Contacts of the helix formed by residues 1137 - 1148 (chain A) in PDB entry 4KSC
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 SER1137 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1128A ALA* 5.1 1.2 - - - +
1134A ARG* 4.2 11.6 + - - -
1135A VAL* 3.2 14.8 + - - -
1136A VAL* 1.3 75.2 - - - +
1138A TYR* 1.3 58.8 + - - +
1139A GLU* 2.5 30.9 + - - +
1140A GLU* 3.5 20.9 - - - +
1141A ILE* 2.9 38.4 + - - +
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Residues in contact with TYR1138 (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* 4.0 3.8 + - - +
1137A SER* 1.3 73.7 + - - +
1139A GLU* 1.3 68.2 + - - +
1141A ILE* 3.1 20.0 - - + +
1142A VAL* 2.9 45.3 + - + +
1160A LYS* 5.1 8.8 - - - -
1161A TYR* 3.5 43.4 - + + -
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Residues in contact with GLU1139 (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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1137A SER* 2.5 21.6 + - - +
1138A TYR* 1.3 85.9 + - + +
1140A GLU* 1.3 64.4 + - + +
1142A VAL* 3.2 12.9 - - - +
1143A ARG* 3.2 19.1 + - - +
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Residues in contact with GLU1140 (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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1134A ARG* 4.1 18.2 + - - +
1137A SER* 3.2 25.0 + - - +
1138A TYR 3.2 0.6 - - - -
1139A GLU* 1.3 78.4 - - + +
1141A ILE* 1.3 60.6 + - + +
1142A VAL 3.0 4.0 - - - -
1143A ARG* 2.8 18.9 + - - +
1144A ALA* 2.8 24.8 + - - +
1186A LEU* 4.3 5.5 - - - +
1187A VAL* 3.7 38.6 - - + +
1189A GLN* 4.3 11.6 + - - +
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Residues in contact with ILE1141 (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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1124A ALA* 3.9 31.9 - - + +
1127A ILE* 4.1 17.5 - - + +
1128A ALA* 3.6 31.2 - - + -
1136A VAL* 4.4 8.3 - - + -
1137A SER 2.9 26.2 + - - +
1138A TYR* 3.1 34.8 - - + +
1140A GLU* 1.3 69.9 - - + +
1142A VAL* 1.3 58.9 + - - +
1144A ALA* 3.4 10.1 - - - +
1145A ALA* 2.9 24.1 + - - +
1161A TYR* 3.3 21.1 + - + -
1187A VAL* 4.9 2.2 - - + -
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Residues in contact with VAL1142 (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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1138A TYR* 2.9 46.3 + - + +
1139A GLU* 3.2 13.7 - - - +
1141A ILE* 1.3 76.7 - - - +
1143A ARG* 1.3 59.5 + - - +
1145A ALA* 3.1 4.3 + - - +
1146A LYS* 2.8 55.8 + - + +
1151A HIS* 4.2 6.9 - - - +
1161A TYR* 3.3 20.0 - - + +
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Residues in contact with ARG1143 (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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1139A GLU 3.2 7.2 + - - +
1140A GLU* 2.8 25.0 + - - +
1142A VAL* 1.3 76.6 - - - +
1144A ALA* 1.3 63.7 + - - +
1146A LYS* 4.1 12.9 - - - +
1147A GLU* 3.0 37.6 + - - +
1186A LEU* 4.0 7.4 - - + +
1189A GLN* 5.4 7.2 - - - +
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Residues in contact with ALA1144 (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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1127A ILE* 3.6 14.4 - - + -
1140A GLU* 2.8 7.3 + - - +
1141A ILE* 3.4 12.6 - - - +
1142A VAL 3.1 0.2 - - - -
1143A ARG* 1.3 76.4 - - - +
1145A ALA* 1.3 57.9 + - - +
1147A GLU* 3.4 2.6 + - - +
1148A ALA* 3.0 30.1 + - - +
1183A ALA* 3.8 10.6 - - + +
1186A LEU* 3.5 14.2 - - + +
1187A VAL* 3.5 32.1 - - + -
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Residues in contact with ALA1145 (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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1127A ILE* 4.7 2.6 - - + +
1141A ILE 2.9 9.5 + - - +
1142A VAL 3.6 0.4 - - - +
1144A ALA* 1.3 73.4 - - - +
1146A LYS* 1.3 61.9 + - - +
1149A ASN* 2.9 27.0 + - - -
1150A ILE* 3.3 32.4 + - + -
1151A HIS* 3.6 18.4 + - + +
1154A ILE* 4.6 0.4 - - + -
1161A TYR* 3.1 33.2 - - + +
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Residues in contact with LYS1146 (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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1142A VAL* 2.8 39.6 + - + +
1143A ARG* 3.6 15.9 - - - +
1145A ALA* 1.3 74.4 - - - +
1147A GLU* 1.3 61.0 + - - +
1149A ASN* 3.7 14.6 + - - -
1151A HIS* 3.6 36.3 - - + -
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Residues in contact with GLU1147 (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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1143A ARG* 3.0 29.6 + - - +
1146A LYS* 1.3 78.9 - - - +
1148A ALA* 1.3 60.6 + - - +
1149A ASN* 3.3 11.9 + - - +
1182A ILE* 5.3 0.2 - - - +
1186A LEU* 3.6 31.4 - - + +
1212A GLU* 5.2 0.2 - - - +
1213A ALA* 3.8 12.5 - - - +
1216A LYS* 3.2 41.5 - - + +
1217A ALA* 5.1 2.9 - - - +
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Residues in contact with ALA1148 (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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1144A ALA 3.0 18.1 + - - +
1145A ALA 3.3 2.4 + - - +
1147A GLU* 1.3 75.6 - - - +
1149A ASN* 1.3 74.6 + - - +
1150A ILE* 3.1 6.0 + - + +
1179A ARG* 3.2 44.6 - - - +
1182A ILE* 3.8 19.3 - - + -
1183A ALA* 3.9 7.4 - - + -
1209A VAL 5.3 0.3 - - - +
1213A ALA* 4.3 6.0 - - - +
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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