Contacts of the helix formed by residues 1135 - 1141 (chain A) in PDB entry 6KJV
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 SER1135 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1113A PHE* 3.3 30.5 - - - -
1131A ASN 3.9 1.9 + - - -
1132A LEU* 2.9 28.2 + - - -
1133A ALA 3.0 4.4 + - - -
1134A LYS* 1.3 77.9 + - - +
1136A ARG* 1.3 65.8 + - - +
1137A TRP* 3.2 12.3 - - - -
1138A TYR 4.0 4.9 - - - -
1139A ASN* 3.2 26.5 + - - +
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Residues in contact with ARG1136 (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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1105A MET* 4.0 12.6 - - + +
1109A GLY 3.4 17.2 + - - -
1112A GLY* 4.5 13.1 + - - -
1113A PHE* 3.4 47.9 - - - +
1135A SER* 1.3 73.1 - - - +
1137A TRP* 1.3 64.7 + - + +
1139A ASN* 3.3 3.6 + - - +
1140A GLN* 3.0 33.1 + - - +
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Residues in contact with TRP1137 (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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1100A ASN* 5.6 0.7 - - - -
1101A MET* 3.9 40.3 - - + +
1104A GLN* 3.0 29.5 + - - -
1105A MET* 4.0 23.0 - - + -
1113A PHE* 4.0 18.2 - + + -
1132A LEU* 4.2 22.0 - - + -
1135A SER* 3.2 1.1 - - - -
1136A ARG* 1.3 84.0 - - - +
1138A TYR* 1.3 63.0 + - - +
1140A GLN* 4.8 3.6 - - - -
1141A THR* 3.3 33.1 + - - +
1144A ARG* 4.8 1.0 - - + +
1145A ALA* 3.5 32.6 - - + +
1148A VAL* 3.7 37.0 - - + -
1149A ILE* 4.0 20.2 - - + -
1152A PHE* 5.3 0.2 - + - -
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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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1132A LEU 3.7 11.9 - - - +
1133A ALA* 3.4 39.5 - - + +
1135A SER* 3.6 4.5 + - - +
1136A ARG 3.3 0.8 - - - -
1137A TRP* 1.3 78.9 - - + +
1139A ASN* 1.3 69.7 + - - +
1142A PRO* 3.2 40.7 - - + +
1145A ALA* 3.7 22.0 - - + -
1146A LYS* 4.4 20.2 - - + +
1149A ILE* 3.8 19.7 - - + -
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Residues in contact with ASN1139 (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 ALA 3.9 4.3 - - - +
1135A SER 3.2 18.3 + - - +
1136A ARG* 3.3 4.5 + - - +
1137A TRP 3.3 0.2 - - - -
1138A TYR* 1.3 91.9 - - - +
1140A GLN* 1.3 65.3 + - - +
1142A PRO* 4.3 7.4 - - - +
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Residues in contact with GLN1140 (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 ARG 3.0 20.0 + - - +
1137A TRP* 4.2 3.8 - - - +
1139A ASN* 1.3 79.5 - - - +
1141A THR* 1.3 70.6 + - + +
1142A PRO* 3.6 6.2 - - - +
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Residues in contact with THR1141 (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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1104A GLN* 3.2 30.2 + - - +
1137A TRP* 3.3 18.5 + - - +
1138A TYR 3.8 2.0 - - - -
1140A GLN* 1.3 92.1 - - + +
1142A PRO* 1.3 66.8 - - - +
1143A ASN 3.5 1.8 - - - -
1144A ARG* 3.8 8.9 + - - +
1145A ALA* 3.2 21.0 + - - +
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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