Contacts of the strand formed by residues 63 - 75 (chain A) in PDB entry 2VGM
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 VAL 63 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A LYS* 3.2 6.5 - - - +
45A LYS 2.7 35.4 + - - +
46A LYS* 4.9 5.2 - - - +
47A PHE 5.9 1.8 - - - +
61A ASP* 3.6 13.5 - - + +
62A LEU* 1.3 84.4 - - - +
64A LYS* 1.3 61.2 + - - +
65A LEU* 3.5 30.8 + - + +
99A ILE* 4.4 13.2 - - + -
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Residues in contact with LYS 64 (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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42A ILE* 3.8 25.3 - - + +
43A PHE* 3.1 6.2 - - - +
44A LYS* 3.2 44.5 - - + +
63A VAL* 1.3 73.4 - - - +
65A LEU* 1.3 64.4 + - - +
94A ALA* 3.8 15.5 - - + +
95A SER* 3.2 13.2 - - - -
96A ASN 3.0 22.0 + - - -
97A VAL 4.8 0.2 + - - -
99A ILE* 4.9 1.0 - - - +
116A THR* 5.1 4.9 + - - -
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Residues in contact with LEU 65 (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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41A LEU 4.3 0.4 - - - -
42A ILE* 3.5 4.5 - - - +
43A PHE* 2.8 46.0 + - + +
45A LYS* 3.4 33.0 - - + -
46A LYS 5.0 0.2 - - - +
47A PHE 5.4 7.4 - - - +
63A VAL* 3.5 16.1 + - + +
64A LYS* 1.3 75.2 - - - +
66A LYS* 1.3 66.2 + - - +
95A SER* 3.6 6.0 + - - -
96A ASN* 3.4 18.4 - - - +
99A ILE* 3.7 33.0 - - + -
105A LEU* 3.5 29.6 - - + -
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Residues in contact with LYS 66 (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* 3.6 21.8 + - - -
41A LEU 3.2 9.0 - - - +
42A ILE* 3.8 29.5 - - + +
65A LEU* 1.3 81.3 - - - +
67A ILE* 1.3 73.8 + - - +
87A THR* 3.4 10.0 - - - +
88A VAL* 3.4 27.9 + - + +
89A THR 3.9 13.1 + - - -
90A ASP* 3.8 30.8 + - + +
95A SER* 3.4 9.6 - - - +
96A ASN* 3.2 22.7 - - - +
118A ILE* 5.2 4.0 - - - +
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Residues in contact with ILE 67 (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* 3.2 8.3 - - - +
41A LEU* 2.9 47.2 + - + -
43A PHE* 3.9 28.3 - - + -
66A LYS* 1.3 82.7 - - - +
68A LYS* 1.3 67.5 + - - +
69A VAL* 4.0 3.8 - - - +
83A TYR* 4.0 20.2 - - + +
84A LYS 4.4 2.2 - - - +
85A GLY* 3.9 18.8 - - - +
86A VAL 3.2 17.0 - - - +
87A THR* 4.1 4.3 - - + +
88A VAL* 4.3 5.2 - - - -
105A LEU* 4.0 23.8 - - + +
107A PHE* 5.0 1.3 - - + -
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Residues in contact with LYS 68 (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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38A ASP* 3.2 33.4 - - - +
39A ASP 3.5 7.0 - - - +
40A GLU* 4.4 9.6 - - - +
67A ILE* 1.3 73.0 - - - +
69A VAL* 1.3 72.0 + - - +
70A ILE* 3.7 10.8 - - + +
85A GLY* 3.3 19.1 - - - -
86A VAL* 2.9 29.5 + - + +
88A VAL* 3.8 18.8 - - + +
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Residues in contact with VAL 69 (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 VAL* 3.9 13.0 - - + -
36A ASP 3.7 20.0 - - - +
37A LYS* 4.0 8.5 - - + +
38A ASP* 3.1 19.3 + - - +
39A ASP 2.9 18.0 + - - +
41A LEU* 3.7 35.7 - - + -
67A ILE* 4.5 3.8 - - + -
68A LYS* 1.3 79.9 - - - +
70A ILE* 1.3 67.1 + - - +
71A SER 4.0 11.4 - - - +
83A TYR* 3.9 25.1 - - + -
84A LYS 3.9 5.2 - - - +
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Residues in contact with ILE 70 (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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37A LYS* 3.1 26.6 - - - +
68A LYS* 3.7 16.6 - - + +
69A VAL* 1.3 79.9 - - - +
71A SER* 1.3 64.5 + - - +
84A LYS* 2.7 15.1 + - + +
85A GLY* 3.6 13.0 - - - -
86A VAL* 4.1 31.4 - - + +
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Residues in contact with SER 71 (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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37A LYS* 4.1 13.0 - - - +
69A VAL* 4.0 2.4 - - - +
70A ILE* 1.3 84.4 - - - +
72A GLU* 1.3 63.1 + - - +
83A TYR* 3.4 10.2 - - - -
84A LYS* 3.0 56.0 + - - +
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Residues in contact with GLU 72 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A TYR* 3.5 39.2 + - + +
35A VAL 5.5 2.1 - - - +
37A LYS* 3.0 27.1 + - - +
71A SER* 1.3 79.4 - - - +
73A ASP* 1.3 63.3 + - - +
74A PHE* 4.3 4.2 + - + +
81A LEU* 4.9 1.6 - - + -
82A LYS 3.3 4.7 - - - -
83A TYR* 4.1 20.2 - - + -
84A LYS* 4.2 10.6 + - - -
325A HIS* 5.7 3.8 - - - -
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Residues in contact with ASP 73 (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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72A GLU* 1.3 73.4 - - - +
74A PHE* 1.3 63.3 + - - +
75A ASP* 6.1 0.2 - - - +
80A TYR* 3.2 25.6 - - + +
81A LEU* 3.3 5.6 - - - -
82A LYS* 2.7 68.2 + - - +
84A LYS* 4.5 8.3 - - - -
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Residues in contact with PHE 74 (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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28A LEU* 4.1 24.9 - - + -
29A PHE* 3.6 25.8 - + - -
32A TYR* 3.5 50.0 - + + +
72A GLU* 4.1 3.8 + - + +
73A ASP* 1.3 78.1 + - - +
75A ASP* 1.3 61.7 + - - +
76A MET* 3.2 41.5 - - + -
80A TYR* 3.2 11.7 - - - -
81A LEU* 3.6 17.5 - - + -
355A LEU* 4.5 9.2 - - + -
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Residues in contact with ASP 75 (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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74A PHE* 1.3 74.4 - - - +
76A MET* 1.3 66.2 + - - +
77A LYS* 3.5 22.3 + - - +
78A ASP* 2.9 33.5 + - + +
79A GLU 2.9 9.5 + - - -
80A TYR* 2.8 26.5 + - + +
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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
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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