Contacts of the helix formed by residues 82 - 101 (chain A) in PDB entry 1KVO
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 82 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A ARG* 3.2 19.8 + - - -
80A GLN 3.7 1.0 + - - -
81A ASP* 1.3 73.4 - - - +
83A CYS* 1.3 58.0 + - - +
85A SER* 4.1 6.5 - - - -
86A GLN* 2.8 54.6 + - - +
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Residues in contact with CYS 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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54A LEU* 4.5 2.3 - - - +
57A ARG* 4.5 7.0 - - - -
58A GLY 5.0 0.9 - - - -
59A CYS* 2.0 55.4 - - + +
64A LEU* 4.1 5.8 - - + -
81A ASP* 3.3 11.0 + - - +
82A SER* 1.3 80.1 + - - +
84A ARG* 1.3 57.5 + - - +
86A GLN* 3.9 3.3 - - - +
87A LEU* 2.9 32.1 + - - +
57B ARG 4.9 3.6 - - - -
58B GLY* 3.5 24.0 - - - +
83B CYS* 5.5 4.5 - - - -
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Residues in contact with ARG 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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64A LEU* 3.6 22.5 - - + +
65A SER* 2.6 35.0 + - - +
66A TYR* 3.9 7.1 - - + +
80A GLN* 3.7 31.9 - - + +
81A ASP* 2.9 34.1 + - - +
83A CYS* 1.3 74.6 - - - +
85A SER* 1.3 57.0 + - - +
87A LEU* 3.6 6.4 - - - +
88A CYS* 2.8 31.4 + - - +
55B GLU* 3.0 26.9 + - - +
56B LYS* 3.2 23.6 + - - +
58B GLY 3.9 2.4 - - - +
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Residues in contact with SER 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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77A CYS* 5.5 2.0 - - - -
78A ALA 4.2 4.4 + - - -
79A LYS* 5.2 0.2 - - - -
80A GLN* 2.8 43.4 + - - +
81A ASP 2.9 9.4 + - - -
82A SER* 3.5 8.1 - - - -
84A ARG* 1.3 73.0 - - - +
86A GLN* 1.3 68.5 + - - +
88A CYS* 3.0 4.8 + - - +
89A GLU* 2.9 31.4 + - - +
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Residues in contact with GLN 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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50A CYS* 4.6 0.2 - - - -
53A ARG* 4.4 22.1 + - - +
54A LEU* 3.6 18.8 - - + +
57A ARG* 2.9 28.2 + - - +
82A SER* 2.8 42.9 + - - +
85A SER* 1.3 74.0 - - - +
87A LEU* 1.3 56.0 + - - +
89A GLU* 3.3 8.7 + - + +
90A CYS* 2.9 34.3 + - - -
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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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1A ASN 4.3 0.7 - - - +
51A TYR* 3.5 38.6 - - + +
54A LEU* 3.7 16.7 - - + +
60A GLY 4.0 2.9 - - - +
61A THR* 3.7 22.9 - - - +
64A LEU* 3.3 46.2 - - + +
66A TYR* 3.7 17.0 - - + -
83A CYS 2.9 18.9 + - - +
84A ARG* 3.6 3.8 - - - +
86A GLN* 1.3 75.2 - - - +
88A CYS* 1.3 65.2 + - - +
90A CYS* 3.2 3.7 + - - +
91A ASP* 3.1 23.8 + - - +
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Residues in contact with CYS 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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8A MET* 3.7 8.3 - - - +
66A TYR* 3.6 38.6 - - + -
67A LYS 4.4 1.1 - - - -
68A PHE* 3.9 4.3 - - - -
77A CYS* 2.0 55.6 - - + -
80A GLN* 4.2 3.8 - - - +
84A ARG 2.8 22.3 + - - +
85A SER 3.0 3.8 + - - +
87A LEU* 1.3 72.6 - - - +
89A GLU* 1.3 56.1 + - - +
91A ASP* 3.5 2.9 + - - +
92A LYS* 2.9 22.7 + - - +
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Residues in contact with GLU 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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77A CYS* 3.3 26.8 + - - +
85A SER* 2.9 20.9 + - - +
86A GLN* 3.7 9.6 - - - +
88A CYS* 1.3 76.7 - - - +
90A CYS* 1.3 64.8 + - - +
91A ASP 3.2 0.2 - - - -
92A LYS* 3.6 24.2 + - - +
93A ALA* 3.0 25.6 + - - +
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Residues in contact with CYS 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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47A HIS* 3.2 16.7 - - + -
50A CYS* 2.0 56.7 - - + +
51A TYR* 4.1 13.2 - - + -
53A ARG* 3.9 2.7 - - - -
54A LEU* 3.6 23.3 - - - -
86A GLN 2.9 23.3 + - - -
87A LEU 3.5 6.7 - - - +
89A GLU* 1.3 76.3 - - - +
91A ASP* 1.3 63.0 + - - +
93A ALA* 3.6 5.0 + - - +
94A ALA 3.3 13.0 + - - -
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Residues in contact with ASP 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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1A ASN 4.1 1.7 - - - +
5A PHE* 3.2 39.8 - - + +
8A MET* 3.8 3.8 - - - -
47A HIS* 2.8 23.9 + - - -
51A TYR* 2.9 21.6 + - - -
66A TYR* 2.7 36.9 + - - +
87A LEU* 3.1 9.1 + - - +
88A CYS 3.6 5.8 - - - +
90A CYS* 1.3 75.9 - - - +
92A LYS* 1.3 59.8 + - - +
94A ALA 3.4 0.3 + - - -
95A ALA* 3.0 26.0 + - - +
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Residues in contact with LYS 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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8A MET* 3.7 9.6 - - - -
75A ILE* 3.2 50.6 + - + +
76A THR* 5.0 3.8 + - - +
77A CYS* 4.6 3.3 - - - +
88A CYS 2.9 17.8 + - - +
89A GLU* 3.6 28.4 + - - +
91A ASP* 1.3 75.9 - - - +
93A ALA* 1.3 57.8 + - - +
95A ALA* 3.3 2.6 + - - +
96A THR* 2.8 43.5 + - - +
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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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46A THR* 6.2 3.8 - - + -
89A GLU 3.0 17.9 + - - +
90A CYS* 3.8 5.6 - - - +
92A LYS* 1.3 77.5 - - - +
94A ALA* 1.3 58.1 + - - +
96A THR* 3.6 5.1 + - - -
97A CYS* 2.9 28.6 + - - +
100A ARG* 4.5 3.8 + - - +
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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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5A PHE* 3.9 11.2 - - + -
43A CYS* 4.8 6.7 - - - +
47A HIS* 3.6 39.7 - - + -
90A CYS 3.3 3.3 + - - +
91A ASP 3.9 3.1 - - - +
92A LYS 3.3 0.8 - - - -
93A ALA* 1.3 75.8 - - - +
95A ALA* 1.3 60.2 + - - +
97A CYS* 3.3 6.9 + - - +
98A PHE* 2.9 43.9 + - + -
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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* 4.3 4.0 - - + -
8A MET* 4.1 28.5 - - + +
9A ILE* 4.4 4.9 - - + +
12A THR* 3.0 33.6 + - + +
13A THR* 6.0 0.2 - - - -
75A ILE* 5.9 0.7 - - + -
91A ASP 3.0 17.9 + - - +
92A LYS* 3.3 4.9 + - - +
94A ALA* 1.3 78.0 - - - +
96A THR* 1.3 63.1 + - - +
98A PHE* 3.5 10.2 + - - +
99A ALA 3.3 14.0 + - - -
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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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12A THR* 4.7 8.4 - - + +
75A ILE* 6.2 0.5 - - - +
92A LYS* 2.8 28.9 + - - +
93A ALA* 3.9 5.8 - - - -
95A ALA* 1.3 74.3 - - - +
97A CYS* 1.3 59.7 - - - +
99A ALA* 3.3 8.3 + - + +
100A ARG* 2.9 46.3 + - + +
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Residues in contact with CYS 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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39A ALA 4.7 0.4 - - - -
42A ARG 5.3 0.4 - - - -
43A CYS* 2.0 51.4 - - + -
93A ALA 2.9 20.5 + - - +
94A ALA* 3.4 7.4 - - - +
96A THR* 1.3 73.9 - - - +
98A PHE* 1.3 64.7 + - - +
100A ARG* 3.2 26.2 + - - +
101A ASN* 2.8 35.1 + - - -
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Residues in contact with PHE 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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5A PHE* 4.7 2.2 - + - -
9A ILE* 3.9 33.4 - - + -
13A THR* 4.0 7.2 - - + -
21A TYR* 3.7 40.8 + + - +
40A THR* 3.7 20.3 + - + -
43A CYS* 3.5 30.3 - - + -
44A CYS* 3.5 28.0 - - - -
94A ALA* 2.9 27.6 + - + +
95A ALA* 3.7 4.9 - - - +
96A THR 3.3 0.2 - - - -
97A CYS* 1.3 75.3 - - - +
99A ALA* 1.3 63.1 + - - +
101A ASN* 3.1 6.4 + - - +
102A LYS* 3.1 21.7 + - - +
190A OAP 4.2 16.4 - - + -
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Residues in contact with ALA 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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12A THR* 3.2 31.4 - - - +
13A THR* 3.7 9.1 - - - +
95A ALA 3.3 10.5 + - - +
96A THR* 3.3 12.0 + - + +
97A CYS 3.3 0.2 - - - -
98A PHE* 1.3 77.2 - - - +
100A ARG* 1.3 62.2 + - - +
102A LYS* 3.2 22.6 + - + +
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Residues in contact with ARG 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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93A ALA* 4.5 3.4 + - - +
96A THR* 2.9 39.8 + - + +
97A CYS* 3.3 37.2 - - - +
99A ALA* 1.3 76.3 - - - +
101A ASN* 1.3 66.7 + - - +
102A LYS 3.5 0.4 + - - -
103A THR* 5.2 3.3 + - - +
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Residues in contact with ASN 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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39A ALA* 3.4 31.0 + - + +
40A THR* 3.6 17.3 + - - +
43A CYS* 3.5 17.0 - - - -
97A CYS* 2.8 30.7 + - - +
98A PHE 3.1 5.8 + - - +
100A ARG* 1.3 92.3 - - - +
102A LYS* 1.3 63.6 + - - +
103A THR* 3.3 4.3 - - - -
104A THR* 3.3 17.9 + - - +
105A TYR* 3.4 8.0 + - - +
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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