Contacts of the strand formed by residues 956 - 962 (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 SER 956 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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828A PHE* 4.5 5.9 - - - +
831A ARG* 2.9 27.6 + - - -
832A MET* 3.2 6.2 - - - -
833A PHE 2.9 23.3 + - - -
954A LYS* 4.8 1.1 - - - +
955A LYS* 1.3 73.5 - - - +
957A VAL* 1.3 62.6 + - - +
958A TRP* 2.8 29.6 + - - -
985A ASN* 3.7 3.1 + - - +
1057A GLU* 2.7 32.3 + - - +
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Residues in contact with VAL 957 (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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833A PHE* 3.9 27.6 - - + -
876A GLY* 3.4 35.0 - - - +
879A MET* 4.4 8.5 - - + -
880A ASN* 4.3 20.2 - - + +
883A MET* 4.8 7.2 - - + -
954A LYS* 5.7 0.2 - - - +
955A LYS* 4.0 4.1 + - + +
956A SER* 1.3 74.4 + - - +
958A TRP* 1.3 63.3 - - - +
959A ILE* 5.2 0.2 - - + -
983A ASP 4.6 7.3 + - - +
984A VAL* 3.7 17.6 - - + -
985A ASN* 3.0 32.0 + - - +
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Residues in contact with TRP 958 (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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824A ILE* 4.4 11.0 - - + -
828A PHE* 3.6 31.6 - + - +
832A MET* 3.6 23.2 - - + +
833A PHE 2.8 14.1 + - - +
834A ILE* 3.3 4.0 - - + -
835A ALA* 2.9 24.8 + - - +
956A SER* 2.8 36.6 + - - -
957A VAL* 1.3 77.7 - - - +
959A ILE* 1.3 65.3 + - - +
960A PHE* 3.8 28.5 - + + -
985A ASN* 3.2 32.9 - - + +
986A VAL 5.0 1.3 - - - -
987A PHE* 4.1 20.0 - + + -
1053A LEU* 4.1 25.4 - - + -
1056A ALA* 5.3 4.7 - - + -
1057A GLU* 3.8 16.8 - - + +
1065A VAL* 5.5 4.5 - - + -
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Residues in contact with ILE 959 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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835A ALA* 3.3 6.3 - - + +
872A ALA* 3.7 27.4 - - + +
873A ALA* 3.7 28.0 - - + +
876A GLY* 3.9 13.7 - - - -
877A PHE 4.5 0.4 - - - +
957A VAL* 5.2 0.4 - - + -
958A TRP* 1.3 78.4 - - - +
960A PHE* 1.3 57.9 + - - +
965A TRP* 3.6 29.8 - - + -
977A VAL* 4.3 2.5 - - + -
984A VAL* 4.1 30.5 - - + -
985A ASN 2.8 7.6 + - - +
986A VAL* 3.4 15.0 - - + +
987A PHE 2.8 31.7 + - - +
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Residues in contact with PHE 960 (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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821A VAL* 3.7 25.4 - - + -
824A ILE* 4.2 18.8 - - + -
825A THR* 6.0 0.9 - - + -
832A MET* 3.9 19.1 - - + -
834A ILE* 3.7 23.3 - - + -
835A ALA 2.9 6.2 + - - +
836A ASN* 3.4 23.9 - - - +
837A ALA* 2.7 26.5 + - - +
841A SER* 4.9 2.9 - - - +
844A TRP* 5.8 0.9 - + - -
853A TYR* 3.7 19.3 - + - -
872A ALA* 4.5 1.7 - - - +
958A TRP* 3.8 34.7 - + + -
959A ILE* 1.3 84.1 - - - +
961A GLY* 1.3 58.4 + - - +
965A TRP* 4.7 0.9 - - - -
987A PHE* 3.5 19.7 - + + +
989A MET* 5.5 3.6 - - - -
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Residues in contact with GLY 961 (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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837A ALA* 3.8 10.8 - - - -
841A SER* 4.3 8.0 + - - -
960A PHE* 1.3 76.2 - - - +
962A GLY* 1.3 63.1 + - - -
965A TRP* 3.7 16.8 - - - -
987A PHE 3.3 5.7 + - - -
988A VAL* 3.2 6.2 - - - -
989A MET* 2.9 33.1 + - - +
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Residues in contact with GLY 962 (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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837A ALA* 4.9 0.8 - - - +
838A THR 5.5 1.2 + - - -
839A GLY* 6.1 0.8 - - - -
841A SER* 4.9 2.0 + - - -
961A GLY* 1.3 75.9 - - - +
963A ASP* 1.3 61.2 + - - -
964A GLY 3.3 3.1 - - - -
965A TRP* 3.4 4.1 + - - +
966A ALA* 3.0 26.0 + - - +
988A VAL* 4.1 2.7 - - - -
989A MET* 3.2 15.0 - - - -
2236A HTL 3.5 30.0 + - - -
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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