Contacts of the strand formed by residues 1172 - 1177 (chain D) in PDB entry 6K4Y
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 LYS1172 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1167D LYS* 3.7 3.1 - - - +
1169D THR* 3.1 23.6 + - - -
1170D LYS* 3.1 15.6 + - + +
1171D GLY* 1.3 85.0 - - - +
1173D ARG* 1.3 60.1 + - - +
1174D ARG* 4.2 0.6 - - - +
1189D MET* 3.7 25.8 - - + -
1190D ILE 3.2 15.7 - - - +
1191D PRO* 3.5 40.4 - - + -
1192D LYS* 5.0 4.0 - - - +
1193D TRP* 5.6 3.7 - - - -
4T G 4.9 8.0 + - - +
5T C 3.4 28.1 + - - -
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Residues in contact with ARG1173 (chain D).
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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1075D ARG* 5.7 3.2 - - - +
1102D PRO* 5.6 7.9 - - - +
1165D PHE* 3.5 44.6 - - + -
1166D GLY 4.8 0.2 - - - +
1167D LYS 3.4 11.4 - - - +
1168D GLU* 4.0 21.1 - - - +
1169D THR 5.1 2.2 - - - +
1172D LYS* 1.3 74.7 - - - +
1174D ARG* 1.3 72.4 + - - +
1188D GLU 3.5 0.2 - - - +
1189D MET* 4.1 0.9 - - - -
1190D ILE* 2.9 47.0 + - + +
1192D LYS* 4.8 30.8 - - + +
1196D LEU* 3.4 44.1 - - - +
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Residues in contact with ARG1174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1165D PHE* 3.5 7.8 - - - +
1166D GLY* 2.9 21.6 + - - -
1167D LYS* 3.3 56.9 + - + +
1170D LYS* 5.1 3.0 - - - +
1172D LYS 4.2 0.8 - - - +
1173D ARG* 1.3 80.6 - - - +
1175D LEU* 1.3 59.4 + - - +
1187D GLU* 3.1 36.9 + - + +
1188D GLU 3.3 8.3 - - - +
1189D MET* 3.5 46.5 - - + +
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Residues in contact with LEU1175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1155D ILE* 5.8 1.6 - - + -
1163D VAL* 3.7 20.4 - - + -
1164D SER 3.3 14.8 - - - +
1165D PHE* 3.7 24.5 - - + -
1174D ARG* 1.3 76.4 - - - +
1176D VAL* 1.3 56.6 + - - +
1177D ILE* 3.3 30.1 + - + +
1186D TYR 3.4 0.5 - - - +
1187D GLU* 2.7 27.5 - - - -
1188D GLU* 2.9 24.7 + - + +
1190D ILE* 3.7 26.0 - - + -
1196D LEU* 4.8 3.4 - - + -
1198D VAL* 5.5 5.2 - - + -
1210D ILE* 5.3 15.5 - - + -
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Residues in contact with VAL1176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1163D VAL* 3.3 2.1 - - - +
1164D SER* 2.9 49.0 + - - +
1165D PHE 3.9 16.6 - - - +
1166D GLY* 4.7 0.7 - - - -
1175D LEU* 1.3 68.7 - - - +
1177D ILE* 1.3 61.5 + - - +
1178D THR* 3.5 5.0 + - - +
1184D ASP* 3.4 34.5 - - + +
1186D TYR 3.8 5.8 - - - +
1187D GLU* 3.4 28.5 - - + +
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Residues in contact with ILE1177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1156D LEU 5.4 2.5 - - - +
1157D ALA* 5.0 9.2 - - + -
1158D GLU 4.6 11.0 - - - +
1159D ILE* 3.4 38.4 - - + +
1160D SER 4.1 3.4 - - - +
1161D GLY 5.1 2.5 - - - +
1163D VAL* 3.8 13.5 - - + -
1175D LEU* 3.7 37.2 - - + +
1176D VAL* 1.3 68.3 - - - +
1178D THR* 1.3 60.5 + - - +
1179D PRO* 3.4 6.1 - - - +
1184D ASP* 3.2 16.0 - - - +
1186D TYR* 3.0 45.7 + - + +
1188D GLU* 5.0 4.3 - - + +
1204D VAL* 5.8 3.1 - - + -
1210D ILE* 6.4 0.7 - - + -
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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