Contacts of the helix formed by residues 1131 - 1141 (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 GLN1131 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1068A TYR* 4.0 3.1 + - - -
1074A GLN* 3.4 17.1 - - - +
1075A GLY 3.5 5.8 - - - -
1076A LEU* 4.1 19.1 - - + -
1077A ARG* 4.3 1.3 - - - -
1086A VAL* 4.4 5.9 - - + +
1127A PHE* 3.3 54.7 + - - +
1128A LEU 3.4 7.5 - - - +
1129A MET 3.2 0.8 - - - -
1130A ALA* 1.3 85.4 - - + +
1132A ASN* 1.3 64.4 + - - +
1133A ARG* 2.9 41.4 + - + +
1134A PHE* 3.1 8.1 + - + -
1135A ALA* 3.0 21.0 + - - +
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Residues in contact with ASN1132 (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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1074A GLN 3.4 1.2 + - - -
1075A GLY* 2.8 28.5 + - - +
1077A ARG* 4.3 3.7 - - - +
1131A GLN* 1.3 70.9 - - - +
1133A ARG* 1.3 57.4 + - - +
1134A PHE 3.0 0.2 - - - -
1135A ALA* 4.1 3.5 - - - +
1136A VAL* 2.9 39.5 + - - +
1139A ARG* 2.9 36.7 - - - +
1188B PHE 2.9 23.3 - - - +
1189B GLY 3.8 1.7 - - - -
1190B GLU 2.9 19.5 + - - +
1191B GLY 4.0 1.2 + - - -
1192B ALA* 3.8 20.9 - - + +
1193B GLU* 4.8 4.4 + - - +
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Residues in contact with ARG1133 (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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991A THR 4.9 0.2 + - - -
992A GLU* 2.9 43.6 + - - +
1006A PRO* 3.8 14.3 - - - +
1008A GLY 4.0 0.2 - - - +
1009A ALA* 3.7 8.5 - - - +
1010A VAL* 2.8 55.2 + - - +
1068A TYR* 3.0 21.8 + - - -
1073A ASN 4.6 3.8 - - - +
1074A GLN* 3.2 44.5 + - - +
1095A TYR* 3.5 6.7 + - - -
1131A GLN* 2.9 29.1 + - + +
1132A ASN* 1.3 76.0 - - - +
1134A PHE* 1.3 79.0 + - + +
1136A VAL* 4.4 3.6 - - - -
1188B PHE* 4.6 5.5 + - + -
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Residues in contact with PHE1134 (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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1006A PRO* 3.8 23.3 - - + -
1007A THR 3.7 11.4 - - - -
1008A GLY* 3.6 16.2 - - - -
1009A ALA* 3.6 25.4 - - + -
1095A TYR* 3.9 4.9 - + - -
1128A LEU* 3.1 65.1 - - + +
1129A MET* 3.4 12.7 - - + +
1131A GLN* 3.1 9.4 + - + -
1133A ARG* 1.3 110.2 - - + +
1135A ALA* 1.3 63.0 + - - +
1136A VAL 3.4 0.2 - - - -
1137A LEU* 3.1 16.9 + - - +
1138A ASP 3.3 8.3 + - - -
1145A ALA* 5.2 0.2 - - - +
1149A ARG* 4.8 7.2 + - + -
1152A VAL* 5.1 2.2 - - + -
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Residues in contact with ALA1135 (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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1077A ARG* 3.6 21.8 - - - +
1129A MET* 3.6 26.6 - - + +
1131A GLN 3.0 15.8 + - - +
1132A ASN* 4.2 2.0 - - - -
1134A PHE* 1.3 75.2 - - - +
1136A VAL* 1.3 64.7 + - - +
1138A ASP* 3.2 3.5 + - - +
1139A ARG* 3.1 42.3 + - + +
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Residues in contact with VAL1136 (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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1010A VAL* 3.9 31.6 - - + -
1132A ASN* 2.9 40.5 + - - +
1133A ARG* 4.5 0.7 - - - -
1135A ALA* 1.3 74.1 - - - +
1137A LEU* 1.3 55.5 - - - +
1139A ARG* 3.5 16.0 + - - +
1140A SER* 2.6 35.5 + - - -
1186B VAL* 3.9 10.1 - - + -
1187B ASP 3.8 7.9 - - - +
1188B PHE* 4.5 2.0 - - - -
1190B GLU* 3.0 45.1 - - + +
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Residues in contact with LEU1137 (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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1008A GLY 4.0 13.2 - - - +
1010A VAL* 3.6 22.2 - - + -
1015A ALA 4.7 0.9 - - - +
1016A ALA* 3.5 26.9 - - - +
1017A GLY* 4.2 0.2 - - - -
1134A PHE 3.1 11.6 + - - +
1136A VAL* 1.3 81.6 - - - +
1138A ASP* 1.3 59.8 + - - +
1140A SER* 4.0 1.3 - - - -
1141A PHE* 2.7 66.2 + - + -
1144A ASP* 4.5 1.3 - - + -
1145A ALA* 3.7 22.9 - - + +
1148A LEU* 3.7 31.2 - - + -
1186B VAL* 4.8 1.6 - - + -
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Residues in contact with ASP1138 (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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1129A MET* 3.7 17.3 - - + +
1134A PHE 3.3 2.2 + - - -
1135A ALA 3.2 9.2 + - - +
1137A LEU* 1.3 80.7 - - - +
1139A ARG* 1.3 62.5 + - + +
1142A PRO* 3.4 32.1 - - - +
1145A ALA* 3.4 12.1 - - - +
1146A LYS* 4.5 1.6 + - - +
1149A ARG* 2.8 39.3 + - - +
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Residues in contact with ARG1139 (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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1077A ARG* 3.8 11.9 - - - +
1132A ASN* 2.9 33.5 - - - +
1135A ALA* 3.1 33.6 + - - +
1136A VAL* 3.6 19.9 - - - +
1137A LEU 3.1 0.2 - - - -
1138A ASP* 1.3 82.4 - - + +
1140A SER* 1.3 59.2 + - - +
1142A PRO* 4.0 6.5 - - - +
1190B GLU 3.0 18.8 + - - -
1191B GLY* 3.8 13.4 + - - -
1193B GLU* 5.8 0.6 + - - -
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Residues in contact with SER1140 (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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1136A VAL 2.6 26.0 + - - -
1139A ARG* 1.3 76.1 - - - +
1141A PHE* 1.3 82.5 + - - +
1142A PRO* 3.3 9.2 - - - +
1186B VAL* 3.7 24.5 - - - +
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Residues in contact with PHE1141 (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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1015A ALA 4.7 1.8 - - - -
1016A ALA* 5.0 7.2 - - + -
1019A ARG* 6.2 0.7 - - - -
1137A LEU* 2.7 38.2 + - + +
1140A SER* 1.3 94.5 - - - +
1142A PRO* 1.3 61.8 - - - +
1143A GLU* 3.1 4.9 - - - -
1144A ASP* 3.0 22.8 + - + -
1145A ALA* 2.8 26.2 + - - +
1181B LYS 5.3 7.2 - - - -
1183B ASP 4.0 16.6 - - - -
1184B GLY* 3.5 28.5 - - - -
1185B SER* 3.7 20.9 - - - -
1186B VAL* 4.5 1.8 - - + -
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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