Contacts of the strand formed by residues 188 - 192 (chain B) in PDB entry 3P3W
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 ARG 188 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B TYR 5.5 1.2 + - - -
130B TRP* 3.5 48.5 - - + +
132B LYS 3.9 10.8 + - - +
133B PHE* 3.5 21.1 - - + -
134B VAL* 3.0 32.3 + - - +
186B GLU* 3.7 1.1 - - - +
187B LYS* 1.3 90.2 + - - +
189B TYR* 1.3 60.4 + - - +
214B GLY 4.4 11.5 + - - -
215B TYR 5.8 0.2 - - - -
216B HIS* 3.6 25.3 + - + +
238B ASN* 5.3 5.7 - - - +
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Residues in contact with TYR 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B TRP* 3.8 6.6 - - - -
134B VAL* 3.7 28.9 - - + -
136B LEU* 4.5 20.0 - - + -
177B ILE* 6.3 0.7 - - + -
178B ILE* 3.6 28.6 - - + +
181B MET* 3.3 29.2 - - + +
182B ASP* 3.7 8.8 + - - -
186B GLU 4.0 8.8 + - - -
187B LYS 4.1 0.9 - - - -
188B ARG* 1.3 80.2 - - - +
190B LEU* 1.3 54.4 + - - +
191B ILE* 4.1 6.1 - - + -
215B TYR* 3.6 31.9 - + - -
216B HIS 2.8 11.1 + - - +
217B TYR* 3.5 37.1 - + + -
218B MET* 2.8 31.2 + - - -
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Residues in contact with LEU 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B ILE* 4.2 18.8 - - + -
125B LEU* 4.5 7.2 - - + -
130B TRP* 4.6 4.9 - - + -
133B PHE* 4.2 23.6 - - + -
134B VAL 2.7 16.8 + - - +
135B TYR* 3.4 28.1 - - + -
136B LEU* 2.8 29.7 + - - +
149B ILE* 4.8 7.0 - - + -
189B TYR* 1.3 73.0 - - - +
191B ILE* 1.3 61.5 + - - +
218B MET* 3.4 39.3 - - + +
220B ALA* 4.1 19.5 - - + -
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Residues in contact with ILE 191 (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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136B LEU* 3.7 31.4 - - + +
189B TYR* 4.2 16.6 - - + +
190B LEU* 1.3 76.3 - - - +
192B ASP* 1.3 61.0 + - - +
193B CYS* 3.7 15.6 + - - -
198B ILE* 3.8 29.7 - - + +
201B ILE* 4.7 17.0 - - + -
202B LEU* 5.9 1.1 - - + -
217B TYR* 4.4 15.5 - - + -
218B MET 2.8 11.6 + - - +
219B LEU* 3.7 27.9 - - + -
220B ALA* 2.7 34.9 + - - +
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Residues in contact with ASP 192 (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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117B LEU* 5.9 0.3 - - - +
135B TYR* 3.5 20.6 + - + +
136B LEU 2.7 15.9 + - - +
137B TYR* 4.1 4.0 - - + +
138B ASP* 3.1 23.0 + - - +
141B ARG* 3.6 22.5 - - - +
142B GLY 4.9 0.9 - - - +
145B VAL* 3.4 33.8 - - - +
190B LEU* 5.6 0.2 - - + -
191B ILE* 1.3 72.3 - - - +
193B CYS* 1.3 62.0 + - - +
220B ALA* 3.6 27.2 - - + +
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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