Contacts of the strand formed by residues 52 - 57 (chain A) in PDB entry 2KWI
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 ARG 52 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A LEU* 6.2 2.2 - - - -
16A LYS* 5.9 0.8 - - - +
35A MET* 4.6 3.8 - - - +
51A TYR* 1.3 81.1 - - - +
53A LYS* 1.3 62.7 + - - +
54A LYS 4.0 1.4 + - - -
63A GLN* 5.0 26.0 + - + +
64A ILE 3.5 11.2 - - - +
65A ASP* 3.3 39.0 - - - +
434B ARG* 3.2 43.3 + - - +
437B THR* 4.2 18.0 + - + +
438B ALA* 4.3 13.7 - - - +
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Residues in contact with LYS 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A PHE* 3.4 33.6 + - + +
35A MET* 2.9 43.4 + - + +
37A ASP* 5.9 0.6 + - - -
51A TYR 4.2 0.4 + - - -
52A ARG* 1.3 75.2 - - - +
54A LYS* 1.3 82.1 + - - +
55A VAL* 3.6 23.7 + - + -
62A VAL 3.7 1.4 - - - +
63A GLN* 3.8 3.3 - - - -
64A ILE* 3.3 42.8 + - + +
66A ILE* 5.4 2.0 - - + +
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Residues in contact with LYS 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A ARG 4.0 2.0 + - - -
53A LYS* 1.3 92.3 + - - +
55A VAL* 1.3 67.1 + - - +
56A VAL* 6.1 0.4 - - + -
61A GLU* 2.6 42.2 + - + +
62A VAL 3.8 6.1 - - - +
63A GLN* 5.0 16.8 + - + +
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Residues in contact with VAL 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A HIS* 6.2 0.2 - - + -
34A PHE* 4.0 18.2 - - + -
53A LYS* 3.7 28.3 - - + +
54A LYS* 1.3 81.1 - - - +
56A VAL* 1.3 55.1 + - - +
57A LEU* 3.7 21.5 - - + -
61A GLU* 3.5 1.5 - - - -
62A VAL* 2.6 53.0 + - + +
64A ILE* 5.0 4.0 - - + +
170A PHE* 4.3 14.4 - - + -
173A MET* 4.6 12.8 - - + -
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Residues in contact with VAL 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A LYS* 6.1 0.4 - - + -
55A VAL* 1.3 75.7 - - - +
57A LEU* 1.3 62.0 + - - +
58A ASP 3.6 2.6 + - - -
59A GLY* 3.6 22.7 - - - +
60A GLU 3.1 22.2 - - - +
61A GLU* 3.9 17.7 - - + +
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Residues in contact with LEU 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A HIS* 6.3 0.2 - - - +
55A VAL* 3.7 28.9 - - + -
56A VAL* 1.3 74.7 - - - +
58A ASP* 1.3 69.7 + - - +
59A GLY 3.0 8.6 + - - -
60A GLU* 3.0 26.4 + - + +
62A VAL* 3.7 16.4 - - + -
170A PHE* 3.8 28.7 - - + -
173A MET* 4.5 7.2 - - - -
174A ARG* 3.4 43.1 - - - +
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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