Contacts of the helix formed by residues 2 - 13 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1B ASN* 1.3 75.0 - - - +
3B VAL* 1.3 62.0 + - + +
5B PHE* 3.9 13.2 - - + -
6B HIS* 2.9 28.9 + - - +
51B TYR* 4.8 3.6 - - - +
62B LYS* 3.2 40.7 + - + +
63B PHE* 5.8 2.9 - - + -
190B OAP 3.6 71.4 - - + -
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Residues in contact with VAL 3 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B ASN* 3.0 14.3 + - - +
2B LEU* 1.3 76.0 - - + +
4B ASN* 1.3 72.5 + - - +
6B HIS* 3.0 8.6 + - + +
7B ARG* 2.9 24.7 + - + +
111C TYR* 4.0 44.0 - - + +
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Residues in contact with ASN 4 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B ASN* 2.7 40.4 + - - +
3B VAL* 1.3 76.5 - - - +
5B PHE* 1.3 63.7 + - - +
7B ARG* 3.1 9.5 + - - +
8B MET* 3.0 23.9 + - - +
65B SER* 3.4 2.9 - - - -
66B TYR* 3.3 55.3 + - + -
68B PHE* 3.9 13.7 - - + -
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Residues in contact with PHE 5 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B ASN 3.1 14.9 + - - +
2B LEU* 3.7 9.2 - - + +
4B ASN* 1.3 79.5 - - - +
6B HIS* 1.3 62.7 + - - +
8B MET* 3.3 5.6 + - - +
9B ILE* 3.1 44.5 + - + +
47B HIS* 3.5 30.1 - + - -
51B TYR* 4.5 1.1 - - - -
66B TYR* 3.6 5.6 + - - -
91B ASP* 3.6 46.9 - - + +
94B ALA* 4.0 14.6 - - + -
95B ALA* 4.5 1.3 - - + -
98B PHE* 4.7 0.9 - + - -
190B OAP 3.6 51.6 - + + -
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Residues in contact with HIS 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B LEU 2.9 20.3 + - - +
3B VAL* 3.3 9.9 - - + +
5B PHE* 1.3 77.0 - - - +
7B ARG* 1.3 63.0 + - - +
9B ILE* 3.6 3.5 + - - +
10B LYS* 3.3 24.9 + - + +
15B LYS 5.0 1.1 - - - +
16B GLU* 2.8 34.3 + - + -
17B ALA* 3.5 30.4 + - + +
18B ALA* 3.7 10.1 - - + +
190B OAP 3.9 17.0 - + + -
111C TYR* 6.3 1.6 - + - -
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Residues in contact with ARG 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B VAL* 2.9 13.5 + - + +
4B ASN* 3.4 9.2 - - - +
6B HIS* 1.3 78.1 + - - +
8B MET* 1.3 64.6 + - - +
10B LYS* 3.3 8.3 + - - +
11B LEU* 3.0 39.3 + - + +
68B PHE* 3.1 33.3 + - + -
69B SER* 5.6 0.4 - - - +
70B ASN* 2.9 28.9 + - - +
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Residues in contact with MET 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B ASN 3.0 19.3 + - - +
5B PHE* 3.3 6.7 + - + +
7B ARG* 1.3 76.2 - - - +
9B ILE* 1.3 58.4 + - - +
11B LEU* 2.9 13.2 + - - +
12B THR* 2.8 32.8 + - - +
66B TYR* 3.6 31.0 - - + +
68B PHE* 3.9 17.5 - - + -
75B ILE* 3.8 30.5 - - + -
88B CYS* 4.0 12.1 - - - +
91B ASP* 3.8 10.8 - - - +
92B LYS* 3.6 34.5 - - - +
95B ALA* 3.9 10.1 - - + -
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Residues in contact with ILE 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B PHE* 3.1 48.2 + - + +
6B HIS 3.9 5.8 - - - +
7B ARG 3.3 0.2 - - - -
8B MET* 1.3 76.2 - - - +
10B LYS* 1.3 54.8 + - - +
12B THR* 3.7 6.3 - - - -
13B THR* 2.6 50.3 + - + +
15B LYS 4.4 3.6 - - - +
17B ALA* 3.7 29.4 - - + -
21B TYR* 4.0 17.9 - - + -
95B ALA* 4.2 8.1 - - + -
98B PHE* 4.0 21.3 - - + -
190B OAP 3.9 10.3 - - + -
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Residues in contact with LYS 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B HIS* 3.3 18.4 + - + +
7B ARG* 3.3 11.8 + - - +
8B MET 3.1 0.4 - - - -
9B ILE* 1.3 77.1 - - - +
11B LEU* 1.3 62.1 + - + +
14B GLY* 2.8 51.9 + - - +
15B LYS 3.2 29.6 + - - +
16B GLU* 4.3 8.1 - - + +
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Residues in contact with LEU 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B ARG* 3.0 45.2 + - - +
8B MET* 2.9 8.6 + - - +
10B LYS* 1.3 82.4 - - + +
12B THR* 1.3 60.4 + - - +
14B GLY* 4.6 0.5 + - - -
68B PHE* 4.0 13.2 - - + -
70B ASN* 3.5 43.5 - - + +
72B GLY 4.5 6.9 - - - +
73B SER* 2.8 21.3 + - - -
75B ILE* 4.1 11.7 - - + -
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Residues in contact with THR 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B MET 2.8 20.2 + - - +
9B ILE* 3.4 9.9 + - - -
11B LEU* 1.3 76.4 - - - +
13B THR* 1.3 64.9 + - - +
14B GLY 3.7 0.2 - - - -
73B SER* 4.0 19.0 + - - +
75B ILE* 3.7 23.1 - - + -
95B ALA* 2.8 40.5 + - + +
96B THR* 4.5 8.5 - - - +
99B ALA* 3.5 19.3 - - - +
102B LYS* 3.6 9.2 + - - -
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Residues in contact with THR 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ILE* 2.6 29.2 + - + +
12B THR* 1.3 80.3 + - - +
14B GLY* 1.3 63.1 + - - +
15B LYS* 3.0 29.3 + - - +
21B TYR* 3.7 19.7 - - + +
98B PHE* 3.9 7.2 - - + -
99B ALA* 3.6 32.3 - - - +
102B LYS* 3.9 22.9 + - + +
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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