Contacts of the helix formed by residues 65 - 87 (chain A) in PDB entry 5NJ8
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 ASP 65 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LYS 3.6 4.8 + - - -
64A LEU* 1.3 71.1 - - - +
66A LYS* 1.3 83.9 + - - +
67A LEU* 3.1 16.3 - - - +
68A SER* 2.8 31.3 + - - +
69A VAL* 2.9 12.5 + - - +
3E T 2.9 39.9 + - - +
4E C 2.6 28.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ASN* 3.4 29.5 + - - +
47A LEU* 4.4 24.4 - - + +
64A LEU 3.6 2.3 + - - +
65A ASP* 1.3 76.5 + - - +
67A LEU* 1.3 62.7 + - + +
69A VAL* 3.3 25.9 - - + +
70A LEU* 3.5 10.4 + - - +
101B ARG* 5.9 1.3 - - - +
105B MET* 4.9 10.3 - - + -
4E C 3.4 38.2 + - + +
5E A 2.2 39.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ASP* 3.1 27.9 - - - +
66A LYS* 1.3 73.4 - - - +
68A SER* 1.3 66.3 + - - +
70A LEU* 3.2 5.6 + - - +
71A ARG* 2.9 20.0 + - - -
101B ARG* 3.1 51.6 - - + +
104B LYS* 5.2 8.3 - - + -
105B MET* 3.3 41.5 - - + +
108B TYR* 3.5 19.5 - - + +
3E T 3.4 9.0 - - - +
4E C 3.8 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A LEU* 4.8 7.6 - - - -
65A ASP* 2.8 30.2 + - - +
67A LEU* 1.3 77.7 - - - +
69A VAL* 1.3 66.8 + - - +
71A ARG* 4.2 6.5 - - - -
72A LEU* 2.9 38.9 + - - +
151A SER 6.0 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LEU* 3.7 20.9 - - + +
50A LEU* 4.3 12.8 - - + -
51A ALA* 3.6 36.8 - - + +
54A LEU* 4.4 4.7 - - + -
64A LEU* 4.1 18.6 - - + +
65A ASP 2.9 17.1 + - - +
66A LYS* 3.3 17.7 - - + +
67A LEU 3.2 0.4 - - - -
68A SER* 1.3 74.7 - - - +
70A LEU* 1.3 61.1 + - + +
72A LEU* 3.7 8.4 - - - +
73A SER* 2.8 29.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LEU* 4.8 13.7 - - + -
50A LEU* 4.4 9.0 - - + -
66A LYS 3.5 7.8 + - - +
67A LEU* 3.2 5.4 + - - +
69A VAL* 1.3 77.7 - - + +
71A ARG* 1.3 66.8 + - - +
73A SER* 2.7 15.2 + - - -
74A VAL* 2.9 18.7 + - + +
105B MET* 3.4 41.1 - - - +
108B TYR* 3.6 20.6 - - + -
109B ILE* 3.8 16.4 - - + -
112B LEU* 3.7 28.0 - - + -
132B LEU* 3.7 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LEU 2.9 14.9 + - - +
68A SER* 3.7 7.9 - - - +
70A LEU* 1.3 75.1 - - - +
72A LEU* 1.3 63.5 + - - +
74A VAL* 3.1 9.7 + - - +
75A SER* 3.0 21.0 + - - -
155A HIS* 3.9 18.8 - - + -
156A GLN* 5.9 4.0 - - - +
108B TYR* 3.1 37.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A LEU* 3.4 33.4 - - + -
55A PRO* 5.3 0.9 - - + -
56A PHE* 3.7 34.5 - - + -
64A LEU* 4.4 17.0 - - + -
68A SER* 2.9 31.4 + - - +
69A VAL* 3.7 1.3 - - - +
71A ARG* 1.3 78.7 - - - +
73A SER* 1.3 65.5 + - - +
75A SER* 2.9 14.1 + - - -
76A TYR* 2.9 22.7 + - - +
151A SER* 4.3 21.5 - - - +
154A ILE* 5.1 11.0 - - + +
155A HIS* 5.4 1.3 - - - -
158B PHE* 4.5 5.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A LEU* 3.3 33.6 - - - +
54A LEU* 4.0 13.0 - - - -
69A VAL 2.8 24.3 + - - -
70A LEU* 2.7 15.1 + - - -
72A LEU* 1.3 79.1 - - - +
74A VAL* 1.3 57.0 + - - -
76A TYR* 3.5 14.5 - - - +
77A LEU* 3.6 15.8 + - - +
112B LEU* 4.5 8.4 - - - +
139B MET* 4.1 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A LEU* 2.9 20.3 + - - +
71A ARG* 3.5 9.4 - - - +
73A SER* 1.3 74.5 - - - +
75A SER* 1.3 71.8 + - - +
76A TYR 3.2 0.4 - - - -
77A LEU* 3.2 4.5 + - - +
78A ARG* 2.9 37.5 + - + +
155A HIS* 5.5 6.3 - - + -
108B TYR* 4.3 6.7 - - + +
111B GLU* 3.9 27.1 - - + +
112B LEU* 4.0 41.7 - - + +
115B MET* 4.8 4.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ARG 3.0 12.9 + - - -
72A LEU* 2.9 11.0 + - - -
74A VAL* 1.3 79.6 - - - +
76A TYR* 1.3 62.4 + - - +
78A ARG* 3.3 8.4 + - - +
79A ALA* 3.0 23.4 + - - +
136A PHE* 4.5 10.7 - - - +
154A ILE* 3.4 33.2 - - - +
155A HIS* 3.5 18.2 + - - +
158B PHE* 3.9 7.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A LEU* 5.5 3.6 - - + -
55A PRO* 3.6 24.8 - - + +
72A LEU 2.9 11.2 + - - +
73A SER* 3.5 11.9 - - - +
75A SER* 1.3 74.5 - - - +
77A LEU* 1.3 81.1 + - + +
79A ALA* 3.1 6.3 + - + +
80A LYS* 2.9 56.5 + - + +
139B MET* 3.1 37.1 - - + +
142B LEU* 4.3 19.1 + - + +
143B ARG* 5.3 5.4 - - - +
157B SER 4.2 4.5 + - - -
158B PHE* 3.5 43.6 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A SER* 3.6 10.9 + - - +
74A VAL 3.2 6.3 + - - +
76A TYR* 1.3 105.2 - - + +
78A ARG* 1.3 62.5 + - - +
80A LYS* 3.2 8.2 + - + +
81A SER* 2.9 24.6 + - - -
112B LEU* 3.6 30.5 - - + -
115B MET* 3.7 37.7 - - + +
116B VAL* 4.8 2.5 - - + -
135B ALA* 5.5 1.8 - - + -
138B HIS* 4.6 18.8 - - + +
139B MET* 4.7 14.8 - - + -
142B LEU* 5.1 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A VAL* 2.9 30.6 + - + +
75A SER* 3.5 7.4 - - - +
77A LEU* 1.3 77.2 - - - +
79A ALA* 1.3 62.6 + - - +
81A SER* 3.3 3.2 + - - -
82A PHE* 3.0 23.9 + - - +
130A THR* 4.7 10.5 - - - +
136A PHE* 3.5 25.3 - - + -
155A HIS* 6.0 5.0 - - - -
246A LEU* 3.6 20.8 - - - +
247A HIS 5.3 0.5 - - - +
248A GLY 5.3 3.2 - - - +
249A GLN* 3.1 33.5 - - + +
262A GLN* 5.3 6.5 + - - -
115B MET* 3.6 33.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A SER 3.0 13.1 + - - +
76A TYR 3.4 7.4 - - - +
78A ARG* 1.3 75.3 - - - +
80A LYS* 1.3 65.3 + - + +
82A PHE* 3.4 0.9 + - - +
83A PHE* 2.9 33.9 + - + -
136A PHE* 3.3 25.2 - - + +
137A TYR* 6.0 1.1 - - + -
158B PHE* 4.3 10.3 - - + +
159B LEU* 4.2 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A TYR* 2.9 52.7 + - + +
77A LEU* 3.2 10.9 + - + +
79A ALA* 1.3 77.5 - - + +
81A SER* 1.3 62.8 + - - +
83A PHE* 3.3 1.2 + - - +
84A ASP* 2.9 36.7 + - - +
142B LEU* 4.6 20.4 - - + -
157B SER 4.5 2.2 + - - -
158B PHE 2.7 30.1 + - - -
159B LEU* 3.8 1.9 - - - +
160B THR* 4.1 11.3 - - - +
163B GLU* 2.6 35.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A LEU 2.9 13.1 + - - -
78A ARG* 3.6 9.0 - - - -
80A LYS* 1.3 75.4 - - - +
82A PHE* 1.3 66.1 + - - +
84A ASP* 2.9 19.2 + - - +
85A VAL* 3.0 21.4 + - - +
248A GLY* 3.4 29.2 + - - -
115B MET* 5.2 6.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ARG 3.0 16.7 + - - +
79A ALA 3.8 2.2 - - - +
81A SER* 1.3 76.6 + - - +
83A PHE* 1.3 83.5 + + - +
85A VAL* 3.1 11.9 - - + +
86A ALA* 3.0 41.3 + - + +
136A PHE* 4.5 12.8 - + + -
244A LYS* 5.0 11.9 - - + -
245A TYR 3.8 12.8 - - - -
246A LEU* 3.6 20.0 - - + -
247A HIS* 3.4 47.3 - - + +
248A GLY* 4.6 0.6 - - - -
266A PHE* 3.7 29.2 - + - -
166B HIS* 5.5 4.5 - + - -
167B LEU* 6.1 0.4 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
79A ALA* 2.9 32.1 + - + +
80A LYS 3.8 1.3 - - - +
82A PHE* 1.3 92.9 - + - +
84A ASP* 1.3 60.4 + - - +
86A ALA* 4.5 2.2 - - + +
87A LEU* 2.9 53.4 + - + +
136A PHE* 5.7 3.1 - + - -
266A PHE* 6.0 0.9 - + - -
159B LEU* 3.5 31.0 - - + -
163B GLU* 2.9 67.1 - - + +
166B HIS* 4.1 18.4 - + - -
167B LEU* 4.2 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A LYS* 2.9 24.3 + - - +
81A SER* 2.9 11.2 + - - +
83A PHE* 1.3 81.8 - - - +
85A VAL* 1.3 63.5 + - + +
87A LEU* 5.2 0.9 - - - -
88A LYS* 3.3 24.1 + - - +
142B LEU* 5.9 2.6 - - - +
163B GLU* 4.8 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A SER* 3.0 21.4 + - - +
82A PHE* 3.1 24.9 - - + +
84A ASP* 1.3 81.3 - - + +
86A ALA* 1.3 63.9 + - + +
88A LYS* 3.7 12.5 - - - +
247A HIS* 4.2 28.5 - - + +
248A GLY* 4.9 6.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A PHE* 3.0 34.3 + - + +
83A PHE* 4.3 2.5 - - - +
85A VAL* 1.3 83.8 - - + +
87A LEU* 1.3 60.1 + - + +
88A LYS 3.2 5.1 + - - -
244A LYS* 5.8 3.1 - - - +
247A HIS* 6.1 1.1 - - - +
166B HIS* 4.3 24.7 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
83A PHE* 2.9 45.3 + - + +
84A ASP* 4.1 2.0 - - - +
86A ALA* 1.3 74.8 - - - +
88A LYS* 1.3 63.9 + - - +
162B GLN* 3.8 33.9 - - + +
163B GLU* 4.1 4.3 - - + -
165B LYS* 5.7 4.9 - - - +
166B HIS* 3.4 37.7 - - + +
----------------------------------------------------------
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