Contacts of the helix formed by residues 178 - 182 (chain A) in PDB entry 1WUR
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 LEU 178 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A LEU* 4.6 6.5 - - + -
114A PRO* 3.1 44.8 + - + +
116A PHE* 4.3 21.3 - - + -
176A VAL 4.1 0.6 - - - -
177A HIS* 1.3 73.2 - - - +
179A CYS* 1.3 56.8 + - - +
180A MET 3.0 0.2 - - - -
181A MET* 4.1 28.3 - - + +
182A MET* 2.8 61.9 + - + +
183A ARG 4.1 0.2 + - - -
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Residues in contact with CYS 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A CYS* 4.0 5.2 - - - -
111A HIS* 3.5 19.5 - - + +
113A LEU* 3.8 20.7 - - + +
114A PRO 4.6 0.6 + - - -
177A HIS* 3.1 16.2 - - - -
178A LEU* 1.3 78.5 - - - +
180A MET* 1.3 65.4 + - - +
183A ARG* 2.9 37.6 + - - +
184A GLY* 4.7 0.3 - - - -
185A VAL 5.2 0.2 + - - -
821A 8DG 3.2 15.7 + - - -
1001A ZN 2.3 37.0 - - - -
133B SER* 5.5 0.2 - - - -
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Residues in contact with MET 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A VAL* 6.0 0.2 - - - -
177A HIS* 3.0 42.2 + - + +
179A CYS* 1.3 87.2 - - - +
181A MET* 1.3 61.2 + - + +
183A ARG 3.8 2.9 - - - -
185A VAL* 3.5 11.6 - - + +
186A GLU 3.1 9.0 + - - -
187A LYS* 2.9 28.8 + - + +
190A SER* 4.8 20.6 - - - +
191A ARG* 6.3 0.2 - - - -
192A THR* 4.1 9.0 - - - +
821A 8DG 5.3 0.4 - - + -
99B VAL* 5.5 2.7 - - + -
132B LEU* 3.7 25.4 - - + +
133B SER* 3.7 39.9 - - - +
136B ALA* 5.7 2.9 - - - -
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Residues in contact with MET 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A PHE* 6.1 1.3 - - + -
176A VAL* 3.8 33.7 - - + -
177A HIS 3.3 20.0 - - - +
178A LEU* 3.1 22.1 + - + +
180A MET* 1.3 81.3 - - + +
182A MET* 1.3 61.6 + - - +
183A ARG 3.4 3.1 + - - -
186A GLU* 3.7 9.4 - - - +
187A LYS 3.4 18.8 - - - +
188A GLN* 3.0 48.0 + - - +
190A SER* 5.2 5.6 - - - +
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Residues in contact with MET 182 (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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113A LEU* 4.5 20.4 - - + -
114A PRO* 6.0 0.2 - - - -
178A LEU* 2.8 50.7 + - + +
181A MET* 1.3 72.9 - - - +
183A ARG* 1.3 66.9 + - + +
186A GLU* 4.4 7.2 - - - +
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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