Contacts of the helix formed by residues 1168 - 1193 (chain A) in PDB entry 5KHU
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 LEU1168 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1167A GLU* 3.8 26.9 - - - +
1169A ALA* 3.8 29.6 - - - +
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Residues in contact with ALA1169 (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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1168A LEU* 3.8 25.4 - - - +
1170A ASN* 3.8 29.2 - - - +
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Residues in contact with ASN1170 (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 PHE* 4.2 19.1 - - - +
1169A ALA* 3.8 25.4 - - - +
1171A GLU* 3.7 29.4 - - - +
1173A ALA* 4.1 18.6 - - - +
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Residues in contact with GLU1171 (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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1170A ASN* 3.7 29.8 - - - +
1172A TYR* 3.8 25.6 - - - +
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Residues in contact with TYR1172 (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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1171A GLU* 3.8 25.6 - - - +
1173A ALA* 3.8 29.2 - - - +
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Residues in contact with ALA1173 (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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1170A ASN* 4.1 18.4 - - - +
1172A TYR* 3.8 29.2 - - - +
1174A GLY* 3.8 28.3 - - - +
1176A LEU* 4.7 14.4 - - - +
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Residues in contact with GLY1174 (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 PHE* 4.6 18.2 - - - +
1141A VAL* 4.3 20.2 - - - +
1173A ALA* 3.8 23.8 - - - +
1175A PHE* 3.7 29.2 - - - +
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Residues in contact with PHE1175 (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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1140A GLY* 4.6 16.2 - - - +
1174A GLY* 3.7 30.3 - - - +
1176A LEU* 3.8 24.9 - - - +
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Residues in contact with LEU1176 (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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1173A ALA* 4.7 14.4 - - - +
1175A PHE* 3.8 25.6 - - - +
1177A MET* 3.7 29.6 - - - +
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Residues in contact with MET1177 (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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1176A LEU* 3.7 29.6 - - - +
1178A ALA* 3.8 27.4 - - - +
1207A GLY* 4.3 23.6 - - - +
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Residues in contact with ALA1178 (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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1177A MET* 3.8 29.6 - - - +
1179A LEU* 3.8 27.1 - - - +
1181A LEU* 4.2 22.2 - - - +
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Residues in contact with LEU1179 (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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1178A ALA* 3.8 24.9 - - - +
1180A GLY* 3.8 29.8 - - - +
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Residues in contact with GLY1180 (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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1179A LEU* 3.8 26.5 - - - +
1181A LEU* 3.7 26.5 - - - +
1182A ASN* 4.6 0.7 - - - +
1183A GLY* 3.5 32.1 - - - +
1211A GLY* 4.0 23.3 - - - +
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Residues in contact with LEU1181 (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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1178A ALA* 4.2 20.9 - - - +
1180A GLY* 3.7 29.2 - - - +
1182A ASN* 3.7 22.2 - - - +
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Residues in contact with ASN1182 (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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1180A GLY* 4.6 2.5 - - - +
1181A LEU* 3.7 26.9 - - - +
1183A GLY* 3.7 30.3 - - - +
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Residues in contact with GLY1183 (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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1180A GLY* 3.5 32.1 - - - +
1182A ASN* 3.7 22.2 - - - +
1184A HIS* 3.7 23.8 - - - +
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Residues in contact with HIS1184 (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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1183A GLY* 3.7 30.3 - - - +
1185A LEU* 3.8 26.7 - - - +
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Residues in contact with LEU1185 (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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1184A HIS* 3.8 29.2 - - - +
1186A THR* 3.8 26.0 - - - +
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Residues in contact with THR1186 (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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1185A LEU* 3.8 25.8 - - - +
1187A LYS* 3.8 29.6 - - - +
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Residues in contact with LYS1187 (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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1186A THR* 3.8 29.8 - - - +
1188A LEU* 3.8 25.8 - - - +
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Residues in contact with LEU1188 (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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1187A LYS* 3.8 28.9 - - - +
1189A ALA* 3.8 29.2 - - - +
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Residues in contact with ALA1189 (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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1188A LEU* 3.8 26.5 - - - +
1190A THR* 3.8 29.4 - - - +
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Residues in contact with THR1190 (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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1189A ALA* 3.8 28.0 - - - +
1191A LEU* 3.7 29.8 - - - +
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Residues in contact with LEU1191 (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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1190A THR* 3.7 29.6 - - - +
1192A ASN* 3.8 25.4 - - - +
1194A HIS* 4.3 19.5 - - - +
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Residues in contact with ASN1192 (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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1191A LEU* 3.8 24.9 - - - +
1193A ILE* 3.7 29.4 - - - +
1195A ASP* 4.3 15.7 - - - +
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Residues in contact with ILE1193 (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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1192A ASN* 3.7 29.6 - - - +
1194A HIS* 3.8 26.2 - - - +
1196A TYR* 4.6 15.0 - - - +
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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