Contacts of the strand formed by residues 1013 - 1018 (chain A) in PDB entry 6KJV
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 ARG1013 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1010A GLU 6.1 0.7 - - - +
1011A GLY 5.8 0.9 - - - -
1012A LEU* 1.3 87.3 - - - +
1014A LEU* 1.3 61.3 + - - +
1015A LYS 4.0 10.1 - - - +
1017A TYR* 3.3 54.7 - - - +
1019A ASP* 4.9 7.7 + - - -
1025A THR* 3.6 32.3 - - - +
1026A ILE* 4.0 1.5 - - - +
1027A GLY* 2.9 39.9 + - - +
1057A ILE* 5.0 2.4 - - - +
1062A ALA* 5.2 1.6 - - - +
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Residues in contact with LEU1014 (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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1012A LEU* 4.4 6.7 + - + -
1013A ARG* 1.3 76.2 - - - +
1015A LYS* 1.3 70.9 + - + +
1026A ILE* 3.7 5.7 - - - +
1055A GLY 3.6 1.0 - - - +
1056A VAL* 3.6 21.7 - - + -
1057A ILE 3.0 52.4 + - - +
1058A THR* 4.7 9.2 - - - -
1059A LYS* 4.9 5.2 - - + +
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Residues in contact with LYS1015 (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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1013A ARG* 4.0 10.6 - - - +
1014A LEU* 1.3 89.2 - - + +
1016A ILE* 1.3 70.3 + - - +
1017A TYR* 3.5 4.5 + - - +
1025A THR 4.0 2.6 - - - +
1026A ILE* 3.6 12.0 - - - +
1055A GLY 3.3 7.9 - - - +
1056A VAL* 3.8 31.4 - - + -
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Residues in contact with ILE1016 (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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1015A LYS* 1.3 80.0 - - - +
1017A TYR* 1.3 63.8 + - - +
1024A TYR* 3.7 33.7 - - + -
1025A THR 3.6 7.9 - - - +
1026A ILE* 3.8 17.7 - - + -
1032A LEU* 4.6 4.9 - - + -
1038A LEU* 4.0 18.6 - - + +
1041A ALA* 4.4 4.3 - - + +
1042A LYS* 3.9 32.3 - - + +
1045A LEU* 3.8 20.0 - - + -
1053A THR* 5.5 0.2 - - - +
1055A GLY* 3.5 19.0 + - - +
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Residues in contact with TYR1017 (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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1013A ARG* 3.3 54.7 - - - +
1015A LYS 4.3 1.3 - - - +
1016A ILE* 1.3 77.1 - - - +
1018A LYS* 1.3 84.1 + - - +
1019A ASP* 4.0 13.5 - - - -
1020A THR 5.3 0.4 - - - -
1024A TYR* 3.4 6.0 - - - -
1025A THR* 2.8 35.6 + - + +
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Residues in contact with LYS1018 (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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1017A TYR* 1.3 90.7 + - - +
1019A ASP* 1.3 67.1 + - - +
1022A GLY* 5.6 3.6 - - - +
1023A TYR 3.8 5.4 - - - +
1024A TYR* 3.7 31.9 - - + +
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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