Contacts of the helix formed by residues 1189 - 1196 (chain A) in PDB entry 6CNB
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 ASP1189 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1169A VAL* 4.2 2.6 + - - +
1171A PHE* 4.0 23.3 - - + +
1188A ILE* 1.3 76.8 - - - +
1190A LEU* 1.3 62.8 + - - +
1191A GLY* 3.1 13.8 + - - -
1192A THR* 2.5 48.5 + - - +
1193A ILE* 3.2 15.1 - - - +
1195A LYS* 4.3 6.0 + - - -
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Residues in contact with LEU1190 (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 ILE 3.7 1.8 + - - +
1189A ASP* 1.3 68.9 + - - +
1191A GLY* 1.3 58.2 + - - +
1192A THR 3.0 5.2 - - - -
1193A ILE* 2.9 37.7 + - + +
1194A ASP* 2.9 17.1 + - - +
1200A LEU* 4.9 2.0 - - + -
1201A THR* 4.2 15.9 - - + +
1227A LYS* 5.2 15.0 - - + -
1228A ASP* 3.2 33.2 - - - +
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Residues in contact with GLY1191 (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 ASP* 3.1 15.4 + - - -
1190A LEU* 1.3 77.7 - - - +
1192A THR* 1.3 55.9 + - - +
1194A ASP* 3.2 18.1 + - - +
1195A LYS* 2.9 36.0 + - - +
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Residues in contact with THR1192 (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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1165A LEU* 5.8 4.3 - - + -
1168A ASP* 4.5 31.2 + - - +
1169A VAL* 5.2 11.4 - - + -
1189A ASP* 2.5 37.5 + - - +
1190A LEU 3.0 0.6 - - - -
1191A GLY* 1.3 72.1 - - - +
1193A ILE* 1.3 62.7 + - + +
1194A ASP 3.0 1.1 - - - -
1195A LYS* 2.8 33.0 + - + +
1196A LEU* 2.8 25.3 + - + +
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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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1169A VAL* 5.1 7.9 - - + -
1188A ILE* 4.2 9.9 - - + -
1189A ASP 3.2 27.6 - - - +
1190A LEU* 2.9 23.8 + - + +
1192A THR* 1.3 77.8 - - + +
1194A ASP* 1.3 62.0 + - - +
1196A LEU 2.7 22.5 - - - +
1197A GLN* 3.3 8.3 - - - +
1198A LEU* 3.8 33.9 - - + +
1200A LEU* 3.6 44.9 - - + +
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Residues in contact with ASP1194 (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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1190A LEU* 2.9 16.3 + - - +
1191A GLY* 3.3 20.9 - - - +
1192A THR 3.0 0.2 - - - -
1193A ILE* 1.3 82.7 - - - +
1195A LYS* 1.3 64.7 + - - +
1197A GLN* 4.5 9.8 + - - +
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Residues in contact with LYS1195 (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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1155A ARG* 5.1 6.8 - - - -
1189A ASP* 4.3 7.5 + - - -
1191A GLY* 2.9 25.6 + - - +
1192A THR* 2.8 20.3 + - + +
1194A ASP* 1.3 81.0 - - - +
1196A LEU* 1.3 68.4 + - + +
1197A GLN* 3.6 5.7 + - - +
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Residues in contact with LEU1196 (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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1155A ARG* 3.8 35.2 - - + +
1158A LYS* 5.1 10.3 - - + +
1159A GLY* 5.9 2.9 - - - -
1162A GLU* 5.1 10.3 - - - +
1165A LEU* 4.3 18.8 - - + -
1168A ASP* 5.0 10.3 - - - +
1192A THR* 2.8 18.5 + - + +
1193A ILE* 2.7 22.4 - - - +
1195A LYS* 1.3 79.6 - - + +
1197A GLN* 1.3 61.6 + - - +
1198A LEU* 3.1 20.2 + - + +
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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