Contacts of the helix formed by residues 2 - 13 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1F ASN* 1.3 73.2 - - - +
3F VAL* 1.3 59.8 + - + +
5F PHE* 4.2 6.5 - - + -
6F HIS* 3.0 28.7 + - - +
51F TYR* 4.5 7.2 - - - +
62F LYS* 2.9 46.6 + - + +
63F PHE* 5.6 5.2 - - + -
190F OAP 3.5 69.7 - - + -
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Residues in contact with VAL 3 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D TYR* 4.1 44.6 - - + +
1F ASN* 2.9 15.5 + - - +
2F LEU* 1.3 73.0 - - + +
4F ASN* 1.3 72.3 + - - +
6F HIS* 3.1 8.2 + - - +
7F ARG* 2.9 30.0 + - + +
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Residues in contact with ASN 4 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1F ASN* 3.0 34.1 + - - +
3F VAL* 1.3 80.1 - - - +
5F PHE* 1.3 63.8 + - - +
7F ARG* 3.1 9.0 + - - +
8F MET* 3.0 22.2 + - - +
65F SER* 3.5 5.5 - - - +
66F TYR* 3.0 61.7 + - + +
68F PHE* 3.7 14.0 - - + -
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Residues in contact with PHE 5 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1F ASN 3.2 13.7 + - - +
2F LEU* 3.8 9.0 - - + +
4F ASN* 1.3 77.9 - - - +
6F HIS* 1.3 63.2 + - - +
8F MET* 3.1 8.4 + - - +
9F ILE* 3.0 47.1 + - + +
47F HIS* 3.5 29.4 - + - -
51F TYR* 4.4 3.8 - - - -
66F TYR* 3.5 5.7 + - - -
91F ASP* 3.4 49.6 - - + +
94F ALA* 3.7 15.9 - - + -
95F ALA 4.3 1.1 - - - -
98F PHE* 4.5 1.3 - + - -
190F OAP 3.5 50.7 - + + -
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Residues in contact with HIS 6 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2F LEU 3.0 20.2 + - - +
3F VAL* 3.1 8.2 + - + +
5F PHE* 1.3 77.2 - - - +
7F ARG* 1.3 61.9 + - - +
9F ILE* 3.7 2.3 + - - +
10F LYS* 3.4 24.1 + - + +
15F LYS 5.2 1.0 - - - +
16F GLU* 2.6 39.3 + - + -
17F ALA* 3.4 31.3 + - + +
18F ALA* 3.5 10.4 + - + +
190F OAP 4.0 16.5 - + + -
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Residues in contact with ARG 7 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D LYS* 5.4 12.1 - - - +
3F VAL* 2.9 21.5 + - + +
4F ASN* 3.1 10.2 + - - +
6F HIS* 1.3 76.3 - - + +
8F MET* 1.3 65.8 + - - +
10F LYS* 3.3 8.2 + - - +
11F LEU* 3.1 59.7 + - - +
68F PHE* 3.7 32.2 + - + -
69F SER* 5.9 1.0 - - - +
70F ASN* 4.7 5.3 + - - -
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Residues in contact with MET 8 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4F ASN 3.0 8.7 + - - +
5F PHE* 3.3 9.4 - - - +
7F ARG* 1.3 77.7 - - - +
9F ILE* 1.3 62.5 + - - +
11F LEU* 3.1 19.1 + - - +
12F THR* 3.2 17.9 + - - +
66F TYR* 3.6 23.3 - - + +
68F PHE* 3.9 25.7 - - + -
75F ILE* 3.6 40.6 - - + -
88F CYS* 4.2 4.3 - - - -
91F ASP* 3.5 32.8 - - - +
92F LYS* 3.5 15.9 - - - +
95F ALA* 3.8 11.4 - - + -
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Residues in contact with ILE 9 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F PHE* 3.0 38.9 + - + +
6F HIS 4.0 4.3 - - - +
7F ARG 3.4 0.2 - - - -
8F MET* 1.3 74.2 - - - +
10F LYS* 1.3 56.6 + - - +
12F THR* 3.7 6.3 - - - -
13F THR* 2.5 52.4 + - + +
15F LYS 4.3 2.9 - - - +
17F ALA* 3.6 15.0 - - + -
21F TYR* 3.7 22.7 - - + -
95F ALA* 4.5 5.2 - - + -
98F PHE* 4.1 22.2 - - + -
190F OAP 3.6 32.1 - - + -
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Residues in contact with LYS 10 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F HIS* 3.4 17.0 + - + +
7F ARG* 3.3 12.3 + - - +
8F MET 3.2 0.2 - - - -
9F ILE* 1.3 78.3 - - - +
11F LEU* 1.3 60.2 + - + +
14F GLY* 2.7 43.9 + - - +
15F LYS 3.5 26.4 + - - +
16F GLU* 4.6 7.6 - - + +
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Residues in contact with LEU 11 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7F ARG* 3.1 40.8 + - - +
8F MET* 3.1 7.6 + - - +
10F LYS* 1.3 82.5 - - + +
12F THR* 1.3 62.1 + - + +
14F GLY 4.9 0.3 + - - -
68F PHE* 4.0 16.8 - - + -
70F ASN* 3.3 41.7 - - + +
72F GLY 4.7 5.2 - - - +
73F SER* 4.1 14.5 + - - -
75F ILE* 4.8 4.9 - - + -
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Residues in contact with THR 12 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F MET 3.2 12.4 + - - +
9F ILE* 3.3 9.4 + - - -
11F LEU* 1.3 80.3 - - - +
13F THR* 1.3 63.5 + - - +
14F GLY 3.7 0.2 - - - -
73F SER* 3.8 30.6 - - - +
75F ILE* 4.3 10.3 - - + -
95F ALA* 2.9 39.2 + - + +
96F THR* 4.6 7.2 - - - +
99F ALA* 3.7 18.8 - - - +
102F LYS* 4.4 4.2 + - - +
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Residues in contact with THR 13 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F ILE* 2.5 34.7 + - + +
12F THR* 1.3 81.5 - - - +
14F GLY* 1.3 59.3 + - - +
15F LYS* 3.0 24.2 + - - +
21F TYR* 3.6 14.1 + - - +
98F PHE* 3.5 33.2 - - + -
99F ALA* 3.5 15.7 - - - +
102F LYS* 3.0 34.7 + - + -
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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