Contacts of the strand formed by residues 132 - 137 (chain A) 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 LYS 132 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A TRP* 5.8 0.7 - - - -
131A GLU* 1.3 81.1 - - + +
133A PHE* 1.3 60.9 + - - +
159A GLN* 3.7 15.7 - - + -
185A GLN 6.0 1.3 - - - +
186A GLU* 3.3 16.9 - - - +
187A LYS 5.3 1.0 + - - -
188A ARG* 3.9 14.7 + - - +
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Residues in contact with PHE 133 (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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125A LEU* 4.2 18.2 - - + -
130A TRP* 3.6 57.9 - + + -
131A GLU 4.1 0.7 - - - -
132A LYS* 1.3 81.3 - - - +
134A VAL* 1.3 71.6 + - - +
135A TYR* 4.9 0.7 - - + -
149A ILE* 5.5 5.8 - - + -
158A TRP* 4.1 17.3 - + + -
159A GLN 3.0 18.6 + - - +
160A VAL* 3.5 49.4 - - + -
161A THR* 3.6 2.6 + - - -
186A GLU* 3.4 13.1 + - - +
188A ARG* 3.5 11.4 - - + +
190A LEU* 4.2 23.1 - - + -
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Residues in contact with VAL 134 (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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133A PHE* 1.3 79.6 - - - +
135A TYR* 1.3 60.1 + - - +
136A LEU* 3.8 25.1 - - + -
161A THR* 3.6 13.2 - - - +
163A ARG* 5.3 2.5 - - + -
181A MET* 3.7 24.9 - - + -
186A GLU* 3.7 26.2 - - + -
188A ARG 3.0 15.5 + - - +
189A TYR* 3.7 26.2 - - + -
190A LEU* 2.7 36.1 + - - +
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Residues in contact with TYR 135 (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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133A PHE* 4.3 1.1 + - + -
134A VAL* 1.3 73.1 - - - +
136A LEU* 1.3 63.0 + - - +
137A TYR* 3.4 38.4 - + + +
142A GLY 5.2 0.2 + - - -
145A VAL* 3.5 12.2 - - + +
146A LEU* 3.4 44.8 + - + +
149A ILE* 4.9 13.2 - - + -
150A MET* 6.0 0.2 - - + -
160A VAL* 3.9 17.5 - - + -
161A THR 2.8 22.7 + - - +
162A ALA* 4.3 7.0 - - + -
163A ARG 3.2 15.6 + - - -
190A LEU* 3.4 32.8 - - + -
192A ASP* 3.5 30.9 + - + -
220A ALA* 6.3 0.2 - - + -
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Residues in contact with LEU 136 (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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134A VAL* 3.8 24.0 - - + -
135A TYR* 1.3 71.4 - - - +
137A TYR* 1.3 57.3 + - - +
163A ARG* 3.7 30.3 - - + +
165A VAL* 5.1 9.9 - - + -
177A ILE* 4.7 11.4 - - + -
178A ILE* 5.9 6.5 - - + -
181A MET* 5.8 0.9 - - + -
189A TYR* 4.4 14.1 - - + -
190A LEU 2.9 9.1 + - - +
191A ILE* 3.7 31.4 - - + -
192A ASP* 2.7 35.3 + - - +
193A CYS* 4.3 5.5 - - - -
201A ILE* 4.1 15.5 - - + -
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Residues in contact with TYR 137 (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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135A TYR* 3.4 38.8 - + + +
136A LEU* 1.3 75.6 - - - +
138A ASP* 1.3 74.4 + - - +
139A THR* 5.0 1.8 - - + -
142A GLY 5.4 2.7 - - - -
143A PHE* 4.7 12.7 - + - -
146A LEU* 3.6 43.5 - - + +
162A ALA* 3.9 6.9 - - + +
163A ARG 3.0 56.4 + - - +
164A SER* 3.4 22.7 + - - -
165A VAL* 3.0 21.5 + - - +
192A ASP* 3.4 13.7 - - + +
193A CYS* 4.4 0.2 - - - -
137C TYR* 5.3 3.6 + - - -
150C MET* 5.8 2.4 - - - +
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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