Contacts of the strand formed by residues 182 - 186 (chain A) in PDB entry 1WSQ
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 ILE 182 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A GLN* 3.5 4.5 - - - +
134A VAL* 2.9 44.4 + - + -
154A ILE* 4.2 13.0 - - + -
158A THR* 3.4 24.9 - - + +
178A LYS 3.9 7.2 - - - +
179A VAL* 3.2 13.9 + - + +
180A GLU 3.4 0.2 - - - -
181A ASN* 1.3 84.5 - - - +
183A LEU* 1.3 63.9 + - - +
190A TYR* 3.9 22.2 - - + -
191A VAL 3.5 7.6 - - - +
192A LEU* 4.7 10.8 - - + -
251A LEU* 3.7 36.6 - - + -
255A LEU* 5.5 0.7 - - + -
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Residues in contact with LEU 183 (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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104A VAL* 3.7 24.9 - - + -
129A CYS* 4.0 13.0 - - + -
132A GLY 3.3 6.3 - - - +
133A GLN* 4.0 15.3 - - + -
134A VAL* 4.7 0.7 - - - -
180A GLU 4.7 0.7 - - - +
182A ILE* 1.3 81.0 - - - +
184A LEU* 1.3 60.8 + - - +
190A TYR* 3.2 12.2 - - - -
191A VAL* 2.9 41.0 + - + +
193A CYS* 4.0 12.8 - - - -
405A KSA 3.5 68.4 - - + +
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Residues in contact with LEU 184 (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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129A CYS* 3.5 12.3 - - - +
131A GLY* 3.4 38.6 + - - +
132A GLY 2.8 16.5 + - - +
134A VAL* 4.9 1.2 - - + +
137A LEU* 4.3 26.5 - - + -
183A LEU* 1.3 71.9 - - - +
185A HIS* 1.3 59.5 + - - +
186A ASP* 3.3 36.3 - - - +
187A ARG* 4.2 4.5 - - - +
190A TYR* 3.6 34.3 - - + +
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Residues in contact with HIS 185 (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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127A ASP* 3.7 6.1 - - - -
128A PHE 4.6 3.4 - - - -
129A CYS* 3.8 18.8 - - + +
130A ARG 5.6 1.6 + - - -
131A GLY* 5.0 4.9 + - - -
183A LEU 3.6 2.6 + - - -
184A LEU* 1.3 74.6 - - - +
186A ASP* 1.3 74.4 + - - +
189A HIS* 2.9 28.2 + + + +
191A VAL* 4.3 11.4 - - + -
401A ZN 2.1 35.9 - - - -
402A ZN 2.1 36.3 - - - -
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Residues in contact with ASP 186 (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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184A LEU* 3.3 16.1 - - - +
185A HIS* 1.3 83.2 + - - +
187A ARG* 1.3 60.2 + - - +
188A GLY 3.1 0.5 + - - -
189A HIS* 2.8 37.9 + - - +
401A ZN 2.0 37.3 - - - -
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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