Contacts of the helix formed by residues 67 - 97 (chain A) in PDB entry 4DYL
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 67 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A PRO 3.2 5.0 - - - -
66A ASP* 1.3 84.6 - - - +
68A PRO* 1.4 63.4 - - - +
69A ILE* 4.1 0.2 - - - +
70A SER* 3.2 22.9 + - - -
71A GLN* 3.0 27.4 + - - +
260A GLU* 2.2 38.3 + - - -
263A GLY* 6.4 0.4 - - - -
264A PHE* 6.1 1.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ASP 3.7 3.1 - - - +
67A SER* 1.4 81.3 - - - +
69A ILE* 1.3 60.8 + - + +
71A GLN* 4.0 5.2 - - + +
72A SER* 2.8 34.6 + - - +
254A ARG 5.2 2.7 - - - +
255A ILE* 4.8 5.6 - - - -
256A GLN* 4.7 18.2 - - + +
259A ALA* 4.2 20.2 - - + +
260A GLU* 3.4 24.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A SER* 3.3 0.2 + - - -
68A PRO* 1.3 73.0 - - - +
70A SER* 1.3 58.2 + - - +
72A SER* 3.2 5.5 + - - -
73A TRP* 2.7 44.6 + - + +
255A ILE* 3.6 36.3 - - + +
257A PRO* 6.2 2.2 - - + -
260A GLU* 3.1 37.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A PRO* 3.8 24.3 - - - +
67A SER* 3.2 28.2 + - - -
69A ILE* 1.3 81.3 - - - +
71A GLN* 1.3 55.9 + - - -
73A TRP* 3.3 9.2 + - - +
74A ALA* 3.0 28.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A PRO 3.6 11.4 - - - +
66A ASP 3.5 14.1 - - - +
67A SER 3.0 21.7 + - - +
68A PRO* 4.0 6.3 - - + +
70A SER* 1.3 72.5 - - - +
72A SER* 1.3 64.8 + - - +
74A ALA* 3.5 7.1 + - - +
75A GLU* 3.0 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A PRO 2.8 24.3 + - - -
69A ILE 3.7 3.4 - - - -
71A GLN* 1.3 73.3 - - - +
73A TRP* 1.3 65.1 + - - +
75A GLU* 3.3 4.0 + - - +
76A ILE* 3.1 31.0 + - - +
251A ALA* 2.8 36.4 + - - +
254A ARG* 4.4 7.4 + - - +
255A ILE* 3.6 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ILE* 2.7 28.5 + - + +
70A SER* 3.5 8.3 - - - +
72A SER* 1.3 70.3 - - - +
74A ALA* 1.3 68.5 + - + +
76A ILE* 3.1 22.4 + - + +
77A THR* 2.9 51.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A SER 3.0 16.3 + - - +
71A GLN* 3.7 8.1 - - - +
73A TRP* 1.3 78.2 - - + +
75A GLU* 1.3 63.8 + - - +
77A THR* 3.0 9.8 + - - -
78A SER* 3.0 26.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A GLN 3.0 13.9 + - - +
72A SER* 3.5 10.1 - - - +
73A TRP 3.2 0.4 - - - -
74A ALA* 1.3 77.8 - - - +
76A ILE* 1.3 55.2 + - - +
78A SER* 3.7 7.7 + - - -
79A GLN* 2.8 65.2 + - + +
247A GLU* 3.8 15.8 - - - +
251A ALA* 3.7 21.8 - - + -
254A ARG* 4.5 9.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A SER* 3.1 23.2 + - - +
73A TRP* 3.1 24.2 + - + +
75A GLU* 1.3 73.1 - - - +
77A THR* 1.3 66.9 + - - +
79A GLN* 3.4 1.6 + - - +
80A THR* 2.9 36.2 + - - +
248A MET* 3.8 44.1 - - + +
251A ALA* 4.0 4.5 - - + -
252A ALA* 3.9 22.9 - - + +
255A ILE* 5.8 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A SER* 6.1 5.8 - - - -
73A TRP* 2.9 58.3 + - + +
74A ALA* 3.0 14.2 + - - -
76A ILE* 1.3 76.4 - - + +
78A SER* 1.3 58.9 + - - +
80A THR* 3.2 8.6 + - - -
81A GLU* 2.9 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ALA 3.0 19.8 + - - -
75A GLU* 3.7 11.5 + - - -
77A THR* 1.3 78.7 + - - +
79A GLN* 1.3 59.6 + - - +
81A GLU* 3.3 9.7 + - - +
82A GLY* 3.0 21.7 + - - -
85A ARG* 5.0 2.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A GLU* 2.8 51.1 + - + +
76A ILE 3.8 0.4 - - - +
78A SER* 1.3 76.5 + - - +
80A THR* 1.3 60.6 + - - +
82A GLY* 2.9 5.3 + - - +
83A LEU 2.8 23.6 + - - -
244A ILE* 3.5 39.5 - - + +
247A GLU* 3.7 28.1 + - + +
248A MET* 3.5 22.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LEU* 4.8 15.8 - - + +
51A MET* 3.9 38.1 - - + +
76A ILE* 2.9 23.5 + - - +
77A THR* 3.4 7.6 - - - -
79A GLN* 1.3 75.9 - - - +
81A GLU* 1.3 61.2 + - - +
83A LEU* 3.1 15.4 + - + +
84A SER* 3.1 20.1 + - - -
248A MET* 3.6 17.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LEU 4.3 2.0 - - - +
49A HIS* 2.6 58.0 + - - +
52A SER* 3.7 15.0 + - - -
77A THR 2.9 12.7 + - - +
78A SER* 3.4 13.2 - - - +
80A THR* 1.3 75.9 - - - +
82A GLY* 1.3 62.7 + - - +
84A SER* 3.1 19.7 + - - -
85A ARG* 3.2 37.9 + - - +
88A ARG* 5.6 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A SER 3.0 9.5 + - - -
79A GLN* 2.9 11.1 + - - -
81A GLU* 1.3 77.2 - - - +
83A LEU* 1.3 59.9 + - - +
85A ARG* 3.5 25.0 + - - +
86A LEU* 3.2 21.5 + - - +
244A ILE* 3.7 12.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A TYR* 5.6 4.3 - - + +
48A LEU* 4.4 19.5 - - + -
79A GLN 2.8 11.2 + - - +
80A THR* 3.1 16.5 + - + +
82A GLY* 1.3 74.0 - - - +
84A SER* 1.3 65.0 + - - +
86A LEU* 3.4 4.5 + - + +
87A LEU* 3.1 42.1 + - + +
241A VAL* 4.1 29.8 - - + -
244A ILE* 3.7 17.2 - - + +
245A HIS* 4.2 20.2 - - + +
248A MET* 5.1 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ALA* 2.8 38.7 + - - +
48A LEU* 4.1 11.4 - - - +
49A HIS* 3.3 26.3 + - - +
80A THR 3.1 11.3 + - - -
81A GLU* 3.1 18.6 + - - -
83A LEU* 1.3 77.0 - - - +
85A ARG* 1.3 61.8 + - - +
87A LEU* 3.3 2.6 + - - +
88A ARG* 3.2 21.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A SER 5.0 2.4 + - - -
81A GLU* 3.2 39.5 + - - +
82A GLY* 3.6 24.8 - - - +
84A SER* 1.3 72.7 - - - +
86A LEU* 1.3 60.7 + - - +
88A ARG* 3.2 37.5 + - - +
89A GLN* 3.0 37.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A GLY 3.2 12.8 + - - +
83A LEU* 3.5 11.9 - - + +
84A SER 3.3 0.2 - - - -
85A ARG* 1.3 77.3 - - - +
87A LEU* 1.3 57.9 + - + +
89A GLN* 3.0 23.8 + - + +
90A HIS* 2.8 51.5 + - + +
240A GLU* 3.4 60.6 - - + +
241A VAL* 3.7 16.6 - - + -
244A ILE* 3.9 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ASP* 3.7 53.4 - - + +
44A TYR* 3.8 32.1 - - + -
45A ALA* 4.1 6.1 - - + +
48A LEU* 4.8 2.5 - - + -
83A LEU* 3.1 40.6 + - + +
84A SER 3.3 8.9 + - - +
86A LEU* 1.3 79.7 - - + +
88A ARG* 1.3 62.2 + - - +
90A HIS* 3.2 16.3 + - + +
91A ALA* 3.1 17.7 + - - +
236A LEU* 4.3 23.6 - - + -
241A VAL* 5.8 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ASP 5.0 0.4 - - - -
42A ARG* 5.1 13.2 - - + +
45A ALA* 3.7 16.5 + - + +
49A HIS* 5.5 4.8 + - - +
81A GLU* 5.6 1.4 + - - -
84A SER* 3.2 16.3 + - - +
85A ARG* 3.2 56.5 + - - +
86A LEU 3.1 0.6 - - - -
87A LEU* 1.3 79.4 - - - +
89A GLN* 1.3 62.2 + - + +
91A ALA* 3.0 8.9 + - + +
92A GLU* 3.0 35.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ARG* 3.0 22.9 + - - +
86A LEU* 3.0 30.3 + - + +
88A ARG* 1.3 72.8 - - + +
90A HIS* 1.3 62.1 + - + +
92A GLU* 4.2 14.1 - - - -
93A ASP* 2.9 45.9 + - - +
240A GLU* 5.2 3.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ASP* 3.6 17.1 + - - +
86A LEU* 2.8 48.2 + - + +
87A LEU* 3.3 20.4 - - + +
89A GLN* 1.3 79.0 - - + +
91A ALA* 1.3 57.1 + - - +
93A ASP* 5.9 0.7 - - - -
94A LEU* 3.0 32.4 + - - +
233A ILE* 3.2 31.8 + - + +
234A SER* 3.9 9.9 + - - -
235A SER 3.2 28.0 - - - -
236A LEU* 4.9 4.2 - - + +
238A GLN* 3.6 11.6 + - - -
240A GLU* 5.5 0.2 - - - -
241A VAL* 4.4 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A VAL* 3.6 35.7 - - + +
41A ASP* 4.1 4.6 - - + +
42A ARG* 3.8 20.6 - - + +
87A LEU 3.1 10.9 + - - +
88A ARG* 3.0 10.8 + - + +
90A HIS* 1.3 75.4 - - - +
92A GLU* 1.3 65.9 + - + +
94A LEU* 3.7 5.0 - - - +
95A ASN* 3.0 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ARG* 3.0 28.1 + - + +
89A GLN* 3.8 20.9 - - - +
91A ALA* 1.3 75.3 - - + +
93A ASP* 1.3 64.1 + - - +
95A ASN* 3.2 6.9 + - - +
96A SER* 2.8 32.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A GLN* 2.9 31.4 + - - +
90A HIS* 5.1 0.9 - - - -
92A GLU* 1.3 79.0 - - - +
94A LEU* 1.3 60.4 + - - +
96A SER* 3.9 7.1 + - - -
97A GLY* 2.9 24.4 + - - -
233A ILE* 3.5 34.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A MET* 4.2 13.9 - - + +
37A ARG* 3.8 23.1 - - + -
38A VAL* 3.6 18.6 - - + +
41A ASP* 4.9 2.9 - - - +
90A HIS 3.0 19.1 + - - +
91A ALA 3.7 3.4 - - - +
93A ASP* 1.3 78.4 - - - +
95A ASN* 1.3 61.9 + - - +
98A PRO* 3.5 23.8 - - + +
99A LEU* 3.2 24.5 + - + +
230A TYR* 3.5 45.8 - - + +
233A ILE* 3.7 7.0 - - + +
234A SER* 4.4 9.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A VAL* 4.0 18.6 - - + +
91A ALA 3.0 18.3 + - - +
92A GLU* 3.4 7.6 - - - +
94A LEU* 1.3 79.7 - - - +
96A SER* 1.3 63.2 + - - +
97A GLY 3.6 0.2 + - - -
99A LEU* 3.8 27.3 - - - +
100A SER* 3.6 18.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A GLU 2.8 20.9 + - - -
93A ASP* 3.9 8.8 + - - -
95A ASN* 1.3 75.0 - - - +
97A GLY* 1.3 58.2 + - - +
100A SER* 2.7 16.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ASP 2.9 12.4 + - - -
95A ASN 3.4 1.4 - - - -
96A SER* 1.3 76.1 + - - +
98A PRO* 1.3 72.9 - - - +
99A LEU 3.4 0.7 - - - -
100A SER* 2.6 19.8 + - - -
101A LYS* 3.0 23.7 + - - +
229A GLU* 4.5 7.4 - - - -
233A ILE* 5.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il