Contacts of the helix formed by residues 87 - 102 (chain A) in PDB entry 1VFQ
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 SER 87 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A ASN 3.5 4.7 + - - -
86A VAL* 1.3 76.7 - - - +
88A GLY* 1.3 65.1 + - - +
89A LEU* 4.1 4.4 + - - +
90A GLN* 3.1 26.2 + - - +
91A ARG* 2.8 20.1 + - - +
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Residues in contact with GLY 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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86A VAL 3.6 2.0 + - - -
87A SER* 1.3 72.5 - - - +
89A LEU* 1.3 63.1 + - - +
91A ARG* 3.1 18.8 + - - +
92A ALA* 3.3 14.0 + - - +
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Residues in contact with LEU 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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87A SER* 3.3 4.8 + - - +
88A GLY* 1.3 74.2 - - - +
90A GLN* 1.3 65.8 + - + +
92A ALA* 3.5 6.7 + - + +
93A LYS* 3.1 26.0 + - - +
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Residues in contact with GLN 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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57A ARG* 3.3 35.6 + - - +
86A VAL* 4.0 12.8 - - + -
87A SER* 3.1 20.9 + - - +
89A LEU* 1.3 84.9 - - + +
91A ARG* 1.3 55.7 + - - +
92A ALA 3.3 0.2 - - - -
93A LYS* 3.6 30.2 - - - +
94A THR* 2.6 38.4 + - - -
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Residues in contact with ARG 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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82A ILE* 3.4 32.3 - - + +
83A GLY 2.8 24.5 + - - -
84A GLU* 3.3 22.8 + - - +
86A VAL* 3.8 17.8 + - + +
87A SER 2.8 15.4 + - - +
88A GLY* 3.1 10.2 + - - +
90A GLN* 1.3 77.8 - - - +
92A ALA* 1.3 57.2 + - - +
94A THR* 3.4 3.0 + - - -
95A GLY* 3.0 23.6 + - - -
115A SER* 3.1 29.3 + - - -
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Residues in contact with ALA 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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88A GLY 3.3 8.9 + - - +
89A LEU* 3.7 10.8 - - + +
91A ARG* 1.3 78.2 - - - +
93A LYS* 1.3 67.0 + - - +
95A GLY* 3.1 2.2 + - - -
96A THR* 3.1 28.9 + - + +
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Residues in contact with LYS 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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1A MET 4.6 11.4 + - - +
2A ALA* 6.1 0.2 - - - -
3A THR* 3.3 24.9 + - - +
31A TYR* 3.8 20.0 - - - -
33A GLY 5.2 0.4 + - - -
34A SER* 4.3 17.6 - - - -
57A ARG* 4.0 5.1 - - - +
89A LEU 3.1 14.6 + - - +
90A GLN* 3.6 36.5 - - - +
92A ALA* 1.3 78.9 - - - +
94A THR* 1.3 55.6 + - - +
96A THR* 3.2 8.1 + - - +
97A ASP* 2.9 47.9 + - - +
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Residues in contact with THR 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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31A TYR* 3.6 10.1 + - - +
57A ARG* 2.7 39.2 + - + +
58A LEU 5.3 0.2 - - - +
59A PHE* 3.7 23.2 - - + -
80A THR* 4.1 7.5 - - + +
81A TRP 4.9 0.9 - - - +
82A ILE* 3.9 23.6 - - + -
90A GLN 2.6 23.6 + - - -
91A ARG* 3.5 6.6 - - - -
92A ALA 3.1 0.4 - - - -
93A LYS* 1.3 74.5 - - - +
95A GLY* 1.3 67.0 + - - +
97A ASP* 3.0 12.3 + - - +
98A LYS* 3.4 8.0 + - - +
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Residues in contact with GLY 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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80A THR* 5.2 2.0 - - - -
82A ILE* 4.2 11.2 - - - +
91A ARG 3.0 15.3 + - - -
92A ALA* 3.1 4.7 + - - -
94A THR* 1.3 75.2 - - - +
96A THR* 1.3 60.1 + - - +
98A LYS* 2.8 44.9 + - - +
113A VAL* 5.8 2.2 - - - -
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Residues in contact with THR 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 ALA* 3.1 13.1 + - + +
93A LYS* 3.2 14.6 + - - +
95A GLY* 1.3 73.8 - - - +
97A ASP* 1.3 63.6 + - - +
98A LYS* 3.1 3.0 + - - -
99A THR* 3.0 27.6 + - - +
100A LEU 4.5 0.2 + - - -
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Residues in contact with ASP 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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3A THR* 2.8 39.5 + - - -
31A TYR* 2.6 31.1 + - - +
36A ILE* 4.3 5.6 - - + -
59A PHE* 3.9 6.7 - - + -
93A LYS* 2.9 30.3 + - - +
94A THR 3.0 4.4 + - - +
96A THR* 1.3 77.9 + - - +
98A LYS* 1.3 58.4 + - - +
99A THR 3.2 0.4 - - - -
100A LEU* 2.9 27.9 + - + +
101A VAL* 3.1 11.8 + - - +
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Residues in contact with LYS 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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59A PHE* 3.8 14.1 - - + -
78A LEU* 5.4 2.7 - - + -
80A THR* 3.6 30.3 - - + +
94A THR 3.4 4.6 + - - +
95A GLY* 2.8 33.7 + - - +
96A THR 3.1 2.0 - - - -
97A ASP* 1.3 77.4 - - - +
99A THR* 1.3 64.5 + - + +
101A VAL* 3.2 4.4 + - + +
102A LYS* 2.9 42.2 + - + +
111A GLU* 3.7 23.1 - - - +
113A VAL* 3.4 28.4 - - + +
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Residues in contact with THR 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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96A THR* 3.0 18.2 + - - +
98A LYS* 1.3 85.1 - - + +
100A LEU* 1.3 64.0 + - - +
102A LYS* 3.5 22.9 + - - +
103A GLU* 3.5 17.3 + - - +
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Residues in contact with LEU 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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3A THR* 3.9 41.3 - - + +
4A LYS* 4.5 0.7 - - - -
5A ILE* 4.0 37.3 - - + +
7A LYS* 5.2 2.0 - - - +
36A ILE* 4.7 3.6 - - + -
97A ASP* 2.9 15.8 + - - +
99A THR* 1.3 82.8 + - - +
101A VAL* 1.3 64.4 + - + +
103A GLU* 3.0 46.0 + - - +
104A VAL* 4.1 1.4 + - - +
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Residues in contact with VAL 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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5A ILE* 4.0 15.0 - - + -
29A PHE* 4.6 8.1 - - + -
36A ILE* 3.8 26.9 - - + -
59A PHE* 3.9 38.1 - - + -
78A LEU* 4.5 9.6 - - + -
97A ASP 3.1 12.2 + - - +
98A LYS* 3.6 8.3 - - + +
100A LEU* 1.3 75.8 - - - +
102A LYS* 1.3 58.0 + - + +
103A GLU 3.0 0.2 - - - -
104A VAL* 3.0 9.7 + - + +
105A VAL* 2.8 40.7 + - + -
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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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78A LEU* 3.4 21.3 - - + -
98A LYS* 2.9 31.4 + - + +
99A THR* 3.9 19.2 - - - +
100A LEU 3.2 0.4 - - - -
101A VAL* 1.3 71.8 - - - +
103A GLU* 1.3 62.7 + - - +
104A VAL 3.1 2.4 + - - -
105A VAL* 3.4 24.6 - - - +
106A GLN* 3.6 11.4 + - - +
108A PHE* 4.1 11.7 - - + -
111A GLU* 2.6 41.9 + - - +
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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