Contacts of the helix formed by residues 1067 - 1072 (chain A) in PDB entry 3B8R
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 LEU1067 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1032A ARG* 5.3 0.7 - - - -
1068A PRO* 1.3 78.0 - - + +
1069A LEU* 3.1 34.9 + - + +
1070A LYS* 3.5 21.0 + - - +
1071A TRP* 3.5 19.8 - - - -
1111A ILE* 4.6 19.4 - - + +
1108B GLY 5.5 2.0 - - - +
1110B LYS* 5.6 14.1 - - + +
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Residues in contact with PRO1068 (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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1028A ASP* 4.5 9.6 - - - +
1032A ARG* 4.1 20.0 - - - +
1067A LEU* 1.3 94.8 - - + +
1069A LEU* 1.3 64.6 + - + +
1070A LYS 3.0 2.9 - - - -
1071A TRP* 2.9 26.3 + - + +
1072A MET* 3.2 24.9 + - + +
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Residues in contact with LEU1069 (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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1067A LEU* 3.1 19.9 - - + -
1068A PRO* 1.3 79.3 - - + +
1070A LYS* 1.3 61.7 + - - +
1071A TRP 3.1 1.6 + - - -
1072A MET* 3.1 42.0 + - - +
1077A ILE* 4.0 21.6 - - + +
1111A ILE* 3.3 35.0 - - + +
1115A PHE* 4.5 9.2 - - + -
1116A CYS* 5.0 7.4 - - - -
1119A LEU* 5.3 0.7 - - - +
1108B GLY* 3.6 42.2 - - - +
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Residues in contact with LYS1070 (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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1067A LEU 3.6 16.5 - - - +
1068A PRO 3.0 0.4 - - - -
1069A LEU* 1.3 78.3 - - - +
1071A TRP* 1.3 78.3 + - + +
1072A MET 3.5 0.7 - - - -
1089A TRP* 4.8 1.7 + - - -
1093A VAL* 3.6 13.9 - - - +
1104A SER* 3.3 19.6 + - - -
1105A PRO* 3.1 37.3 + - + +
1106A TYR* 3.5 39.1 + - + -
1109A VAL 5.3 2.4 + - - -
1111A ILE* 3.9 37.2 - - + -
1115A PHE* 4.6 2.9 - - - -
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Residues in contact with TRP1071 (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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1028A ASP* 5.1 7.6 - - - +
1029A LEU 3.2 27.6 - - - +
1030A ALA* 2.9 17.7 - - + +
1032A ARG* 3.8 22.2 - - - -
1067A LEU 3.5 22.2 - - - -
1068A PRO 2.9 9.7 + - - +
1070A LYS* 1.3 95.3 - - + +
1072A MET* 1.3 61.4 + - + +
1089A TRP* 3.4 11.4 - - - -
1090A SER* 2.6 30.1 + - - +
1093A VAL* 3.5 27.0 - - + +
1094A LEU 4.6 0.4 - - - -
1097A GLU* 2.8 43.7 + - - -
1104A SER* 5.3 2.5 - - - -
1105A PRO* 3.6 20.9 - - + -
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Residues in contact with MET1072 (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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1027A ARG 5.4 4.7 - - - +
1068A PRO* 3.2 22.7 - - + +
1069A LEU* 3.1 40.0 + - - +
1070A LYS 5.1 0.3 - - - -
1071A TRP* 1.3 79.7 - - + +
1073A ALA* 1.3 64.7 + - - +
1074A PRO 3.8 0.3 - - - -
1076A THR* 4.1 19.7 - - + +
1077A ILE* 3.6 24.9 - - + +
1082A TYR* 3.1 31.0 - - + +
1089A TRP* 3.4 11.4 + - - -
1090A SER* 4.7 0.7 - - - -
1119A LEU* 4.0 3.6 - - - +
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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