Contacts of the strand formed by residues 9 - 14 (chain B) in PDB entry 1KO1
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 HIS 9 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B HIS 5.3 2.4 + - - -
8B HIS* 1.3 74.5 + - - +
10B ILE* 1.3 84.9 + - - +
11B TYR* 3.4 40.0 + + + +
77B GLN* 5.2 0.8 - - - +
80B ASN 4.9 0.9 - - - +
81B LYS 2.9 13.5 + - - +
82B VAL* 3.6 2.5 - - + -
83B SER* 3.0 25.1 + - - +
103B PRO 4.6 3.1 - - - -
104B ASN* 3.3 31.4 + - - +
105B LEU 3.9 2.0 - - - -
106B SER* 3.4 24.4 + - - -
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Residues in contact with ILE 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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9B HIS* 1.3 83.1 - - - +
11B TYR* 1.3 67.0 + - - +
12B VAL* 4.1 0.9 - - + -
73B ALA* 3.5 34.3 - - + +
77B GLN* 3.7 23.6 - - + -
83B SER* 3.3 16.4 - - - +
85B ILE* 3.8 31.9 - - + -
102B ASN* 4.7 5.2 - - - +
104B ASN* 2.9 24.4 + - - +
105B LEU* 3.9 25.1 - - + -
106B SER 2.8 26.0 + - - -
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Residues in contact with TYR 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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9B HIS* 3.4 30.4 - + + +
10B ILE* 1.3 74.3 - - - +
12B VAL* 1.3 63.1 + - - +
13B LEU* 3.7 2.1 + - + +
82B VAL* 4.1 18.6 - - + -
83B SER 2.6 14.1 + - - -
84B LEU* 3.2 19.1 - - + +
85B ILE 2.9 22.7 + - - +
106B SER* 3.0 31.9 - - - -
108B ILE* 3.9 32.5 - - + -
152B LEU* 4.5 11.2 - - + -
170B VAL 4.9 1.0 + - - -
171B ILE* 3.4 48.2 + - + +
174B GLY* 6.1 0.3 - - - -
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Residues in contact with VAL 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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10B ILE* 4.3 5.4 - - + -
11B TYR* 1.3 71.6 - - - +
13B LEU* 1.3 63.5 + - - +
14B MET 3.4 1.6 + - - -
85B ILE* 3.2 17.5 - - + +
87B CYS* 3.9 35.7 - - + +
89B ALA* 4.7 0.2 - - + -
98B LEU* 4.0 10.5 - - + -
105B LEU* 3.5 37.2 - - + -
106B SER 2.7 9.2 + - - +
107B PHE* 3.2 31.8 - - + +
108B ILE 2.8 24.1 + - - -
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Residues in contact with LEU 13 (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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11B TYR* 4.2 10.8 - - + +
12B VAL* 1.3 72.5 - - - +
14B MET* 1.3 59.9 + - - +
21B LYS* 3.4 18.3 - - + +
24B VAL* 3.9 17.7 - - + -
25B ALA* 3.8 38.8 - - + +
84B LEU* 4.5 9.0 - - + -
85B ILE 2.8 14.5 + - - +
86B VAL* 3.7 7.7 - - + -
87B CYS 3.1 23.4 + - - -
108B ILE* 3.3 39.9 - - + +
110B LEU* 4.1 11.7 - - + -
167B THR* 4.5 8.5 - - + -
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Residues in contact with MET 14 (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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12B VAL 4.3 2.0 - - - +
13B LEU* 1.3 73.6 - - - +
15B GLY* 1.3 64.0 + - - +
21B LYS* 3.6 6.3 - - - +
87B CYS 3.2 17.0 - - - +
88B SER 3.4 7.6 - - - +
89B ALA* 3.5 14.1 - - + +
95B ARG* 3.5 42.6 - - - +
107B PHE* 3.9 21.1 - - + -
108B ILE 3.0 10.3 + - - +
109B TYR* 3.6 31.9 - - + +
110B LEU* 3.0 29.3 + - - +
141B LEU* 4.5 8.7 - - + -
144B PRO* 4.1 17.7 - - + -
151B VAL* 4.9 0.2 - - - -
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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