Contacts of the helix formed by residues 2 - 13 (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 LEU 2 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1E ASN* 1.3 78.5 - - - +
3E VAL* 1.3 58.2 + - + +
5E PHE* 4.2 13.5 - - + -
6E HIS* 2.9 29.3 + - - +
51E TYR* 4.4 5.8 - - - +
62E LYS* 3.1 37.5 + - + +
63E PHE* 6.5 0.2 - - + -
190E OAP 3.4 74.9 - - + -
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Residues in contact with VAL 3 (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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111B TYR* 3.6 35.2 - - + +
1E ASN* 2.9 14.3 + - - +
2E LEU* 1.3 73.9 - - + +
4E ASN* 1.3 66.2 + - - +
6E HIS* 3.3 6.4 + - - +
7E ARG* 3.0 58.0 + - + +
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Residues in contact with ASN 4 (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* 2.8 35.7 + - - +
3E VAL* 1.3 76.5 - - - +
5E PHE* 1.3 52.5 + - - +
7E ARG* 3.1 16.5 + - - +
8E MET* 2.8 34.3 + - - +
65E SER* 3.4 7.9 - - - +
66E TYR* 3.1 58.6 - - + +
68E PHE* 3.7 15.2 - - + -
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Residues in contact with PHE 5 (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 3.1 10.1 + - - +
2E LEU* 3.8 17.5 - - + +
4E ASN* 1.3 78.9 - - - +
6E HIS* 1.3 58.6 + - - +
8E MET* 3.1 6.9 + - + +
9E ILE* 2.8 50.0 + - + +
47E HIS* 3.5 33.2 - + - -
51E TYR* 4.7 0.2 - - - -
66E TYR* 3.6 6.0 + - - -
91E ASP* 3.3 51.6 - - + +
94E ALA* 3.7 14.1 - - + -
95E ALA 4.2 0.7 - - - -
98E PHE* 4.6 1.3 - + - -
190E OAP 3.6 42.8 - + + -
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Residues in contact with HIS 6 (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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111B TYR* 6.1 3.8 - - - -
2E LEU 2.9 20.0 + - - +
3E VAL* 3.6 7.6 + - - +
4E ASN 3.2 0.2 - - - -
5E PHE* 1.3 77.8 - - - +
7E ARG* 1.3 65.6 + - - +
9E ILE* 3.5 2.1 + - - +
10E LYS* 3.1 30.3 + - + +
16E GLU* 2.8 32.3 + - + -
17E ALA* 3.7 28.2 + - + +
18E ALA* 3.8 10.5 + - + +
190E OAP 3.7 21.5 - + + -
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Residues in contact with ARG 7 (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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107B LYS* 3.3 59.4 + - - +
108B LYS* 5.2 3.9 + - - -
110B GLN* 4.2 1.0 + - - +
111B TYR* 3.1 39.3 - - + +
3E VAL* 3.0 43.5 + - + +
4E ASN* 3.1 16.7 + - - +
6E HIS* 1.3 75.7 - - - +
8E MET* 1.3 68.3 + - - +
10E LYS* 3.1 8.0 + - - +
11E LEU* 3.0 32.1 + - + +
68E PHE* 4.3 12.5 - - + -
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Residues in contact with MET 8 (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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4E ASN 2.8 14.3 + - - +
5E PHE* 3.1 10.7 + - - +
7E ARG* 1.3 79.4 - - - +
9E ILE* 1.3 61.2 + - - +
11E LEU* 3.1 11.1 + - - +
12E THR* 3.2 15.4 + - - +
66E TYR* 3.3 35.0 - - + +
68E PHE* 4.0 15.4 - - + -
75E ILE* 3.6 41.8 - - + +
88E CYS* 4.1 13.0 - - - +
91E ASP* 3.5 12.8 - - - +
92E LYS* 3.3 32.3 - - - -
95E ALA* 3.8 9.9 - - + -
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Residues in contact with ILE 9 (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* 2.8 54.4 + - + +
6E HIS 3.9 3.4 - - - +
8E MET* 1.3 71.1 - - - +
10E LYS* 1.3 64.1 + - - +
12E THR* 3.2 6.9 + - - -
13E THR* 2.7 44.4 + - + +
15E LYS 4.5 2.0 - - - +
17E ALA* 3.8 30.7 - - + -
21E TYR* 4.0 16.2 - - + -
95E ALA* 4.3 5.2 - - + -
98E PHE* 4.0 19.3 - - + -
190E OAP 3.8 19.7 - - + -
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Residues in contact with LYS 10 (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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6E HIS* 3.1 22.6 + - + +
7E ARG* 3.1 11.7 + - - +
9E ILE* 1.3 76.2 - - - +
11E LEU* 1.3 60.9 + - + +
14E GLY* 2.8 51.3 + - - +
15E LYS 3.3 21.7 + - - +
16E GLU* 4.5 14.5 - - - +
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Residues in contact with LEU 11 (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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7E ARG* 3.0 21.0 + - + +
8E MET 3.1 5.8 + - - +
10E LYS* 1.3 81.8 - - + +
12E THR* 1.3 59.8 + - + +
14E GLY 4.8 0.5 + - - -
68E PHE* 4.3 13.7 - - + -
70E ASN* 3.4 47.6 - - + +
72E GLY 4.3 12.3 - - - +
73E SER* 4.7 4.5 - - - -
75E ILE* 4.1 14.6 - - + -
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Residues in contact with THR 12 (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 3.2 12.4 + - - +
9E ILE* 3.3 7.8 + - - -
11E LEU* 1.3 78.9 - - - +
13E THR* 1.3 64.0 + - - +
73E SER* 3.8 29.8 - - - +
75E ILE* 4.0 15.9 - - + -
95E ALA* 3.0 36.7 + - + +
96E THR* 4.7 7.2 - - - +
99E ALA* 3.5 19.8 - - - +
102E LYS* 4.5 5.7 + - - -
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Residues in contact with THR 13 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E ILE* 2.7 32.5 + - + +
12E THR* 1.3 83.2 - - - +
14E GLY* 1.3 60.7 + - - +
15E LYS* 3.0 25.3 + - - +
21E TYR* 3.7 19.9 - - - +
98E PHE* 3.8 9.0 - - + +
99E ALA* 3.6 33.4 - - - +
102E LYS* 3.5 29.6 + - + +
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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