Contacts of the helix formed by residues 1219 - 1231 (chain B) 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 THR1219 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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748A CYS 3.8 0.6 + - - -
753A ASP* 5.0 2.6 + - - +
1078A LYS 3.0 22.2 - - - +
1079A GLY* 4.9 2.2 - - - -
1081A GLY* 3.4 27.9 + - - -
1082A LYS* 3.6 15.9 - - + -
1194B PHE* 4.6 1.1 - - - -
1218B GLY* 1.3 76.6 - - - +
1220B SER* 1.3 61.2 + - - +
1221B GLU* 2.9 35.0 - - + +
1222B GLN* 2.8 30.3 + - - -
1223B GLN* 2.9 28.1 + - - +
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Residues in contact with SER1220 (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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1077A ARG 4.2 2.1 + - - -
1078A LYS* 3.0 32.6 + - - -
1193B GLU* 5.8 0.3 - - - +
1194B PHE* 3.8 13.2 - - - -
1219B THR* 1.3 71.2 - - - +
1221B GLU* 1.3 65.1 + - - +
1223B GLN* 3.3 10.1 + - - +
1224B GLY* 2.9 26.0 + - - -
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Residues in contact with GLU1221 (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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753A ASP* 5.2 3.8 - - - +
1078A LYS* 3.1 32.7 + - - +
1082A LYS* 3.1 25.1 + - - +
1219B THR* 2.9 29.0 - - + +
1220B SER* 1.3 80.9 - - - +
1222B GLN* 1.3 62.6 + - + +
1224B GLY* 3.2 1.7 + - - -
1225B ASP* 2.9 33.4 + - - +
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Residues in contact with GLN1222 (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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749A GLY* 2.9 36.3 + - - -
752A ALA* 3.9 9.0 - - + +
753A ASP* 3.5 24.4 + - - +
764A MET* 3.7 27.8 - - + +
1217B ALA 5.0 0.9 - - - +
1218B GLY* 3.5 4.6 - - - -
1219B THR* 2.8 38.0 + - - +
1221B GLU* 1.3 82.8 - - + +
1223B GLN* 1.3 62.1 + - - +
1225B ASP* 3.8 10.9 - - - +
1226B LEU* 3.0 26.0 + - - +
1229B ARG* 4.9 0.5 + - - -
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Residues in contact with GLN1223 (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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680A ASN* 4.8 1.8 - - - +
1194B PHE* 4.1 5.7 - - - -
1213B ASP* 3.0 28.8 + - - +
1217B ALA* 3.1 34.8 + - + +
1218B GLY 2.8 21.4 + - - -
1219B THR 2.9 19.2 + - - +
1220B SER* 3.8 6.5 - - - +
1222B GLN* 1.3 75.9 - - - +
1224B GLY* 1.3 58.5 + - - +
1226B LEU* 3.2 9.8 + - - +
1227B SER* 2.9 28.4 + - - -
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Residues in contact with GLY1224 (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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1220B SER 2.9 14.7 + - - -
1221B GLU* 3.2 3.6 + - - -
1223B GLN* 1.3 75.9 - - - +
1225B ASP* 1.3 62.2 + - - +
1227B SER* 3.0 9.4 + - - -
1228B LYS* 2.9 24.5 + - - +
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Residues in contact with ASP1225 (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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763A VAL* 5.1 3.1 - - - +
1221B GLU 2.9 16.3 + - - +
1222B GLN* 3.8 9.6 - - - +
1224B GLY* 1.3 74.6 - - - +
1226B LEU* 1.3 61.6 + - - +
1228B LYS* 3.4 23.0 + - - +
1229B ARG* 3.1 58.1 + - - +
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Residues in contact with LEU1226 (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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680A ASN* 3.4 40.8 - - + +
764A MET* 4.3 9.2 - - + +
765A GLN* 4.1 8.3 - - - +
766A PRO* 4.3 14.8 - - + -
1222B GLN 3.0 21.5 + - - +
1223B GLN* 3.5 6.7 - - - +
1224B GLY 3.2 0.2 - - - -
1225B ASP* 1.3 74.6 - - - +
1227B SER* 1.3 66.6 + - - +
1229B ARG* 3.1 40.8 + - - +
1230B THR* 3.1 38.4 + - + +
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Residues in contact with SER1227 (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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1223B GLN 2.9 12.9 + - - -
1224B GLY* 3.0 11.4 + - - -
1226B LEU* 1.3 77.8 - - - +
1228B LYS* 1.3 57.1 + - - +
1229B ARG 3.0 0.2 - - - -
1230B THR* 3.1 8.2 + - - -
1231B LYS* 2.8 36.4 + - - +
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Residues in contact with LYS1228 (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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1224B GLY 2.9 11.6 + - - +
1225B ASP* 3.5 26.4 - - - +
1226B LEU 3.3 0.2 - - - -
1227B SER* 1.3 75.5 - - - +
1229B ARG* 1.3 60.3 + - + +
1231B LYS* 4.0 20.7 + - - -
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Residues in contact with ARG1229 (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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763A VAL* 3.5 17.8 - - - +
764A MET* 2.8 26.9 + - - +
765A GLN* 2.7 29.5 + - - +
1222B GLN 4.9 0.2 + - - -
1225B ASP* 3.1 42.7 + - - +
1226B LEU* 3.1 27.3 + - - +
1227B SER 3.0 0.6 - - - -
1228B LYS* 1.3 81.7 - - + +
1230B THR* 1.3 64.7 + - + +
1231B LYS* 4.5 8.7 + - - +
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Residues in contact with THR1230 (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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766A PRO* 5.9 4.0 - - + -
1226B LEU* 3.1 34.6 + - + +
1227B SER* 3.1 6.3 + - - -
1229B ARG* 1.3 85.6 - - + +
1231B LYS* 1.3 80.4 + - - +
1232B LYS* 2.8 27.5 + - - +
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Residues in contact with LYS1231 (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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1227B SER* 2.8 24.9 + - - +
1228B LYS* 4.0 19.6 + - - +
1229B ARG* 4.5 7.7 + - - +
1230B THR* 1.3 86.5 + - - +
1232B LYS* 2.0 79.8 + - - +
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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