Contacts of the helix formed by residues 1091 - 1095 (chain B) in PDB entry 3I8E
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 GLY1091 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5B TYR* 2.8 33.0 - - - -
6B VAL 2.7 12.9 + - - -
7B VAL* 4.0 2.2 - - - -
1089B ILE 2.9 5.1 + - - -
1090B ASP* 1.3 66.9 - - - +
1092B ASP* 1.3 58.4 + - - +
1093B LEU 3.2 0.4 - - - -
1094B ILE* 3.7 6.7 - - - -
1095B GLU* 2.8 43.6 + - - +
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Residues in contact with ASP1092 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B VAL 4.1 1.8 + - - -
7B VAL* 4.0 5.5 - - - +
8B THR* 2.6 55.2 + - - +
1074B ARG* 5.0 6.2 + - - +
1090B ASP* 2.9 15.9 - - + +
1091B GLY* 1.3 77.3 - - - +
1093B LEU* 1.3 59.3 + - - +
1095B GLU* 3.8 6.9 - - - +
1096B SER* 3.3 18.7 + - - -
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Residues in contact with LEU1093 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B TYR* 3.9 16.6 - - + +
1055B GLN* 3.6 33.7 - - + +
1058B LEU* 3.5 15.1 - - + +
1059B ASN* 3.6 24.7 - - - +
1062B ILE* 4.1 15.0 - - + -
1070B HIS* 3.6 21.3 - - + +
1090B ASP* 2.8 24.1 + - - +
1092B ASP* 1.3 74.7 - - - +
1094B ILE* 1.3 59.9 + - - +
1095B GLU 3.0 1.3 - - - -
1096B SER* 2.6 43.3 + - - +
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Residues in contact with ILE1094 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B TYR* 4.2 5.8 - - + +
1051B LEU* 3.8 37.7 - - + +
1054B MET* 3.5 29.8 - - + +
1055B GLN* 4.5 11.9 - - + +
1058B LEU* 3.9 5.5 - - + +
1089B ILE* 3.7 25.8 - - + -
1090B ASP 3.8 5.6 - - - +
1091B GLY* 3.7 12.3 - - - -
1093B LEU* 1.3 76.4 - - - +
1095B GLU* 1.3 57.8 + - + +
1097B PHE* 3.1 27.7 - - - +
1133B VAL* 3.4 17.3 - - + +
1136B LEU* 4.1 15.5 - - + -
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Residues in contact with GLU1095 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B TYR* 4.5 6.3 + - - +
7B VAL* 3.7 27.6 - - - +
1091B GLY 2.8 27.5 + - - +
1092B ASP* 3.8 8.7 - - - +
1093B LEU 3.0 0.2 - - - -
1094B ILE* 1.3 69.0 - - + +
1096B SER* 1.3 60.9 + - - +
1097B PHE 3.0 6.2 + - - -
1098B LEU* 3.3 19.7 + - + +
1099B ASP* 4.7 4.5 - - - +
1133B VAL* 3.9 11.2 - - + +
1136B LEU* 4.5 3.6 - - + +
1137B THR* 3.5 34.8 - - + +
1140B HIS* 3.9 11.9 + - - -
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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