Contacts of the helix formed by residues 1091 - 1097 (chain A) in PDB entry 5XJY
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 MET1091 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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932A LEU* 6.0 5.4 - - + -
1089A HIS 3.5 5.6 + - - +
1090A HIS* 1.3 72.9 - - - +
1092A ASP* 1.3 60.1 + - - +
1093A GLU 3.3 1.1 - - - -
1094A ALA* 3.1 12.2 + - + +
1095A ASP* 2.9 25.1 + - - +
1128A LEU 6.2 0.2 - - - -
1130A LEU 5.8 0.7 - - - -
1131A VAL* 4.3 26.9 - - + +
1134A ASP* 5.7 5.2 - - + -
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Residues in contact with ASP1092 (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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1090A HIS* 3.5 3.9 - - + +
1091A MET* 1.3 78.6 - - - +
1093A GLU* 1.3 57.4 + - - +
1095A ASP* 3.1 10.8 + - - +
1096A VAL* 2.9 24.3 + - - +
1128A LEU 5.7 7.6 - - - +
1131A VAL* 5.8 1.0 - - - +
2105A GLU* 4.2 24.7 - - + -
2141A ILE 5.9 5.4 - - - +
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Residues in contact with GLU1093 (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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1060A THR* 5.0 17.0 - - - -
1068A ARG* 5.1 14.1 - - + -
1088A THR* 6.1 2.7 - - - -
1090A HIS* 4.2 12.9 + - + +
1091A MET 3.3 0.4 - - - -
1092A ASP* 1.3 77.4 - - - +
1094A ALA* 1.3 51.5 + - - +
1096A VAL* 3.0 10.7 + - - +
1097A LEU* 2.7 32.8 + - - +
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Residues in contact with ALA1094 (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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930A SER* 4.6 18.6 - - - -
932A LEU* 5.5 10.1 - - + -
1088A THR* 5.3 10.6 - - - -
1090A HIS 4.3 3.7 + - - +
1091A MET* 3.1 18.3 + - + +
1093A GLU* 1.3 77.4 - - - +
1095A ASP* 1.3 58.6 + - - +
1097A LEU* 3.1 31.5 + - - +
1100A ARG 5.4 2.4 - - - +
1101A ILE* 5.9 5.0 - - + +
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Residues in contact with ASP1095 (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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1091A MET 2.9 12.4 + - - +
1092A ASP* 3.1 12.5 + - - +
1094A ALA* 1.3 74.6 - - - +
1096A VAL* 1.3 63.7 + - - +
1097A LEU 3.4 6.2 - - - +
1115A SER* 5.1 17.3 - - - -
1128A LEU 5.5 8.5 - - - +
1130A LEU* 5.7 7.9 - - + -
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Residues in contact with VAL1096 (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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1068A ARG* 5.6 7.9 - - + -
1072A TRP* 5.6 7.2 - - + -
1092A ASP 2.9 13.3 + - - +
1093A GLU* 3.0 13.2 + - - +
1095A ASP* 1.3 73.0 - - - +
1097A LEU* 1.3 65.5 + - - +
1098A GLY* 3.7 2.3 + - - -
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Residues in contact with LEU1097 (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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928A ILE* 4.4 16.6 - - + +
929A THR 5.1 7.2 - - - +
930A SER* 5.1 5.2 - - - -
1086A LEU* 6.5 0.7 - - + -
1093A GLU 2.7 16.8 + - - +
1094A ALA* 3.1 28.1 + - + +
1095A ASP* 3.4 6.9 - - - +
1096A VAL* 1.3 75.8 - - - +
1098A GLY* 1.3 59.9 + - - +
1099A ASP 4.0 1.3 + - - -
1100A ARG 5.4 3.1 + - - +
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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