Contacts of the strand formed by residues 134 - 138 (chain A) in PDB entry 2P2M
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 VAL 134 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A GLY 4.3 6.5 - - - +
133A ASP* 1.3 74.4 - - - +
135A VAL* 1.3 66.3 - - - +
158A VAL* 3.1 23.3 - - + +
160A SER* 3.8 17.7 - - - -
178A SER* 3.5 35.4 - - - +
179A SER 4.7 2.9 + - - +
180A SER* 3.4 19.4 - - - +
181A ARG* 3.0 30.9 + - - +
261A ILE* 5.1 2.7 - - + -
478A PHE* 4.2 22.0 - - + -
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Residues in contact with VAL 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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124A LEU* 5.0 1.3 - - + -
129A ILE* 4.0 30.3 - - + -
133A ASP 4.4 0.9 - - - +
134A VAL* 1.3 78.8 - - - +
136A ALA* 1.3 63.3 + - - +
137A ILE* 3.6 3.4 + - + -
152A CYS* 3.8 27.8 - - - -
157A ALA* 4.3 7.0 - - + -
158A VAL 2.9 9.8 + - - +
159A HIS* 3.3 4.0 - - - +
160A SER 2.8 29.9 + - - -
182A LEU* 3.9 23.3 - - + +
184A ILE* 3.7 29.6 - - + -
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Residues in contact with ALA 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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135A VAL* 1.3 72.1 - - - +
137A ILE* 1.3 63.4 + - - +
138A TYR 4.1 0.4 - - - -
160A SER* 3.4 8.5 - - - +
162A ILE* 4.1 21.3 - - + -
175A ILE* 4.3 4.3 - - + -
180A SER* 3.6 24.2 + - - +
182A LEU 2.9 13.4 + - - +
183A VAL* 3.3 16.9 - - + -
184A ILE 2.9 25.3 + - - -
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Residues in contact with ILE 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 VAL* 4.1 12.6 - - + +
136A ALA* 1.3 75.8 - - - +
138A TYR* 1.3 58.4 + - - +
139A MET* 3.4 30.1 - - + +
145A ALA* 4.9 7.9 - - + +
148A ALA* 3.9 24.7 - - + +
149A MET* 3.8 24.7 - - + +
152A CYS* 4.5 4.0 - - - -
159A HIS* 3.8 25.6 - - + -
160A SER 3.1 7.7 + - - -
161A VAL* 3.4 19.6 - - + +
162A ILE* 2.7 32.6 + - - +
184A ILE* 3.6 10.5 - - + +
307A VAL* 6.3 0.2 - - + -
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Residues in contact with TYR 138 (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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136A ALA 4.1 0.6 - - - -
137A ILE* 1.3 72.0 - - - +
139A MET* 1.3 59.1 + - - +
162A ILE* 3.4 26.0 - - + -
163A PHE 3.4 18.6 - - - -
164A GLY* 3.3 17.5 + - - -
166A PHE 2.7 22.4 + - - -
171A VAL* 3.5 28.3 - - + -
183A VAL* 4.6 10.3 - - + -
184A ILE 2.8 10.6 + - - +
185A THR* 2.6 37.3 + - - +
186A ALA 4.0 0.5 + - - -
198A LEU* 3.5 33.5 - - + +
201A ASN* 3.0 25.5 + - + +
202A VAL* 3.4 21.5 - - + -
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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