Contacts of the strand formed by residues 960 - 967 (chain A) in PDB entry 1KCW
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 GLU 960 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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893A ARG 3.2 12.4 + - - +
894A LYS* 3.4 19.8 - - + +
895A LEU 2.9 24.9 + - - +
958A GLY 5.2 0.4 - - - +
959A ASP* 1.3 72.7 - - - +
961A VAL* 1.3 62.2 + - - +
962A ASN* 5.2 8.4 + - - +
1008A GLU* 6.1 3.8 - - + +
1009A MET 4.0 2.5 - - - +
1010A PHE* 3.6 30.4 - - + -
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Residues in contact with VAL 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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895A LEU* 3.7 7.9 - - + +
897A PHE* 3.5 34.1 - - + -
955A MET* 3.8 17.7 - - + -
959A ASP* 4.4 4.5 - - + -
960A GLU* 1.3 78.6 - - - +
962A ASN* 1.3 73.0 + - - +
963A TRP* 3.6 24.7 - - + +
1007A LEU 3.6 0.5 - - - +
1008A GLU* 3.5 1.0 - - - +
1009A MET* 2.8 42.9 + - + +
1011A PRO* 3.7 26.2 - - + -
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Residues in contact with ASN 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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853A SER* 6.0 1.2 - - - -
855A CYS* 5.2 5.0 + - - +
894A LYS* 4.3 17.6 + - - +
895A LEU 2.8 15.1 + - - +
896A GLU* 3.3 5.0 - - + -
897A PHE 2.8 26.9 + - - +
960A GLU* 5.1 8.7 + - - +
961A VAL* 1.3 85.3 + - - +
963A TRP* 1.3 62.6 + - - +
964A TYR* 3.5 33.3 + - + +
1006A THR* 4.2 7.3 + - - -
1007A LEU 3.6 3.1 - - - -
1008A GLU* 3.8 22.8 - - - +
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Residues in contact with TRP 963 (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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897A PHE* 3.5 25.1 - + + -
899A LEU* 3.5 33.2 - - + -
953A LEU* 3.9 24.7 - - + -
955A MET* 4.2 12.3 - - + -
961A VAL* 3.6 15.9 - - + +
962A ASN* 1.3 72.6 - - - +
964A TYR* 1.3 61.1 + - - +
965A LEU* 3.7 11.4 + - + -
979A PHE* 4.0 31.3 - + + -
984A PHE* 5.7 0.4 - - + -
1005A GLN 3.6 0.9 - - - +
1006A THR* 3.2 5.2 - - - -
1007A LEU* 2.9 54.4 + - + +
1009A MET* 3.2 49.8 - - + +
1019A LEU* 4.3 0.2 - - + -
1035A TYR* 4.3 23.6 - + + -
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Residues in contact with TYR 964 (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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792A GLN* 4.1 5.2 - - - -
855A CYS* 3.6 21.1 - - - +
857A PRO* 4.1 20.6 - - + -
877A PRO* 5.8 1.3 - - + -
879A ILE* 3.4 38.4 - - + -
894A LYS* 4.8 0.5 + - - -
896A GLU* 2.6 44.4 + - + -
897A PHE 2.7 24.4 + - - +
898A ALA* 3.4 7.3 - - + +
899A LEU* 2.8 32.1 + - - +
962A ASN* 3.5 24.5 + - + -
963A TRP* 1.3 72.0 - - - +
965A LEU* 1.3 58.7 + - - +
966A MET* 4.3 4.8 - - + +
1005A GLN 3.5 4.0 - - - -
1006A THR* 3.6 31.9 - - - -
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Residues in contact with LEU 965 (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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857A PRO* 4.6 0.9 - - - +
899A LEU* 3.6 23.1 - - + -
901A PHE* 3.5 31.9 - - + -
963A TRP* 4.7 7.0 - - + -
964A TYR* 1.3 72.5 - - - +
966A MET* 1.3 61.1 - - - +
977A VAL* 4.5 12.6 - - + -
979A PHE* 4.8 4.0 - - + -
997A PHE* 4.4 13.5 - - + -
999A ILE* 3.3 23.5 - - + +
1003A THR 3.8 0.2 - - - +
1004A TYR* 3.2 1.9 - - - -
1005A GLN* 2.6 44.8 + - + +
1007A LEU* 3.3 37.0 - - + -
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Residues in contact with MET 966 (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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789A LEU* 3.9 22.7 - - + -
857A PRO* 5.1 7.9 - - + -
858A TRP 4.9 1.3 - - - +
859A ALA* 4.3 18.4 - - + -
875A ILE* 4.6 7.9 - - + -
876A GLY 4.0 9.4 - - - +
877A PRO* 3.6 38.6 - - + -
898A ALA* 5.5 1.1 - - + -
899A LEU 3.1 11.4 + - - +
900A LEU* 3.1 41.1 - - + +
901A PHE* 3.3 4.1 + - - -
964A TYR* 4.3 7.0 - - - +
965A LEU* 1.3 79.3 - - - +
967A GLY* 1.3 58.7 + - - +
968A MET* 5.9 0.2 - - + -
999A ILE* 4.0 5.3 - - - +
1003A THR 2.9 5.2 - - - -
1004A TYR* 3.1 25.6 - - + -
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Residues in contact with GLY 967 (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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900A LEU* 4.3 0.4 - - - -
901A PHE 3.7 9.4 - - - -
966A MET* 1.3 73.6 - - - +
968A MET* 1.3 70.7 + - - +
975A HIS* 5.4 0.7 - - - -
999A ILE* 3.7 23.1 - - - +
1000A PHE 4.3 2.7 - - - -
1001A PRO* 4.1 3.4 - - - -
1002A GLY* 3.0 22.5 + - - -
1003A THR 2.7 12.1 + - - +
1004A TYR* 3.8 1.9 - - - -
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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