Contacts of the helix formed by residues 1165 - 1170 (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 LEU1165 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1159A GLY* 5.4 6.1 - - - +
1162A GLU* 3.3 40.2 - - + +
1164A THR* 1.3 74.9 + - - +
1166A LEU* 1.3 53.5 + - - +
1167A SER 3.4 2.0 - - - -
1168A ASP* 2.9 21.5 + - + +
1169A VAL* 2.5 50.3 + - + +
1192A THR* 5.8 4.0 - - + -
1196A LEU* 4.3 20.2 - - + -
1198A LEU* 3.7 38.6 - - + -
1272A VAL* 3.3 10.5 - - + +
1273A LYS 4.4 7.0 - - - +
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Residues in contact with LEU1166 (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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1164A THR* 3.4 6.5 + - - +
1165A LEU* 1.3 74.3 - - - +
1167A SER* 1.3 52.6 + - - +
1169A VAL* 2.9 9.6 + - + +
1170A ALA* 2.4 44.7 + - + +
1209A ILE* 4.0 20.6 - - + -
1267A LEU* 3.3 28.9 - - + +
1268A PRO* 3.5 18.2 - - + -
1269A ASP 3.7 3.8 - - - +
1270A VAL* 3.1 38.4 - - + +
1271A VAL 4.8 0.4 - - - +
1272A VAL* 3.3 18.5 - - + +
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Residues in contact with SER1167 (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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1164A THR* 5.8 0.6 - - - +
1165A LEU 3.4 0.2 - - - -
1166A LEU* 1.3 81.6 - - - +
1168A ASP* 1.3 58.7 + - - +
1170A ALA* 2.9 28.9 + - - +
1171A PHE 4.2 2.4 + - - +
1268A PRO* 3.7 21.9 + - - +
1269A ASP* 4.8 2.5 + - - -
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Residues in contact with ASP1168 (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* 2.9 26.0 + - + +
1167A SER* 1.3 77.8 + - - +
1169A VAL* 1.3 57.9 + - - +
1170A ALA 3.3 0.2 - - - -
1171A PHE 4.8 1.9 + - - -
1192A THR* 4.5 24.5 + - - +
1196A LEU* 5.0 10.0 - - - +
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Residues in contact with VAL1169 (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* 2.5 44.9 + - + +
1166A LEU* 3.4 10.8 - - + +
1168A ASP* 1.3 72.9 - - + +
1170A ALA* 1.3 63.4 + - - +
1171A PHE* 3.0 4.9 + - - +
1188A ILE* 3.3 52.8 - - + +
1189A ASP* 4.2 2.4 + - - +
1192A THR* 5.2 11.9 - - + -
1193A ILE* 5.1 10.8 - - + -
1198A LEU* 5.4 5.8 - - + -
1200A LEU* 5.6 8.3 - - + -
1205A ILE* 5.9 1.6 - - + -
1272A VAL* 5.1 9.0 - - + -
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Residues in contact with ALA1170 (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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1166A LEU* 2.4 35.4 + - + +
1167A SER* 2.9 22.5 + - - +
1169A VAL* 1.3 70.6 - - - +
1171A PHE* 1.3 66.8 + - - +
1172A TYR 2.9 10.0 + - - +
1173A VAL* 4.9 9.1 - - + +
1186A VAL* 4.7 4.6 - - - +
1187A ARG 2.8 16.1 - - - +
1188A ILE* 4.8 2.7 - - - -
1268A PRO* 4.9 9.6 - - + -
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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