Contacts of the helix formed by residues 66 - 88 (chain A) in PDB entry 3DOY
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 PRO 66 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A VAL* 3.6 32.8 - - + -
58A HIS* 3.7 11.4 - - + +
64A ILE 3.2 6.2 - - - +
65A PHE* 1.3 92.3 - - + +
67A GLY* 1.3 66.0 + - - +
68A VAL* 4.1 7.2 - - + -
69A LEU* 2.9 34.6 + - + +
70A ILE* 3.1 12.0 + - - +
1001A CL 3.8 9.0 - - + -
27B MET* 3.7 24.9 - - + -
72B GLU* 5.5 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A PHE 3.4 1.6 + - - -
66A PRO* 1.3 72.2 - - - +
68A VAL* 1.3 61.8 + - - +
70A ILE* 3.0 25.2 + - - +
71A VAL* 3.1 9.4 + - - +
109A PHE* 3.2 36.1 - - - -
1001A CL 3.0 20.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A PRO* 4.1 13.9 - - + -
67A GLY* 1.3 76.7 - - - +
69A LEU* 1.3 66.1 + - + +
71A VAL* 3.3 10.9 + - - +
72A GLU* 3.0 25.8 + - - +
109A PHE* 4.0 1.5 - - + -
27B MET* 4.9 0.4 - - + -
68B VAL* 3.6 33.9 - - + +
69B LEU* 4.4 8.5 - - + -
71B VAL* 4.5 11.9 - - + -
72B GLU* 3.6 44.4 + - + +
75B ALA* 6.2 0.4 - - + -
104B ILE* 4.6 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A MET* 4.5 16.4 - - - -
29A LEU* 3.6 26.4 - - + +
54A VAL* 4.0 15.5 - - + -
65A PHE* 3.8 26.1 - - + -
66A PRO* 2.9 40.6 + - + +
68A VAL* 1.3 78.0 - - + +
70A ILE* 1.3 60.9 + - - +
72A GLU* 3.4 4.1 + - + +
73A GLY* 2.9 23.4 + - - -
121A TYR* 4.6 0.5 + - - -
27B MET* 5.1 4.3 - - - -
68B VAL* 4.4 15.7 - - + -
69B LEU* 4.5 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A PHE* 3.8 21.3 - - + +
66A PRO 3.1 10.4 + - - +
67A GLY* 3.0 21.4 + - - +
69A LEU* 1.3 77.1 - - - +
71A VAL* 1.3 63.8 + - + +
73A GLY* 3.2 2.4 + - - -
74A MET* 3.1 25.5 + - - +
109A PHE* 4.8 3.4 - - + -
111A ILE 5.3 2.5 - - - +
113A VAL* 3.7 28.3 - - + +
119A LEU* 3.9 13.5 - - + -
121A TYR* 3.7 2.8 - - + -
139A ALA* 3.4 32.1 - - + -
146A VAL* 4.7 1.8 - - + +
147A ALA* 4.0 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A GLY 3.1 11.6 + - - +
68A VAL* 3.4 11.4 - - + +
70A ILE* 1.3 78.9 - - + +
72A GLU* 1.3 58.3 + - - +
74A MET* 3.0 13.3 + - - +
75A ALA* 2.9 26.3 + - - +
101A PHE* 4.0 8.1 - - + -
104A ILE* 3.9 35.7 - - + -
107A VAL* 3.9 28.7 - - + -
109A PHE* 4.3 6.5 - - + -
147A ALA* 6.2 1.3 - - + -
149A ALA* 4.5 10.5 - - + -
151A LEU* 4.8 5.8 - - + +
68B VAL* 4.4 3.4 - - + -
104B ILE* 6.2 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A HIS* 3.7 13.5 + - - -
27A MET* 3.7 27.1 - - + +
29A LEU* 3.9 6.5 - - + -
68A VAL 3.0 14.5 + - - +
69A LEU* 3.5 12.3 - - - +
70A ILE 3.3 0.2 - - - -
71A VAL* 1.3 75.7 - - - +
73A GLY* 1.3 56.9 + - - +
75A ALA* 3.3 5.7 + - - +
76A GLN* 3.0 63.2 + - - +
101A PHE* 3.4 22.9 - - - -
58B HIS* 4.5 7.3 + - - -
66B PRO* 5.3 1.8 - - - +
67B GLY 5.6 0.7 + - - -
68B VAL* 3.4 18.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LEU* 4.3 12.6 - - - -
30A VAL* 3.8 0.7 - - - +
69A LEU 2.9 12.3 + - - -
70A ILE 3.2 1.5 + - - -
71A VAL 3.1 0.4 - - - -
72A GLU* 1.3 75.5 - - - +
74A MET* 1.3 63.1 - - - +
76A GLN* 3.4 5.7 + - - +
77A SER* 3.1 24.8 + - - -
121A TYR* 3.4 33.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ILE* 3.1 18.9 + - - +
71A VAL* 3.0 11.5 + - - +
73A GLY* 1.3 74.0 - - - +
75A ALA* 1.3 59.3 + - - +
77A SER* 3.2 4.3 + - - -
78A GLY* 2.9 24.8 + - - -
121A TYR* 3.6 18.4 - - + -
123A LEU* 3.5 35.3 - - + +
135A VAL* 5.4 0.2 - - - +
137A GLY 3.6 33.9 - - - +
138A THR* 3.7 8.3 - - - +
139A ALA* 4.1 18.8 - - + -
147A ALA* 5.1 4.3 - - - -
148A GLU 4.6 0.2 - - - -
149A ALA* 3.6 31.4 - - + +
151A LEU* 4.9 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A VAL 2.9 6.3 + - - +
72A GLU* 3.5 8.7 - - - +
74A MET* 1.3 74.5 - - - +
76A GLN* 1.3 55.9 + - + +
78A GLY* 3.2 1.8 + - - -
79A GLY* 2.7 31.7 + - - -
99A VAL* 5.2 4.5 - - - +
101A PHE* 3.1 45.1 - - + -
151A LEU* 4.2 17.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LEU* 3.8 17.0 - - + +
23A HIS* 3.3 20.1 - - + +
27A MET 2.7 23.7 + - - +
28A LEU* 3.8 12.1 - - - +
29A LEU* 2.9 31.1 + - - +
30A VAL* 3.6 22.7 - - + +
72A GLU* 3.0 45.3 + - - +
73A GLY 3.7 0.7 - - - +
74A MET 3.3 0.2 - - - -
75A ALA* 1.3 76.1 - - + +
77A SER* 1.3 61.9 + - - +
79A GLY* 3.2 2.3 + - - -
80A PHE* 2.9 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A VAL* 4.0 7.2 - - - +
42A ILE* 3.7 20.6 - - - +
44A ALA* 3.9 10.4 - - - +
73A GLY 3.1 14.6 + - - -
74A MET 3.2 9.2 + - - -
76A GLN* 1.3 74.0 - - - +
78A GLY* 1.3 65.8 + - - +
80A PHE* 3.1 9.3 + - - +
81A LEU* 3.0 21.3 + - - +
121A TYR* 3.2 23.3 - - - +
123A LEU* 4.0 15.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A MET 2.9 14.0 + - - -
75A ALA 3.6 2.9 - - - -
77A SER* 1.3 76.6 - - - +
79A GLY* 1.3 56.9 + - - +
81A LEU* 3.2 9.2 + - - +
82A ALA* 2.8 30.8 + - - +
123A LEU* 4.2 12.7 - - - +
133A TRP* 5.8 0.2 - - - -
135A VAL* 4.6 22.8 - - - +
151A LEU* 6.0 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LEU* 4.6 6.1 - - - -
75A ALA 2.7 15.3 + - - -
76A GLN* 3.6 4.7 - - - -
77A SER 3.1 0.4 - - - -
78A GLY* 1.3 77.6 - - - +
80A PHE* 1.3 61.1 + - - +
82A ALA* 3.2 4.6 + - - +
83A PHE* 3.0 25.7 + - - +
99A VAL* 4.0 31.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A PHE* 3.9 36.1 - + - -
16A HIS 4.4 0.2 - - - -
17A ILE* 4.2 17.0 - - + -
20A ILE* 3.5 43.9 - - + +
21A LEU* 4.1 19.4 - - + +
33A ILE* 3.4 33.2 - - + -
36A LEU* 4.6 2.5 - - + -
42A ILE* 4.1 9.6 - - + -
76A GLN 2.9 12.6 + - - +
77A SER* 3.4 10.1 - - - +
79A GLY* 1.3 74.7 - - - +
81A LEU* 1.3 59.9 + - - +
83A PHE* 4.0 1.1 - - - +
84A THR* 2.9 57.2 + - + -
89A PHE* 4.7 0.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LEU* 3.3 30.5 - - + -
37A GLN 3.6 12.1 - - - +
39A ASN 4.4 0.7 - - - +
41A LYS* 3.5 36.6 - - - +
42A ILE* 3.7 14.4 - - + -
77A SER 3.0 12.6 + - - +
78A GLY* 3.4 11.4 - - - +
80A PHE* 1.3 78.3 - - - +
82A ALA* 1.3 50.7 + - - +
84A THR* 4.4 0.2 - - - -
85A SER* 2.7 53.8 + - - +
123A LEU* 4.4 5.2 - - + +
124A GLU 5.2 0.2 - - - -
125A VAL* 3.7 23.6 - - + +
133A TRP* 5.1 0.9 - - + -
135A VAL* 5.3 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A GLY 2.8 20.5 + - - +
79A GLY* 3.5 7.4 - - - +
81A LEU* 1.3 76.7 - - - +
83A PHE* 1.3 65.2 + - - +
85A SER* 3.2 7.6 + - - -
86A LEU* 3.2 18.2 + - - +
99A VAL* 5.2 2.5 - - + -
133A TRP* 3.7 43.6 - - + -
135A VAL* 6.3 0.2 - - + -
153A ALA* 6.3 1.8 - - + -
155A ILE* 4.0 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ILE* 4.0 24.9 - - + -
79A GLY 3.0 14.1 + - - +
80A PHE 4.0 1.6 - - - +
82A ALA* 1.3 78.3 - - - +
84A THR* 1.3 57.1 + - - +
86A LEU 3.0 3.3 + - - -
87A TRP* 2.8 79.1 + + + -
88A GLY 3.6 21.1 - - - -
90A ASP 3.5 14.6 - - - -
93A ILE* 3.8 15.9 - - + -
94A ALA* 3.2 42.8 - - + -
97A LYS* 4.3 12.8 - - + -
99A VAL* 5.4 5.4 - - + -
155A ILE* 4.2 5.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU* 3.2 34.3 - - + +
12A PHE* 5.0 0.5 - - - -
20A ILE* 4.9 2.3 - - - +
36A LEU* 3.6 22.9 - - + -
80A PHE* 2.9 38.9 + - + +
81A LEU 3.8 4.7 - - - +
83A PHE* 1.3 78.3 - - - +
85A SER* 1.3 63.7 + - - +
88A GLY* 2.8 44.1 + - - -
89A PHE* 4.6 2.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ALA* 3.5 12.8 - - - +
39A ASN* 2.8 54.9 + - - +
81A LEU* 2.7 35.6 + - - +
82A ALA 3.2 0.6 + - - -
84A THR* 1.3 76.0 - - - +
86A LEU* 1.3 60.8 + - - +
88A GLY 4.9 0.2 + - - -
133A TRP* 3.4 11.8 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
39A ASN* 5.4 2.5 - - - +
82A ALA 3.2 6.0 + - - +
83A PHE 3.0 6.8 + - - +
85A SER* 1.3 82.1 - - - +
87A TRP* 1.3 84.2 + - + +
128A HIS* 5.7 2.5 - - + +
130A GLY* 3.9 13.5 - - - +
131A MET* 3.9 14.1 - - + -
133A TRP* 3.7 25.8 - - + +
155A ILE* 3.4 33.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A PHE* 2.8 69.9 + + + +
86A LEU* 1.3 96.6 - - + +
88A GLY* 1.3 65.0 + - - +
89A PHE 3.9 0.2 + - - -
90A ASP* 3.8 16.5 - - + +
93A ILE* 3.7 31.7 - - + +
97A LYS* 3.8 25.1 - - + -
131A MET* 3.7 35.9 - - + -
155A ILE* 4.0 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU* 4.3 12.6 - - - -
83A PHE* 3.6 14.9 - - - -
84A THR* 2.8 32.4 + - - -
85A SER 4.7 0.2 - - - -
86A LEU 3.6 0.6 - - - -
87A TRP* 1.3 82.6 - - - +
89A PHE* 1.3 57.9 + - - -
90A ASP 2.9 8.0 + - - -
----------------------------------------------------------
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