Contacts of the helix formed by residues 1132 - 1146 (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 THR1132 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1131A MET* 3.8 27.1 - - - +
1133A SER* 3.7 29.6 - - - +
1135A ALA* 4.3 19.7 - - - +
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Residues in contact with SER1133 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1132A THR* 3.7 29.4 - - - +
1134A TRP* 3.8 25.6 - - - +
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Residues in contact with TRP1134 (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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1133A SER* 3.8 26.0 - - - +
1135A ALA* 3.8 28.9 - - - +
1137A PHE* 4.3 17.3 - - - +
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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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1132A THR* 4.3 18.6 - - - +
1134A TRP* 3.8 27.4 - - - +
1136A SER* 3.7 29.4 - - - +
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Residues in contact with SER1136 (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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1135A ALA* 3.7 30.1 - - - +
1137A PHE* 3.8 25.1 - - - +
1139A ASN* 4.4 16.2 - - - +
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Residues in contact with PHE1137 (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 TRP* 4.3 17.7 - - - +
1136A SER* 3.8 26.2 - - - +
1138A HIS* 3.7 29.4 - - - +
1170A ASN* 4.2 23.3 - - - +
1174A GLY* 4.6 15.9 - - - +
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Residues in contact with HIS1138 (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* 3.7 29.8 - - - +
1139A ASN* 3.8 25.8 - - - +
1141A VAL* 4.2 19.5 - - - +
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Residues in contact with ASN1139 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1136A SER* 4.4 18.2 - - - +
1138A HIS* 3.8 25.1 - - - +
1140A GLY* 3.8 29.8 - - - +
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Residues in contact with GLY1140 (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 ASN* 3.8 29.8 - - - +
1141A VAL* 3.8 26.2 - - - +
1143A ALA* 4.2 21.3 - - - +
1175A PHE* 4.6 16.6 - - - +
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Residues in contact with VAL1141 (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 HIS* 4.2 19.3 - - - +
1140A GLY* 3.8 23.8 - - - +
1142A ALA* 3.7 29.6 - - - +
1174A GLY* 4.3 18.8 - - - +
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Residues in contact with ALA1142 (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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1085A GLY* 4.2 24.5 - - - +
1141A VAL* 3.7 29.6 - - - +
1143A ALA* 3.7 26.0 - - - +
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Residues in contact with ALA1143 (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* 4.2 18.2 - - - +
1142A ALA* 3.7 29.6 - - - +
1144A GLY* 3.7 26.2 - - - +
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Residues in contact with GLY1144 (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 ALA* 3.7 26.7 - - - +
1145A LEU* 3.7 30.1 - - - +
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Residues in contact with LEU1145 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1089A LEU* 4.6 12.8 - - - +
1144A GLY* 3.7 29.8 - - - +
1146A LYS* 3.8 28.7 - - - +
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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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1089A LEU* 4.3 8.7 - - - +
1090A PHE* 3.8 19.3 - - - +
1091A SER* 4.3 12.1 - - - +
1145A LEU* 3.8 28.7 - - - +
1147A ILE* 3.8 25.1 - - - +
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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