Contacts of the strand formed by residues 19 - 25 (chain B) in PDB entry 2KH2
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 VAL 19 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11B LEU* 3.7 24.0 - - + -
13B ALA* 4.0 14.1 - - + -
17B ASP 4.3 0.7 - - - +
18B ARG* 1.3 72.5 - - - +
20B THR* 1.3 61.6 + - - +
21B ILE* 4.3 10.3 - - + -
73B LEU 3.7 0.5 - - - +
74B THR* 3.4 5.5 - - - +
75B ILE* 2.8 56.8 + - + +
78B LEU* 3.7 42.0 - - + -
104B VAL* 4.0 19.1 - - + -
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Residues in contact with THR 20 (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 SER 4.7 0.2 - - - +
8B PRO* 4.3 12.1 - - - +
11B LEU* 4.7 5.9 - - - +
18B ARG* 3.4 11.1 + - - +
19B VAL* 1.3 79.0 - - - +
21B ILE* 1.3 64.7 + - - +
22B THR* 4.2 2.8 + - - +
72B THR* 3.6 24.7 - - + -
73B LEU 3.3 6.1 - - - +
74B THR* 4.0 15.3 - - + +
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Residues in contact with ILE 21 (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 GLN* 4.3 1.6 - - - +
7B SER 4.1 2.7 - - - +
8B PRO* 4.9 0.7 - - - -
11B LEU* 5.1 0.4 - - + -
19B VAL* 4.3 12.6 - - + -
20B THR* 1.3 77.9 - - - +
22B THR* 1.3 66.8 + - - +
35B TRP* 3.8 21.1 - - + -
72B THR* 3.1 6.3 - - - -
73B LEU* 2.7 60.8 + - + +
75B ILE* 4.9 3.4 - - + -
86B TYR* 3.8 35.2 - - + -
102B THR* 3.3 39.5 - - + +
104B VAL* 4.2 8.1 - - + -
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Residues in contact with THR 22 (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 THR 4.7 0.2 - - - -
6B GLN* 3.3 5.4 - - - +
7B SER* 2.8 53.3 + - - +
20B THR* 5.0 2.9 + - - -
21B ILE* 1.3 76.2 - - - +
23B CYS* 1.3 68.3 + - - +
24B ARG* 5.3 2.0 - - + +
70B GLN* 4.2 22.2 - - + +
71B PHE 3.7 8.5 - - - +
72B THR* 4.2 11.9 - - - +
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Residues in contact with CYS 23 (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 MET* 3.4 21.8 - - - -
5B THR 3.6 3.4 - - - -
6B GLN* 4.3 2.0 - - + +
21B ILE 3.9 0.2 + - - -
22B THR* 1.3 77.0 - - - +
24B ARG* 1.3 60.6 + - - +
33B LEU* 4.4 7.0 - - - -
35B TRP* 3.5 20.9 - - + -
70B GLN* 3.8 2.4 - - - +
71B PHE* 2.8 44.2 + - + +
88B CYS* 2.0 50.0 - - - -
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Residues in contact with ARG 24 (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 GLN* 5.6 2.6 + - - +
4B MET* 3.4 9.4 - - - +
5B THR* 2.7 79.4 + - - +
22B THR* 5.8 2.2 - - + -
23B CYS* 1.3 74.3 - - - +
25B THR* 1.3 80.2 + - - +
26B SER* 4.9 10.5 - - - +
69B THR* 3.3 17.7 - - + +
70B GLN* 4.3 14.1 - - + -
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Residues in contact with THR 25 (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 ILE* 3.4 12.5 - - - +
3B GLN 3.6 4.5 - - - -
4B MET* 3.8 17.7 - - + -
24B ARG* 1.3 92.4 + - - +
26B SER* 1.3 59.6 + - - +
27B GLY 2.8 30.1 + - - +
29B ILE* 4.0 23.3 - - + +
69B THR* 3.2 41.4 + - - +
71B PHE* 4.4 5.8 - - + -
90B HIS* 4.4 1.6 - - - -
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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