Contacts of the strand formed by residues 1036 - 1040 (chain A) in PDB entry 1KEK
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 TYR1036 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1035A VAL* 1.3 75.5 - - - +
1037A VAL* 1.3 62.6 + - - +
1038A ALA* 3.8 20.6 - - + -
1052A VAL* 4.1 5.3 - - - -
1055A GLU* 2.6 44.3 + - + +
1056A ALA* 3.8 28.7 - - + -
1059A PHE* 3.6 15.3 - - + -
1062A PRO 2.9 7.7 + - - -
1063A SER* 3.3 16.4 - - - +
1064A LEU 2.8 28.6 + - - -
1065A VAL* 4.9 0.2 - - + -
1100A ARG* 3.5 21.6 - - + +
1101A TYR 3.3 15.7 - - - -
1102A ASP* 3.6 36.3 - - + -
1103A PRO* 3.8 3.1 - - + -
1104A ARG* 4.0 6.3 - - - -
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Residues in contact with VAL1037 (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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1026A ALA* 3.9 29.6 - - + +
1029A VAL* 3.4 30.7 - - + -
1030A MET* 3.8 34.1 - - + +
1035A VAL* 3.7 9.9 - - + +
1036A TYR* 1.3 82.9 - - - +
1038A ALA* 1.3 66.7 - - - +
1064A LEU* 3.3 15.5 - - + +
1066A ILE* 5.5 0.7 - - + -
1099A PHE* 4.6 2.3 - - + -
1100A ARG* 3.5 0.7 - - - +
1101A TYR* 2.6 40.6 + - + +
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Residues in contact with ALA1038 (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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1036A TYR* 3.8 11.9 - - + -
1037A VAL* 1.3 79.4 - - - +
1039A THR* 1.3 67.5 + - - +
1052A VAL* 3.5 32.1 - - + -
1064A LEU 3.0 9.0 + - - +
1065A VAL* 3.4 4.0 - - - -
1066A ILE* 2.9 25.6 + - - +
1099A PHE* 3.2 15.5 - - - +
1100A ARG* 3.8 9.0 - - + -
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Residues in contact with THR1039 (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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1026A ALA* 4.6 8.1 - - + -
1038A ALA* 1.3 79.6 - - - +
1040A VAL* 1.3 63.8 - - - +
1048A GLN* 3.0 21.8 - - - +
1066A ILE* 3.3 21.3 - - + +
1096A TRP* 4.1 12.8 - - + +
1097A PRO 2.9 24.9 + - - +
1098A LEU* 3.2 4.6 - - - +
1099A PHE* 3.0 45.8 + - + +
1159A ARG* 5.5 1.8 - - - +
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Residues in contact with VAL1040 (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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820A TYR* 4.0 4.0 - - + -
1039A THR* 1.3 80.1 - - - +
1041A SER* 1.3 62.3 + - - +
1048A GLN* 3.5 18.8 - - - +
1049A PHE* 3.8 33.2 - - + -
1052A VAL* 3.8 28.7 - - + -
1065A VAL* 4.1 8.7 - - + -
1066A ILE 2.9 9.3 + - - +
1067A ALA* 3.5 28.7 - - + +
1068A TYR 3.1 13.9 + - - -
1096A TRP* 3.1 17.0 + - - -
1098A LEU* 3.5 7.2 - - - -
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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