Contacts of the helix formed by residues 2 - 13 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1C ASN* 1.3 76.0 - - - +
3C VAL* 1.3 57.9 + - + +
5C PHE* 3.9 7.9 - - + -
6C HIS* 2.9 30.1 + - - +
51C TYR* 4.9 4.5 - - - +
62C LYS* 3.2 32.3 + - + +
190C OAP 3.5 82.3 - - + -
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Residues in contact with VAL 3 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C ASN* 2.9 15.2 + - - +
2C LEU* 1.3 75.8 - - + +
4C ASN* 1.3 71.3 + - - +
6C HIS* 3.3 6.6 + - + +
7C ARG* 3.1 24.0 + - + +
111E TYR* 3.9 45.5 - - + +
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Residues in contact with ASN 4 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C ASN* 2.7 42.9 + - - +
3C VAL* 1.3 81.2 - - - +
5C PHE* 1.3 63.7 + - - +
7C ARG* 3.2 6.0 + - - +
8C MET* 3.0 21.5 + - - +
65C SER* 3.4 2.4 - - - -
66C TYR* 3.3 58.1 + - + +
68C PHE* 3.8 14.3 - - + -
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Residues in contact with PHE 5 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C ASN 3.0 13.8 + - - +
2C LEU* 3.7 8.1 - - + +
4C ASN* 1.3 80.0 - - - +
6C HIS* 1.3 56.4 + - - +
8C MET* 3.1 9.1 - - + +
9C ILE* 3.0 47.6 + - + +
47C HIS* 3.6 32.1 - + - -
51C TYR* 4.5 2.7 - - - -
66C TYR* 3.5 5.1 + - - -
91C ASP* 3.5 47.8 - - + +
94C ALA* 3.8 15.3 - - + -
95C ALA* 4.2 1.1 - - + -
98C PHE* 4.7 1.3 - + - -
190C OAP 3.5 50.3 - + + -
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Residues in contact with HIS 6 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C LEU 2.9 19.4 + - - +
3C VAL* 3.6 7.6 - - - +
4C ASN 3.3 0.2 - - - -
5C PHE* 1.3 71.9 - - - +
7C ARG* 1.3 65.4 + - - +
9C ILE* 3.4 2.9 + - - +
10C LYS* 3.1 39.3 + - - +
15C LYS 5.5 0.2 - - - -
16C GLU* 2.7 33.7 + - + -
17C ALA* 3.5 27.4 + - + +
18C ALA* 3.5 14.3 + - + +
190C OAP 3.9 17.2 - + + -
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Residues in contact with ARG 7 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C VAL* 3.1 15.2 + - + +
4C ASN* 3.4 10.5 - - - +
6C HIS* 1.3 75.2 + - - +
8C MET* 1.3 62.2 + - - +
10C LYS* 3.2 27.0 - - - +
11C LEU* 3.2 50.1 + - - +
68C PHE* 4.0 14.8 - - + -
70C ASN* 5.0 5.0 + - - -
107E LYS* 4.3 33.7 - - - +
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Residues in contact with MET 8 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C ASN 3.0 11.8 + - - +
5C PHE* 3.1 11.7 - - + +
7C ARG* 1.3 78.0 - - - +
9C ILE* 1.3 62.4 + - - +
11C LEU* 3.3 8.1 + - - +
12C THR* 3.2 25.1 + - - +
66C TYR* 3.4 37.7 - - + +
68C PHE* 4.1 22.6 - - + -
75C ILE* 3.5 26.9 - - + -
88C CYS* 4.1 12.8 - - - -
91C ASP* 3.6 14.8 - - + +
92C LYS* 3.4 34.8 - - - +
95C ALA* 4.0 7.4 - - + -
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Residues in contact with ILE 9 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C PHE* 3.0 40.6 + - + +
6C HIS 3.9 0.4 - - - +
8C MET* 1.3 70.9 - - - +
10C LYS* 1.3 62.9 + - - +
12C THR* 3.9 6.7 - - - +
13C THR* 2.4 46.9 + - + +
15C LYS 4.4 2.0 - - - +
17C ALA* 3.5 36.6 - - + -
21C TYR* 3.9 17.3 - - + -
95C ALA* 4.3 6.3 - - - -
98C PHE* 4.1 23.8 - - + -
190C OAP 3.6 21.8 - - + -
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Residues in contact with LYS 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C HIS* 3.1 32.4 + - - +
7C ARG* 3.2 30.1 - - - +
9C ILE* 1.3 76.4 - - - +
11C LEU* 1.3 60.1 - - + +
14C GLY* 2.7 41.6 + - - +
15C LYS 3.7 20.4 + - - +
16C GLU* 5.3 4.3 - - + +
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Residues in contact with LEU 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C ARG* 3.2 44.5 + - - +
8C MET* 3.5 5.4 - - - +
10C LYS* 1.3 82.2 - - + +
12C THR* 1.3 60.1 + - + +
13C THR 5.2 0.2 - - - -
14C GLY 4.8 0.7 + - - -
68C PHE* 4.2 13.0 - - + -
70C ASN* 3.4 48.2 - - + +
72C GLY 4.6 8.7 - - - +
73C SER* 4.5 11.6 - - - -
75C ILE* 4.5 9.6 - - + -
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Residues in contact with THR 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C MET 3.2 9.9 + - - +
9C ILE* 3.6 5.0 + - - -
11C LEU* 1.3 76.2 - - - +
13C THR* 1.3 62.4 + - - +
73C SER* 4.0 22.7 - - - +
75C ILE* 3.4 31.2 - - + -
95C ALA* 3.0 36.8 + - + +
96C THR* 4.5 7.6 - - - +
99C ALA* 3.4 21.2 - - - +
102C LYS* 3.4 9.9 + - - -
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Residues in contact with THR 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C ILE* 2.4 32.3 + - + +
12C THR* 1.3 80.9 - - - +
14C GLY* 1.3 59.2 + - - +
15C LYS* 3.1 21.7 + - - +
21C TYR* 3.4 25.4 - - + +
98C PHE* 3.6 11.4 - - + +
99C ALA* 3.6 30.5 - - - +
102C LYS* 3.4 28.8 + - + +
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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