Contacts of the strand formed by residues 188 - 192 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130C TRP* 3.7 31.2 - - + -
132C LYS 4.1 8.5 - - - +
133C PHE* 3.8 18.5 - - + -
134C VAL* 3.3 23.4 + - - +
186C GLU* 4.7 1.4 - - - +
187C LYS* 1.3 81.9 + - - +
189C TYR* 1.3 64.3 + - - +
216C HIS* 3.4 8.7 - - + +
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Residues in contact with TYR 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C TRP* 4.0 4.8 - - - -
133C PHE* 5.2 0.4 - - - -
134C VAL* 3.6 36.3 - - + -
136C LEU* 4.4 19.1 - - + -
177C ILE* 6.3 1.6 - - + -
178C ILE* 3.6 27.1 - - + +
181C MET* 3.4 25.3 - - + +
186C GLU 4.4 6.6 + - - -
187C LYS 3.2 30.7 - - - -
188C ARG* 1.3 74.4 - - - +
190C LEU* 1.3 57.2 + - - +
191C ILE* 4.1 5.6 - - + -
201C ILE* 6.5 0.4 - - + -
211C HIS* 5.7 1.2 - - - -
215C TYR* 4.6 10.7 - + - -
216C HIS 2.8 7.1 + - - +
217C TYR* 3.5 42.0 - + + -
218C MET* 2.7 33.8 + - - +
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Residues in contact with LEU 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C ILE* 4.4 14.4 - - + -
125C LEU* 4.8 3.8 - - + -
130C TRP* 5.1 1.6 - - + -
133C PHE* 3.7 26.5 - - + -
134C VAL 2.8 16.1 + - - +
135C TYR* 3.4 31.0 - - + -
136C LEU* 2.9 25.6 + - - -
149C ILE* 4.1 14.8 - - + -
189C TYR* 1.3 74.9 - - - +
191C ILE* 1.3 61.8 + - - +
218C MET* 3.4 41.1 - - + +
220C ALA* 4.3 18.6 - - + -
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Residues in contact with ILE 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136C LEU* 3.7 21.5 - - + +
189C TYR* 5.0 3.4 - - + -
190C LEU* 1.3 75.9 - - - +
192C ASP* 1.3 62.1 + - - +
193C CYS* 3.8 10.0 + - - +
198C ILE* 3.7 25.1 - - + +
201C ILE* 3.7 46.9 - - + -
202C LEU* 4.8 5.4 - - + -
217C TYR* 4.6 20.0 - - + -
218C MET 2.8 10.2 + - - +
219C LEU* 3.7 24.7 - - + -
220C ALA* 2.8 31.7 + - - +
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Residues in contact with ASP 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117C LEU* 5.4 4.0 - - - +
135C TYR* 3.0 35.5 + - + +
136C LEU 2.7 14.6 + - - +
137C TYR* 4.2 4.6 - - - +
138C ASP* 3.4 21.1 + - - +
141C ARG* 5.3 11.8 - - - +
142C GLY 5.3 2.9 - - - +
145C VAL* 3.4 28.0 - - - +
191C ILE* 1.3 73.6 - - - +
193C CYS* 1.3 59.8 + - - +
220C ALA* 3.4 27.6 - - + +
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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