Contacts of the strand formed by residues 1255 - 1260 (chain B) in PDB entry 3KQ4
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 MET1255 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1193B TRP 4.1 0.2 - - - +
1194B TRP* 3.5 2.6 - - - -
1195B LEU* 2.7 44.6 + - + +
1203B PHE* 3.5 26.9 - - + +
1205B LEU* 3.1 33.2 - - + -
1225B VAL* 3.8 26.0 - - + -
1226B TYR 3.8 10.5 - - - +
1228B GLY 3.8 1.8 - - - +
1236B LEU* 5.6 0.9 - - + -
1248B ILE* 3.3 24.2 - - + +
1250B SER* 3.1 34.3 - - - +
1254B SER* 1.3 78.5 - - - +
1256B PHE* 1.3 61.1 + - - +
1257B ILE* 4.1 5.8 - - + -
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Residues in contact with PHE1256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1192B TYR* 4.1 27.1 - + + -
1193B TRP 3.6 4.0 - - - -
1194B TRP* 4.2 18.8 - - + +
1225B VAL* 3.8 1.2 - - - +
1226B TYR* 2.9 48.2 + + + -
1228B GLY 3.1 21.6 + - - +
1229B PRO 3.3 23.1 - - - +
1230B SER* 4.1 5.6 - - - +
1231B SER* 4.5 12.1 - - - -
1255B MET* 1.3 70.9 - - - +
1257B ILE* 1.3 86.4 + - - +
1258B LYS* 3.7 26.0 - - + -
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Residues in contact with ILE1257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1176B PHE* 4.1 26.5 - - + -
1192B TYR* 3.4 1.4 - - - -
1193B TRP* 2.8 60.9 + - + +
1195B LEU* 4.4 13.9 - - + -
1205B LEU* 4.2 12.3 - - + -
1223B LEU* 3.3 32.3 - - + -
1224B ALA 3.4 5.4 - - - +
1225B VAL* 3.5 17.0 - - + -
1255B MET* 4.1 22.0 - - + -
1256B PHE* 1.3 89.0 - - - +
1258B LYS* 1.3 64.2 + - - +
1270B PHE* 5.8 0.2 - - + -
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Residues in contact with LYS1258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1190B GLU* 4.8 14.9 + - - -
1191B CYS 3.4 4.0 - - - -
1192B TYR* 3.1 46.3 + - + -
1222B TYR* 4.3 20.3 - - + +
1223B LEU* 3.0 4.0 - - - +
1224B ALA* 2.8 38.8 + - + +
1226B TYR* 4.9 11.9 - - + -
1231B SER* 5.7 6.5 - - - -
1256B PHE* 3.7 13.6 - - + -
1257B ILE* 1.3 75.4 - - - +
1259B LEU* 1.3 66.1 + - - +
1260B ARG* 5.0 0.7 - - - +
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Residues in contact with LEU1259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1178B SER* 5.1 4.0 - - - -
1179B PRO* 5.4 6.7 - - + -
1185B TYR* 6.2 2.9 - - + -
1189B SER* 4.8 5.8 - - - +
1190B GLU* 3.2 3.0 - - - +
1191B CYS* 2.8 65.4 + - + +
1193B TRP* 5.1 5.1 - - + +
1212B LEU* 4.7 15.7 - - + -
1222B TYR* 3.4 13.9 - - - +
1223B LEU* 3.3 18.8 - - + -
1258B LYS* 1.3 77.2 - - - +
1260B ARG* 1.3 65.4 + - - +
1261B THR* 5.0 12.1 - - + -
1270B PHE* 3.7 29.8 - - + -
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Residues in contact with ARG1260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1188B SER 5.7 0.2 - - - -
1189B SER 3.4 5.2 - - - +
1190B GLU* 3.3 36.6 + - + +
1219B THR 3.8 9.3 + - - -
1220B LEU* 2.5 30.7 + - - +
1221B ASP* 3.1 4.3 - - - +
1222B TYR* 3.0 67.2 + - + +
1258B LYS* 5.0 2.7 - - - -
1259B LEU* 1.3 73.2 - - - +
1261B THR* 1.3 70.6 + - - +
1262B ASP* 3.5 28.9 - - - +
1263B GLU* 5.7 2.2 + - - -
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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