Contacts of the helix formed by residues 83 - 104 (chain A) in PDB entry 3VA2
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 THR 83 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A LEU* 4.2 8.6 - - - +
39A THR* 5.6 0.5 - - - +
40A HIS* 2.6 34.5 + - - -
82A GLY* 1.3 70.7 - - - -
84A VAL* 1.3 62.9 + - - +
85A GLU 3.1 2.0 - - - -
86A ARG* 3.2 48.7 + - - +
87A LEU* 3.3 11.3 + - - +
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Residues in contact with VAL 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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40A HIS* 3.3 34.0 - - + +
43A LEU* 3.8 31.6 - - + -
44A LEU* 5.0 2.5 - - + -
78A THR* 4.4 3.4 - - - +
79A VAL 3.5 27.4 - - - +
80A GLN* 4.5 0.4 - - - -
81A GLY 4.4 2.9 - - - +
82A GLY* 3.0 7.8 - - - +
83A THR* 1.3 78.6 - - - +
85A GLU* 1.3 61.1 + - - +
87A LEU* 3.4 11.3 + - + +
88A PHE* 3.2 39.6 + - + -
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Residues in contact with GLU 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A GLN* 3.9 50.4 - - + +
81A GLY 4.5 5.0 - - - +
82A GLY 3.6 11.8 + - - +
83A THR 3.1 0.6 - - - -
84A VAL* 1.3 79.6 - - - +
86A ARG* 1.3 63.2 + - - +
88A PHE* 3.7 3.6 + - - +
89A LYS* 3.2 24.8 + - + +
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Residues in contact with ARG 86 (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 GLU* 3.3 27.5 + - - -
36A LEU* 3.5 24.9 - - + +
82A GLY 4.6 0.2 + - - -
83A THR* 3.2 38.7 + - + +
85A GLU* 1.3 75.6 - - - +
87A LEU* 1.3 61.2 + - - +
89A LYS* 3.7 10.4 - - + +
90A ASN* 2.9 44.1 + - - +
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Residues in contact with LEU 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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33A THR* 3.7 28.5 - - + +
36A LEU* 3.8 18.3 - - + +
37A LEU* 3.8 37.0 - - + +
40A HIS* 4.8 8.1 - - + -
44A LEU* 4.1 25.8 - - + -
83A THR 3.3 8.6 + - - +
84A VAL* 3.5 11.4 - - + +
85A GLU 3.3 0.4 - - - -
86A ARG* 1.3 77.6 - - - +
88A PHE* 1.3 69.5 + - + +
90A ASN* 3.1 6.2 + - - +
91A LEU* 2.9 44.5 + - + +
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Residues in contact with PHE 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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44A LEU* 3.7 17.9 - - + -
71A ILE* 3.7 21.0 - - + +
74A LEU* 3.5 22.0 - - + -
75A GLU* 3.3 55.4 - - + +
78A THR* 3.4 26.7 - - - -
80A GLN* 5.3 7.2 - - + -
84A VAL* 3.2 37.1 + - + +
85A GLU* 3.7 5.4 + - - +
87A LEU* 1.3 87.9 - - + +
89A LYS* 1.3 56.2 + - - +
91A LEU* 3.9 12.4 - - + +
92A SER* 3.1 25.1 + - - -
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Residues in contact with LYS 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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24A ILE* 6.2 1.0 - - - +
85A GLU* 3.2 20.3 + - + +
86A ARG* 3.7 10.7 - - + +
87A LEU 3.1 0.4 - - - -
88A PHE* 1.3 76.6 - - - +
90A ASN* 1.3 69.3 + - - +
92A SER* 3.2 10.2 - - - -
93A LEU* 3.0 60.8 + - + +
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Residues in contact with ASN 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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29A LEU* 3.7 18.8 - - + +
32A GLU* 3.6 33.7 + - - +
33A THR* 3.2 31.9 + - + +
36A LEU* 4.1 7.3 - - - +
86A ARG* 2.9 26.6 + - - +
87A LEU 3.5 4.0 - - - +
89A LYS* 1.3 87.2 + - - +
91A LEU* 1.3 53.8 + - - +
93A LEU* 3.0 6.1 + - - +
94A ILE* 2.8 39.9 + - - +
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Residues in contact with LEU 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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33A THR* 3.6 22.4 - - + -
37A LEU* 5.7 0.2 - - + -
68A PHE* 3.4 14.6 - - + -
71A ILE* 3.7 41.5 - - + -
87A LEU* 2.9 39.6 + - + +
88A PHE* 3.9 13.7 - - + +
90A ASN* 1.3 75.8 - - - +
92A SER* 1.3 56.9 + - - +
94A ILE* 3.4 8.4 + - + +
95A LYS* 2.9 29.6 + - - +
119B LEU* 4.6 15.0 - - + -
123B LEU* 4.2 19.3 - - + -
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Residues in contact with SER 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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71A ILE* 5.9 0.2 - - - +
75A GLU* 5.9 1.6 - - - -
88A PHE 3.1 17.2 + - - -
89A LYS* 3.2 16.1 + - - +
91A LEU* 1.3 77.0 - - - +
93A LEU* 1.3 57.6 + - - +
95A LYS* 3.3 11.2 + - - +
96A LYS* 3.0 45.4 + - - +
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Residues in contact with LEU 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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24A ILE* 5.3 14.1 - - + -
29A LEU* 3.6 31.0 - - + +
89A LYS* 3.0 45.3 + - + +
90A ASN* 3.0 6.9 + - - +
92A SER* 1.3 74.4 - - - +
94A ILE* 1.3 60.2 + - - +
96A LYS* 3.3 27.5 + - + +
97A TYR* 3.0 25.1 + - - +
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Residues in contact with ILE 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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26A THR* 5.7 2.0 - - + -
29A LEU* 3.7 17.5 - - + -
30A VAL* 4.0 17.7 - - + -
33A THR* 3.7 28.5 - - + +
68A PHE* 4.1 14.8 - - + -
90A ASN 2.8 21.7 + - - +
91A LEU* 3.7 9.6 - - + +
92A SER 3.3 0.2 - - - -
93A LEU* 1.3 69.6 - - - +
95A LYS* 1.3 65.5 + - - +
97A TYR* 3.2 8.6 + - + +
98A ILE* 3.0 23.5 + - + +
123B LEU* 3.7 24.0 - - + -
126B MET* 4.0 28.7 - - + -
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Residues in contact with LYS 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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68A PHE* 3.6 50.2 - - + +
91A LEU 2.9 18.3 + - - +
92A SER* 3.4 9.2 - - - +
93A LEU 3.3 0.2 - - - -
94A ILE* 1.3 76.7 - - - +
96A LYS* 1.3 58.9 + - + +
98A ILE* 3.3 1.7 + - - +
99A ASP* 2.8 59.9 + - - +
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Residues in contact with LYS 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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92A SER* 3.0 31.7 + - - +
93A LEU* 3.5 28.7 - - + +
94A ILE 3.2 0.4 - - - -
95A LYS* 1.3 73.6 - - + +
97A TYR* 1.3 66.4 + - - +
99A ASP* 3.7 10.7 - - - +
100A GLY* 3.1 18.5 + - - -
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Residues in contact with TYR 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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26A THR* 3.6 41.1 - - + +
29A LEU* 6.0 0.2 - - + -
93A LEU 3.0 12.7 + - - +
94A ILE* 3.2 8.9 + - + +
96A LYS* 1.3 77.2 - - - +
98A ILE* 1.3 72.8 + - + +
100A GLY* 3.1 4.9 + - - -
101A GLN* 3.1 55.8 + - + +
59B ASN* 4.7 1.6 + - - -
126B MET* 4.7 6.7 - - - -
130B TRP* 4.3 18.3 - + - -
131B ILE 3.6 10.9 + - - -
132B ILE* 3.4 37.7 + - + +
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Residues in contact with ILE 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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64A THR* 4.1 26.5 - - + +
68A PHE* 3.5 23.6 - - + -
94A ILE* 3.0 17.9 + - + +
95A LYS* 3.7 4.9 - - - +
97A TYR* 1.3 84.1 - - + +
99A ASP* 1.3 66.8 + - - +
101A GLN* 3.0 16.6 + - - +
102A LYS* 3.0 23.9 + - + +
62B LEU* 4.5 10.3 - - + -
122B PHE* 3.5 32.3 - - + -
126B MET* 4.2 9.6 - - + -
130B TRP* 4.3 13.9 - - + -
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Residues in contact with ASP 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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95A LYS* 2.8 54.4 + - - +
96A LYS* 3.7 10.6 - - - +
98A ILE* 1.3 78.4 - - - +
100A GLY* 1.3 56.9 + - - +
102A LYS* 3.4 20.2 + - - +
103A LYS* 3.0 34.1 + - - +
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Residues in contact with GLY 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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96A LYS 3.1 10.9 + - - -
97A TYR* 3.1 9.3 + - - -
99A ASP* 1.3 76.8 - - - +
101A GLN* 1.3 60.7 + - - +
103A LYS* 3.4 11.8 + - - +
104A LYS* 3.0 38.9 + - - +
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Residues in contact with GLN 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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97A TYR* 3.1 54.5 + - + +
98A ILE* 3.0 10.8 + - - +
100A GLY* 1.3 79.7 - - - +
102A LYS* 1.3 61.2 + - - +
104A LYS* 3.2 23.6 + - - +
105A CYS* 3.3 1.8 + - - -
57B HIS* 2.8 46.9 + - - +
59B ASN* 3.4 22.2 + - - +
62B LEU* 3.8 21.5 - - + -
130B TRP* 5.2 0.9 - - + -
131B ILE 4.9 0.7 - - - +
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Residues in contact with LYS 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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61A GLN 5.6 0.7 - - - -
64A THR* 2.5 33.7 + - - -
65A GLU* 4.2 14.3 - - - +
98A ILE* 3.0 24.3 + - + +
99A ASP* 3.7 20.7 + - - +
100A GLY 3.3 0.2 - - - -
101A GLN* 1.3 73.8 - - - +
103A LYS* 1.3 65.8 + - - +
104A LYS 3.1 0.4 - - - -
105A CYS* 3.0 27.7 + - - +
106A GLY 4.3 0.5 + - - -
62B LEU* 4.3 28.0 - - + +
66B GLU* 4.2 7.5 - - - +
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Residues in contact with LYS 103 (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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99A ASP* 3.0 19.6 + - - +
100A GLY* 3.5 15.7 - - - +
102A LYS* 1.3 76.8 - - - +
104A LYS* 1.3 61.0 + - + +
105A CYS 3.2 1.4 + - - -
106A GLY 3.7 1.9 + - - -
107A GLU* 3.1 40.3 + - - +
80C ARG* 3.8 18.0 + - - +
81C ILE* 6.5 0.2 - - + -
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Residues in contact with LYS 104 (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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100A GLY* 3.0 25.4 + - - +
101A GLN* 3.3 26.9 - - - +
102A LYS 3.1 0.6 - - - -
103A LYS* 1.3 77.3 - - + +
105A CYS* 1.3 61.0 + - - +
106A GLY 3.2 1.2 + - - -
107A GLU* 3.6 35.2 + - - +
54B VAL 4.6 0.2 - - - +
55B PRO* 3.5 0.5 - - - +
56B VAL* 3.4 47.9 + - + +
57B HIS* 3.6 15.0 - - + -
81C ILE* 5.7 2.0 - - - -
83C GLU* 6.1 0.7 - - - -
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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
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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