Contacts of the helix formed by residues 82 - 102 (chain A) in PDB entry 3V9M
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 82 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A SER* 3.9 3.1 - - - -
81A LYS* 1.3 100.9 - - + +
83A GLY* 1.3 63.5 + - - +
85A LYS* 4.0 3.3 - - + +
86A SER* 3.1 21.4 + - - +
202A SO4 3.6 8.6 + - - -
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Residues in contact with GLY 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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58A LYS* 3.0 31.7 + - - +
82A PRO* 1.3 72.5 - - - +
84A CYS* 1.3 66.1 + - - -
86A SER* 3.1 13.0 + - - -
87A PHE* 3.2 4.9 + - - +
202A SO4 3.8 8.7 - - - -
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Residues in contact with CYS 84 (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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58A LYS* 4.5 7.9 - - - -
59A GLY 4.2 5.2 - - - -
60A CYS* 2.0 59.9 - - + -
65A THR* 3.8 9.6 - - + +
83A GLY* 1.3 70.7 - - - -
85A LYS* 1.3 60.5 + - - +
87A PHE* 4.6 1.3 - - - +
88A VAL* 2.9 36.0 + - - +
202A SO4 3.1 25.6 + - - +
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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
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65A THR* 3.7 15.7 - - + -
66A LEU* 3.5 29.1 + - - +
67A TYR* 3.4 9.0 - - + +
80A SER* 3.7 20.4 - - - +
82A PRO* 4.0 3.8 - - + +
84A CYS* 1.3 78.2 - - - +
86A SER* 1.3 62.5 + - - +
89A CYS* 3.1 25.8 + - - +
202A SO4 3.0 34.0 + - - +
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Residues in contact with SER 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A LYS* 4.9 1.2 + - - -
78A CYS* 4.7 2.5 - - - +
80A SER* 3.4 28.0 - - - -
81A LYS 3.4 21.5 + - - -
82A PRO 3.1 22.8 + - - -
83A GLY 3.1 3.6 + - - -
85A LYS* 1.3 76.4 - - - +
87A PHE* 1.3 65.6 + - - +
89A CYS* 3.4 3.7 + - - +
90A ALA* 3.0 24.1 + - - +
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Residues in contact with PHE 87 (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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51A CYS* 3.5 31.0 - - - -
54A GLN* 3.8 22.0 - - + -
55A ALA* 3.6 25.4 - - + -
58A LYS* 4.0 23.6 - - + +
60A CYS* 5.3 0.2 - - - -
83A GLY 3.2 14.3 + - - +
84A CYS* 4.0 2.7 - - - +
86A SER* 1.3 79.7 + - - +
88A VAL* 1.3 68.6 + - + +
90A ALA* 3.2 9.4 + - + +
91A CYS* 3.1 26.5 + - - -
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Residues in contact with VAL 88 (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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52A TYR* 4.3 7.4 - - + -
55A ALA* 4.1 18.2 - - + -
60A CYS* 4.1 6.7 - - + -
62A PRO* 3.6 39.0 - - + +
65A THR* 3.5 27.6 - - + +
67A TYR* 4.1 11.4 - - + -
84A CYS 2.9 22.7 + - - +
87A PHE* 1.3 71.5 - - - +
89A CYS* 1.3 66.7 - - - +
91A CYS* 3.2 10.2 + - - +
92A ASP* 3.1 22.7 + - - +
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Residues in contact with CYS 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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8A MET* 3.6 17.7 - - - -
67A TYR* 3.7 28.4 - - + -
68A SER 4.0 3.4 - - - +
69A TRP* 3.8 4.0 - - - -
78A CYS* 2.0 59.0 - - + -
80A SER* 5.1 0.9 - - - -
85A LYS 3.1 22.6 + - - +
86A SER* 3.6 4.3 - - - +
87A PHE 3.2 0.2 - - - -
88A VAL* 1.3 76.6 - - - +
90A ALA* 1.3 57.0 + - - +
92A ASP* 3.1 3.6 + - - +
93A ALA 2.8 25.6 + - - -
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Residues in contact with ALA 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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51A CYS* 5.0 0.2 - - - -
78A CYS* 3.5 8.9 - - + -
86A SER 3.0 14.0 + - - +
87A PHE* 3.5 12.8 - - + +
89A CYS* 1.3 76.9 - - - +
91A CYS* 1.3 61.6 + - - +
93A ALA* 3.9 3.1 - - - +
94A ALA* 3.0 26.5 + - - +
97A LYS* 5.4 0.2 + - - -
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Residues in contact with CYS 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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48A HIS* 3.4 12.8 - - + -
51A CYS* 2.0 65.7 - - + -
52A TYR* 4.0 19.3 - - + -
55A ALA* 4.9 0.9 - - - -
87A PHE* 3.1 28.2 + - - -
88A VAL* 3.4 10.3 - - - +
90A ALA* 1.3 76.2 - - - +
92A ASP* 1.3 63.5 + - - +
94A ALA* 3.9 3.9 - - - +
95A ALA 3.2 17.5 + - - -
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Residues in contact with ASP 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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1A ASN 4.2 3.5 + - - +
5A PHE* 3.5 31.1 - - + +
8A MET* 3.5 10.3 - - - -
48A HIS* 2.9 14.1 + - - -
52A TYR* 2.8 30.4 + - - -
67A TYR* 2.7 36.4 + - - +
88A VAL* 3.1 11.2 + - - +
89A CYS 3.6 4.9 - - - +
91A CYS* 1.3 78.5 - - - +
93A ALA* 1.3 66.2 + - - +
95A ALA 3.3 1.0 + - - -
96A ALA* 2.9 22.0 + - - +
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Residues in contact with ALA 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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8A MET* 3.4 14.3 - - - -
76A PRO* 3.6 27.0 - - - +
78A CYS* 4.2 13.2 - - - +
89A CYS 2.8 19.7 + - - +
90A ALA* 3.9 4.3 - - - +
92A ASP* 1.3 73.2 - - - +
94A ALA* 1.3 61.4 + - - +
96A ALA* 3.4 2.4 + - - +
97A LYS* 3.0 41.1 + - - +
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Residues in contact with ALA 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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47A VAL* 6.1 5.2 - - + -
90A ALA 3.0 17.9 + - - +
91A CYS* 3.9 4.3 - - - +
93A ALA* 1.3 78.3 - - - +
95A ALA* 1.3 57.3 + - - +
97A LYS* 3.4 17.1 + - - +
98A CYS* 2.9 28.5 + - - +
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Residues in contact with ALA 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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5A PHE* 3.7 14.4 - - + -
44A CYS 4.9 2.7 - - - +
48A HIS* 3.4 42.8 - - + -
91A CYS 3.2 7.6 + - - +
92A ASP 3.3 0.4 + - - +
94A ALA* 1.3 74.9 - - - +
96A ALA* 1.3 60.6 + - - +
98A CYS* 3.1 7.0 + - - +
99A PHE* 2.8 44.9 + - + -
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Residues in contact with ALA 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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5A PHE* 4.1 1.4 - - + -
8A MET* 3.6 40.6 - - + +
9A ILE* 3.9 17.7 - - + +
12A ALA* 3.4 11.1 - - - +
76A PRO* 4.0 6.5 - - + -
92A ASP 2.9 16.7 + - - +
93A ALA 3.7 4.3 - - - +
94A ALA 3.3 0.2 - - - -
95A ALA* 1.3 75.7 - - - +
97A LYS* 1.3 62.8 + - - +
99A PHE* 3.4 3.3 + - - +
100A ALA* 3.2 17.3 + - - +
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Residues in contact with LYS 97 (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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12A ALA* 4.2 7.6 - - + -
75A VAL* 4.2 16.2 - - + -
76A PRO* 3.9 29.6 + - + -
93A ALA* 3.0 35.2 + - - +
94A ALA* 3.7 13.8 - - - +
96A ALA* 1.3 75.3 - - - +
98A CYS* 1.3 61.7 + - - +
100A ALA* 3.3 12.3 + - - +
101A LYS* 3.4 18.4 + - + +
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Residues in contact with CYS 98 (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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40A GLU* 6.1 0.9 - - - -
44A CYS* 2.0 59.8 - - + +
47A VAL* 6.3 1.6 - - - -
94A ALA 2.9 17.9 + - - +
95A ALA* 3.1 6.9 + - - +
97A LYS* 1.3 74.0 - - - +
99A PHE* 1.3 63.6 + - - +
101A LYS* 3.3 15.1 + - - +
102A ALA* 3.1 18.0 + - - +
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Residues in contact with PHE 99 (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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5A PHE* 3.9 21.1 - + - -
9A ILE* 3.7 37.7 - - + -
13A ASN* 6.4 0.7 - - + -
22A TYR* 3.7 46.2 + + + -
41A LEU* 3.5 19.1 - - + +
44A CYS* 3.5 23.6 - - + -
45A CYS* 3.6 28.7 - - - -
48A HIS* 5.5 1.8 - + + -
95A ALA* 2.8 30.4 + - + +
96A ALA* 3.7 4.7 - - - +
98A CYS* 1.3 71.9 - - - +
100A ALA* 1.3 63.2 + - - +
102A ALA* 3.2 19.4 + - - +
201A EDO 5.5 2.7 - - - -
204A SO4 5.4 0.5 + - - -
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Residues in contact with ALA 100 (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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12A ALA* 3.4 34.1 - - + +
13A ASN* 3.9 16.6 - - + +
22A TYR* 5.5 0.2 - - - -
96A ALA 3.2 14.7 + - - +
97A LYS* 3.7 5.8 - - - +
98A CYS 3.2 0.4 - - - -
99A PHE* 1.3 79.9 - - - +
101A LYS* 1.3 59.7 + - - +
102A ALA 4.4 2.4 - - - +
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Residues in contact with LYS 101 (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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40A GLU* 3.9 13.4 - - - +
97A LYS* 3.4 11.8 + - + +
98A CYS* 3.3 19.7 + - - +
100A ALA* 1.3 78.4 - - - +
102A ALA* 1.3 61.7 + - - +
103A PRO* 3.9 3.3 - - - +
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Residues in contact with ALA 102 (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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40A GLU* 3.7 12.1 - - + +
41A LEU* 3.8 36.4 - - + +
44A CYS* 4.2 2.9 - - - -
98A CYS 3.1 17.4 + - - +
99A PHE 3.2 14.2 + - - +
100A ALA 4.4 2.4 - - - +
101A LYS* 1.3 79.0 - - - +
103A PRO* 1.3 71.9 - - + +
104A TYR* 3.6 2.1 + - - +
204A SO4 3.9 8.5 + - - -
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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
------------------------------------------------------------
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