Contacts of the helix formed by residues 82 - 100 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57E ARG* 3.4 20.3 + - - -
80E GLN 3.7 0.4 + - - -
81E ASP* 1.3 73.5 - - - +
83E CYS* 1.3 66.0 + - - +
85E SER* 3.3 5.7 + - - -
86E GLN* 3.0 25.6 + - - +
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Residues in contact with CYS 83 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54E LEU* 3.7 5.9 - - - +
57E ARG* 4.5 3.8 - - - +
58E GLY 5.1 0.4 - - - -
59E CYS* 2.0 58.5 - - + -
64E LEU* 4.0 6.5 - - + -
81E ASP* 3.4 9.2 + - - +
82E SER* 1.3 80.4 - - - +
84E ARG* 1.3 58.0 + - - +
86E GLN 3.5 0.2 + - - -
87E LEU* 3.0 30.3 + - - +
57F ARG 4.7 4.9 - - - -
58F GLY* 3.6 20.4 - - - +
83F CYS* 5.8 3.6 - - - -
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Residues in contact with ARG 84 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64E LEU* 3.2 34.5 - - + +
65E SER* 2.9 39.5 + - - +
66E TYR* 3.8 9.1 - - + +
80E GLN* 3.6 33.2 - - + +
81E ASP* 3.1 25.8 + - - +
83E CYS* 1.3 79.2 - - - +
85E SER* 1.3 56.8 + - - +
87E LEU* 3.6 2.0 + - - +
88E CYS* 3.0 29.8 + - - +
55F GLU* 2.7 26.9 + - - +
56F LYS* 3.0 21.2 + - - +
58F GLY* 4.1 0.6 - - - +
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Residues in contact with SER 85 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77E CYS* 4.8 2.1 - - - +
78E ALA 4.4 5.3 + - - -
79E LYS* 5.0 0.3 - - - -
80E GLN* 3.0 29.8 + - - +
81E ASP 2.8 22.9 + - - -
82E SER* 3.5 6.3 - - - -
84E ARG* 1.3 74.8 - - - +
86E GLN* 1.3 66.0 + - - +
88E CYS* 3.2 6.3 + - - +
89E GLU* 3.0 28.9 + - - +
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Residues in contact with GLN 86 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50E CYS* 3.6 8.5 - - - -
53E ARG* 5.5 4.2 + - - -
54E LEU* 3.9 16.7 - - + +
57E ARG* 4.1 19.1 - - - +
82E SER 3.0 16.0 + - - +
85E SER* 1.3 76.8 - - - +
87E LEU* 1.3 58.3 + - - +
89E GLU* 3.1 12.8 + - - +
90E CYS* 2.8 42.4 + - - +
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Residues in contact with LEU 87 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1E ASN 4.4 0.7 - - - +
51E TYR* 3.3 44.0 - - + +
54E LEU* 3.9 7.5 - - + +
60E GLY 3.9 5.6 - - - +
61E THR* 3.2 41.5 - - + +
64E LEU* 3.4 27.6 - - + +
66E TYR* 4.0 14.8 - - + -
83E CYS 3.0 18.3 + - - +
84E ARG 3.9 3.6 - - - +
86E GLN* 1.3 75.0 - - - +
88E CYS* 1.3 63.7 + - - +
90E CYS* 3.1 8.5 + - - +
91E ASP* 3.0 27.3 + - - +
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Residues in contact with CYS 88 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E MET* 4.1 3.4 - - - +
66E TYR* 3.6 39.7 - - + -
67E LYS 4.0 2.2 - - - -
68E PHE* 3.8 7.6 - - - -
77E CYS* 2.0 52.5 - - + -
80E GLN* 4.5 2.7 - - - +
84E ARG 3.0 19.6 + - - +
85E SER* 3.4 5.8 - - - +
86E GLN 3.2 0.2 - - - -
87E LEU* 1.3 74.7 - - - +
89E GLU* 1.3 56.1 + - - +
91E ASP* 3.1 5.4 + - - +
92E LYS* 2.9 27.7 + - - +
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Residues in contact with GLU 89 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77E CYS* 3.3 28.7 + - + +
85E SER* 3.0 17.3 + - - +
86E GLN* 3.1 18.8 + - - +
88E CYS* 1.3 73.6 - - - +
90E CYS* 1.3 64.2 + - - +
92E LYS* 3.9 20.6 + - - +
93E ALA* 3.0 24.9 + - - +
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Residues in contact with CYS 90 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47E HIS* 3.5 11.9 - - + -
50E CYS* 2.0 57.4 - - + -
51E TYR* 4.1 9.4 - - + -
54E LEU* 3.3 19.7 - - - -
86E GLN* 2.8 27.0 + - - +
87E LEU* 3.1 8.0 + - - +
89E GLU* 1.3 75.7 - - - +
91E ASP* 1.3 70.3 + - - +
93E ALA* 3.3 6.2 + - - +
94E ALA 3.1 17.2 + - - -
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Residues in contact with ASP 91 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1E ASN 4.3 1.9 + - - +
5E PHE* 3.3 40.1 - - + +
8E MET* 3.5 3.6 - - - -
47E HIS* 2.9 20.0 + - - -
51E TYR* 2.9 23.8 + - - -
66E TYR* 2.8 36.8 + - - +
87E LEU 3.0 9.7 + - - -
88E CYS 3.4 6.3 - - - +
90E CYS* 1.3 78.8 - - - +
92E LYS* 1.3 55.1 + - - +
94E ALA 3.3 0.5 + - - -
95E ALA* 2.8 32.4 + - - +
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Residues in contact with LYS 92 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E MET* 3.3 16.6 - - + -
74E ARG* 2.6 41.5 - - - +
75E ILE* 2.7 38.7 + - + +
76E THR* 4.8 0.8 - - - +
77E CYS* 4.6 7.8 - - - +
88E CYS 2.9 18.4 + - - +
89E GLU* 3.9 24.3 + - - +
91E ASP* 1.3 71.6 - - - +
93E ALA* 1.3 57.9 + - - +
95E ALA* 3.7 1.7 - - - +
96E THR* 2.7 49.5 + - - +
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Residues in contact with ALA 93 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46E THR* 6.2 4.3 - - + -
89E GLU 3.0 17.3 + - - +
90E CYS* 3.5 7.6 - - - +
92E LYS* 1.3 77.5 - - - +
94E ALA* 1.3 57.1 + - - +
96E THR* 3.8 5.7 - - - +
97E CYS* 2.8 30.9 + - - +
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Residues in contact with ALA 94 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E PHE* 3.7 11.2 - - + -
43E CYS* 4.7 7.6 - - - +
47E HIS* 3.4 40.4 - - + -
90E CYS 3.1 5.0 + - - +
91E ASP 3.6 4.7 - - - +
92E LYS 3.2 0.2 - - - -
93E ALA* 1.3 74.9 - - - +
95E ALA* 1.3 59.5 + - - +
97E CYS* 3.6 6.3 - - - +
98E PHE* 2.8 44.8 + - + -
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Residues in contact with ALA 95 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E PHE* 4.2 1.0 - - - -
8E MET* 3.8 31.4 - - + -
9E ILE* 4.3 15.5 - - + +
12E THR* 3.0 32.6 + - + +
75E ILE* 5.4 0.9 - - + -
91E ASP 2.8 20.4 + - - +
92E LYS* 3.7 4.3 - - - +
94E ALA* 1.3 72.8 - - - +
96E THR* 1.3 61.5 + - - +
98E PHE* 3.4 4.7 + - - +
99E ALA 3.2 14.2 + - - -
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Residues in contact with THR 96 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E THR* 4.7 9.0 - - - +
75E ILE* 5.5 1.9 - - - +
92E LYS* 2.7 39.4 + - - +
93E ALA* 3.8 5.8 - - - +
95E ALA* 1.3 73.1 - - - +
97E CYS* 1.3 58.2 + - - +
99E ALA* 2.9 24.6 + - - +
100E ARG* 2.9 35.7 + - + +
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Residues in contact with CYS 97 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39E ALA 4.7 0.7 - - - -
42E ARG* 5.2 0.4 - - - -
43E CYS* 2.0 51.8 - - + -
93E ALA 2.8 22.7 + - - +
94E ALA* 3.2 4.9 + - - +
96E THR* 1.3 72.7 - - - +
98E PHE* 1.3 61.7 + - - +
100E ARG* 3.5 17.1 + - - +
101E ASN* 2.9 38.7 + - - -
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Residues in contact with PHE 98 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E PHE* 4.6 5.8 - + - -
9E ILE* 4.0 31.9 - - + -
13E THR* 3.8 13.5 - - + -
21E TYR* 3.8 32.3 + + - +
40E THR* 3.6 44.7 + - + -
43E CYS* 3.7 15.5 - - + -
44E CYS* 3.5 22.4 - - - -
94E ALA* 2.8 25.4 + - + +
95E ALA* 3.5 5.4 - - - +
96E THR 3.1 0.2 - - - -
97E CYS* 1.3 72.9 - - - +
99E ALA* 1.3 63.4 + - - +
101E ASN* 3.4 5.1 + - - +
102E LYS* 3.3 20.4 + - - +
190E OAP 4.1 17.9 - - + -
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Residues in contact with ALA 99 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E THR* 3.5 31.0 - - + +
13E THR* 3.6 9.3 - - - +
95E ALA 3.2 8.3 + - - +
96E THR* 2.9 11.1 + - - +
98E PHE* 1.3 79.1 - - - +
100E ARG* 1.3 63.2 + - + +
102E LYS* 3.2 26.1 + - - +
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Residues in contact with ARG 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96E THR* 2.9 41.3 + - + +
97E CYS* 3.9 12.7 - - - +
98E PHE 3.3 0.2 - - - -
99E ALA* 1.3 77.5 - - + +
101E ASN* 1.3 79.4 + - - +
102E LYS 3.4 1.3 + - - -
103E THR* 4.6 5.9 + - - -
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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