Contacts of the helix formed by residues 114 - 121 (chain 3) in PDB entry 2WSC
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 PHE 114 (chain 3).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1103 SER 5.5 1.8 - - - -
1113 TYR 4.4 11.2 - - - +
1123 THR 2.2 26.1 + - - +
1133 LEU* 1.3 69.8 - - - +
1153 VAL* 1.3 65.5 + - - +
1163 PHE 3.4 0.7 - - - -
1173 GLU* 3.6 10.1 + - - +
1183 MET* 3.5 19.3 + - + +
12163 CLA 2.8 70.7 - + + -
12183 CLA 3.7 61.0 - + + -
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Residues in contact with VAL 115 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1123 THR 3.8 2.0 + - - +
1143 PHE* 1.3 77.5 - - - +
1163 PHE* 1.3 77.0 + - + +
1173 GLU 3.1 0.3 + - - -
1183 MET* 3.3 9.5 + - + +
1193 ALA* 2.9 30.7 + - + +
12163 CLA 3.8 26.7 - - + -
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Residues in contact with PHE 116 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12142 CLA 6.0 13.0 - + + -
1123 THR* 5.0 1.1 - - - -
1133 LEU* 3.8 44.0 - - + -
1143 PHE 3.4 0.8 - - - -
1153 VAL* 1.3 85.8 - - + +
1173 GLU* 1.3 56.7 + - - +
1193 ALA* 4.0 4.0 - - - +
1203 LEU* 2.8 49.4 + - + +
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Residues in contact with GLU 117 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1133 LEU 4.8 8.2 - - - +
1143 PHE* 3.6 15.3 + - - +
1153 VAL 3.1 0.4 - - - -
1163 PHE* 1.3 73.2 - - - +
1183 MET* 1.3 73.6 + - - +
1193 ALA 3.0 3.6 - - - -
1203 LEU 2.8 6.1 + - - -
1213 MET* 2.8 68.3 + - + +
12183 CLA 3.5 67.5 + - + +
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Residues in contact with MET 118 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1143 PHE* 3.5 11.5 + - + +
1153 VAL* 3.3 9.2 + - + +
1173 GLU* 1.3 92.8 - - - +
1193 ALA* 1.3 60.4 + - - +
1223 GLY* 3.5 16.8 + - - +
12163 CLA 4.1 31.2 - - + -
12173 CLA 5.0 26.7 - - + -
12183 CLA 4.9 20.0 - - + +
30113 CLA 5.5 11.9 + - - -
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Residues in contact with ALA 119 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1153 VAL* 2.9 26.1 + - + +
1163 PHE* 4.0 4.5 - - - +
1183 MET* 1.3 78.3 - - - +
1203 LEU* 1.3 61.2 + - + +
1223 GLY* 3.1 4.0 + - - -
1233 PHE* 2.8 26.8 + - - +
30113 CLA 5.4 12.2 - - - +
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Residues in contact with LEU 120 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1163 PHE* 2.8 40.1 + - + +
1173 GLU 2.8 3.5 + - - +
1193 ALA* 1.3 73.8 - - + +
1213 MET* 1.3 71.7 + - + +
1223 GLY 3.3 0.2 - - - -
1233 PHE* 3.0 39.0 + - + +
1243 ALA* 4.7 1.0 - - - +
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Residues in contact with MET 121 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1173 GLU* 2.8 48.3 + - + +
1203 LEU* 1.3 85.7 - - + +
1223 GLY* 1.3 58.2 + - - +
1233 PHE 3.1 4.3 - - - -
1243 ALA* 3.6 22.0 + - + +
1253 GLU* 3.7 4.5 + - - +
12183 CLA 3.0 65.7 - - + +
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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