Contacts of the helix formed by residues 76 - 96 (chain A) in PDB entry 2A6O
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 GLY 76 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ILE* 4.4 4.5 - - - +
72A ASP 3.5 7.5 + - - -
73A PRO* 4.0 7.6 + - - -
74A SER 3.7 0.6 - - - -
75A PHE* 1.3 82.9 - - - +
77A VAL* 1.3 66.2 + - - +
78A MET 3.2 2.7 - - - -
79A LYS* 2.9 26.6 + - - +
80A PHE 3.7 2.8 + - - -
73B PRO 5.5 3.6 - - - -
76B GLY* 6.0 5.8 - - - -
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Residues in contact with VAL 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A TYR* 3.3 52.3 - - + +
21A ILE* 4.0 18.8 - - + -
71A ILE* 4.1 17.6 - - + +
76A GLY* 1.3 71.3 - - - -
78A MET* 1.3 63.7 + - + +
80A PHE* 3.1 6.8 + - - +
81A ILE* 3.1 38.9 + - + +
113A ILE* 4.3 13.5 - - + -
19B TYR* 4.8 0.9 - - - +
73B PRO* 5.0 11.8 + - + +
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Residues in contact with MET 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A GLY 3.1 1.8 + - - -
77A VAL* 1.3 75.6 - - - +
79A LYS* 1.3 60.0 + - + +
81A ILE* 3.8 9.1 - - + +
82A LYS* 2.9 29.5 + - - +
111A CYS* 4.3 10.1 - - - -
113A ILE* 3.5 31.6 - - - -
13B VAL* 4.1 20.4 - - + -
73B PRO* 3.9 10.0 + - + +
74B SER* 3.3 33.2 - - - +
15C T 3.8 35.4 - - - +
16C A 3.4 21.5 - - - +
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Residues in contact with LYS 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A LEU* 4.2 2.2 - - - -
74A SER 5.4 0.6 + - - -
75A PHE* 3.2 50.7 + - + +
76A GLY* 2.9 12.6 + - - +
78A MET* 1.3 78.1 - - + +
80A PHE* 1.3 62.0 + - - +
82A LYS* 3.6 5.5 - - - +
83A THR* 2.9 30.8 + - - -
79B LYS* 5.7 5.1 - - - +
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Residues in contact with PHE 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ILE* 3.9 24.0 - - + -
23A TRP* 5.3 0.9 - + - -
44A ILE* 4.2 20.9 - - + -
47A VAL* 4.5 3.8 - - + -
48A ALA* 4.2 21.8 - - + -
51A LEU* 3.6 17.3 - - + -
53A VAL* 3.7 42.8 - - + -
55A ILE* 5.2 1.8 - - + -
67A ILE* 4.4 21.3 - - + -
69A ALA* 4.7 0.7 - - + -
71A ILE* 4.0 19.1 - - + -
75A PHE* 4.0 4.6 - - + -
76A GLY 3.7 1.8 + - - +
77A VAL 3.1 7.5 + - - +
79A LYS* 1.3 77.8 - - - +
81A ILE* 1.3 65.4 + - + +
83A THR* 3.8 1.2 - - - -
84A ALA* 2.8 42.7 + - + +
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Residues in contact with ILE 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ILE* 3.8 32.8 - - + -
23A TRP* 4.4 6.1 - - + -
77A VAL* 3.1 25.7 + - + +
78A MET* 4.0 11.0 - - + +
80A PHE* 1.3 77.7 - - + +
82A LYS* 1.3 68.9 + - - +
84A ALA* 4.4 3.8 - - - -
85A LYS* 2.7 49.9 + - + +
111A CYS* 4.3 14.4 - - - -
113A ILE* 3.6 31.2 - - + -
15C T 4.5 10.8 - - - +
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Residues in contact with LYS 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A MET 2.9 19.9 + - - +
79A LYS* 3.6 7.9 - - - +
81A ILE* 1.3 76.2 - - - +
83A THR* 1.3 61.1 + - - +
85A LYS* 4.0 0.5 - - - +
86A GLY* 2.8 26.5 + - - -
7C G 3.5 9.9 - - - +
8C C 3.3 27.3 + - - -
9C T 4.4 9.4 + - - -
10C T 3.1 24.5 - - + +
13C G 3.6 2.9 - - - +
14C C 3.0 26.7 - - + +
15C T 3.5 34.3 - - - +
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Residues in contact with THR 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A VAL* 3.5 24.2 - - + -
50A GLU* 5.6 0.2 - - - +
51A LEU* 3.5 18.6 - - + +
79A LYS 2.9 18.4 + - - -
82A LYS* 1.3 79.1 - - - +
84A ALA* 1.3 66.9 + - - +
87A ARG* 3.0 36.1 + - - +
9C T 4.8 3.5 - - - +
10C T 3.7 31.2 - - + +
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Residues in contact with ALA 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A TRP* 4.0 14.1 - - + -
44A ILE* 3.8 25.1 - - + +
47A VAL* 3.9 12.6 - - + +
80A PHE* 2.8 40.3 + - + +
81A ILE* 3.8 2.2 - - - +
83A THR* 1.3 75.1 - - - +
85A LYS* 1.3 60.9 + - - +
88A SER* 2.7 28.8 + - - -
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Residues in contact with LYS 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A TRP* 3.4 42.8 - - + +
81A ILE* 2.7 38.5 + - + +
84A ALA* 1.3 71.9 - - - +
86A GLY* 1.3 64.9 + - - +
88A SER* 3.7 0.2 - - - -
89A SER* 3.0 22.7 + - - -
107A TRP* 3.0 42.3 + - + +
108A THR 3.1 11.0 + - - +
110A SER 2.8 26.7 + - - -
111A CYS* 4.2 2.8 - - + +
14C C 3.8 12.6 - - - +
15C T 2.7 24.8 + - - +
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Residues in contact with GLY 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LYS 2.8 15.6 + - - -
85A LYS* 1.3 75.5 - - - +
87A ARG* 1.3 60.4 + - - +
89A SER* 3.5 4.4 + - - -
90A ARG 3.2 15.8 + - - -
10C T 3.1 42.2 + - - -
13C G 3.9 1.8 - - - +
14C C 3.9 12.0 - - - -
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Residues in contact with ARG 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ILE* 3.8 17.0 - - + -
46A GLU* 4.5 9.7 - - - +
47A VAL* 3.6 28.4 - - + +
50A GLU* 3.3 35.8 + - - -
83A THR* 3.0 22.3 + - - +
84A ALA 4.7 0.2 - - - +
86A GLY* 1.3 71.1 - - - +
88A SER* 1.3 69.8 + - - +
89A SER 3.0 1.3 - - - -
90A ARG* 2.8 14.0 + - - +
91A ILE* 2.8 33.7 + - + +
10C T 2.7 67.4 + - - +
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Residues in contact with SER 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A TRP* 5.2 0.2 - - - -
40A LEU* 3.8 24.6 - - - +
43A ILE* 3.8 25.2 - - - +
44A ILE* 4.3 2.1 - - - +
84A ALA 2.7 23.6 + - - -
85A LYS* 3.1 5.5 + - - -
87A ARG* 1.3 78.6 - - - +
89A SER* 1.3 58.5 + - - +
92A LEU* 2.8 40.6 + - - +
107A TRP* 3.1 17.2 + - - -
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Residues in contact with SER 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A LYS 3.0 16.7 + - - -
86A GLY 3.5 4.5 - - - -
88A SER* 1.3 82.8 + - - +
90A ARG* 1.3 62.8 + - - +
93A ARG* 3.0 32.9 + - - +
106A LEU* 3.3 24.7 + - - +
107A TRP* 3.8 1.1 - - - -
13C G 3.1 19.0 - - - -
14C C 3.0 25.3 + - - -
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Residues in contact with ARG 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A GLY 3.2 2.3 + - - +
87A ARG 2.8 12.1 + - - +
89A SER* 1.3 76.3 - - - +
91A ILE* 1.3 63.1 + - - +
93A ARG* 4.0 1.8 - - - +
94A GLN* 2.7 63.6 + - - +
100A LYS* 5.9 3.4 - - - +
10C T 3.6 46.7 - - - +
11C T 3.4 26.1 + - - -
12C A 3.3 52.2 + - - +
13C G 3.8 10.1 + - - -
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Residues in contact with ILE 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A ARG* 3.9 4.9 - - - +
43A ILE* 3.3 36.6 - - + -
46A GLU* 6.2 0.2 - - - +
87A ARG* 2.8 37.7 + - + +
90A ARG* 1.3 77.7 - - + +
92A LEU* 1.3 51.9 + - - +
94A GLN* 2.8 18.8 + - - +
95A GLU* 2.7 60.1 + - + +
10C T 5.5 3.1 - - - +
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Residues in contact with LEU 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A LEU* 5.8 0.2 - - + -
36A VAL* 4.0 17.5 - - + +
39A ARG* 3.6 31.9 - - + -
40A LEU* 3.9 37.0 - - + +
43A ILE* 4.0 9.4 - - + -
88A SER* 2.8 26.1 + - - +
91A ILE* 1.3 74.0 - - - +
93A ARG* 1.3 55.1 + - - +
95A GLU* 4.3 2.0 - - - +
96A PHE* 2.8 52.4 + - + +
99A LEU* 3.8 13.8 - - + +
106A LEU* 3.9 16.8 - - + -
107A TRP* 4.8 1.3 - - + -
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Residues in contact with ARG 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A SER* 3.0 31.2 + - - +
90A ARG* 4.1 1.1 - - - +
92A LEU* 1.3 77.1 - - - +
94A GLN* 1.3 61.6 + - - +
96A PHE 3.6 15.2 - - - +
97A ASN* 4.3 3.5 + - - -
99A LEU* 2.8 42.9 + - + +
100A LYS* 3.2 43.6 + - + +
103A LEU 2.9 21.4 + - - -
104A PRO* 3.2 21.8 + - - +
105A THR* 3.9 5.3 - - - +
106A LEU* 3.9 16.2 - - + +
13C G 2.7 48.3 + - - +
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Residues in contact with GLN 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A ARG* 2.7 65.1 + - - +
91A ILE* 2.8 17.9 + - - +
93A ARG* 1.3 79.8 - - - +
95A GLU* 1.3 63.4 + - + +
97A ASN* 4.5 9.5 + - - +
100A LYS* 5.8 3.1 - - + +
11C T 4.7 1.0 + - - -
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Residues in contact with GLU 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A ARG* 2.8 53.3 + - - +
91A ILE* 2.7 34.4 + - + +
92A LEU* 4.4 0.8 - - - +
94A GLN* 1.3 77.9 - - + +
96A PHE* 1.3 81.3 + - + +
97A ASN* 4.0 3.5 + - - +
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Residues in contact with PHE 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A ALA* 3.3 43.7 - - + -
36A VAL* 3.8 18.2 - - + -
39A ARG* 3.9 10.8 - - + -
92A LEU* 2.8 49.5 + - + +
93A ARG 3.6 6.2 - - - +
95A GLU* 1.3 92.2 - - + +
97A ASN* 1.3 64.3 + - - +
98A HIS* 3.3 24.0 - + + -
99A LEU* 3.1 23.6 + - + +
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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
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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) + - + + + + + -
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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