Contacts of the strand formed by residues 134 - 138 (chain A) in PDB entry 2R2N
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 ASN 134 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A GLY 3.6 1.0 + - - +
133A ASP* 1.3 73.3 - - - +
135A VAL* 1.3 63.0 + - - +
155A ASN* 3.6 29.0 + - - +
157A ILE* 4.0 21.7 - - + +
177A ARG* 5.7 0.2 - - - +
178A TRP* 3.4 15.2 - - - +
188A LYS 5.0 0.2 + - - -
189A ASN* 2.6 42.1 + - - +
190A THR 5.3 1.2 + - - -
191A PRO* 3.2 12.2 - - + +
192A LYS* 3.1 26.5 + - - +
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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
----------------------------------------------------------
129A ILE* 4.4 7.2 - - + -
133A ASP* 4.7 2.0 - - + +
134A ASN* 1.3 79.9 - - - +
136A LEU* 1.3 61.1 + - - +
137A LEU* 5.0 0.9 - - + -
149A LEU* 4.5 6.3 - - + -
154A CYS* 4.1 23.1 - - + -
155A ASN 3.0 9.0 + - - +
156A ILE* 3.6 27.5 - - + -
157A ILE* 2.7 33.0 + - - +
191A PRO* 4.7 0.7 - - - -
192A LYS* 5.0 3.4 - - + -
193A PHE* 3.5 51.6 - - + +
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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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135A VAL* 1.3 75.6 - - - +
137A LEU* 1.3 64.8 + - - +
157A ILE* 3.5 21.3 - - + +
159A VAL* 4.0 9.2 - - + -
171A LEU* 3.7 20.6 - - + -
174A ILE* 3.8 29.2 - - + -
175A LEU* 4.1 9.9 - - + -
191A PRO* 3.9 31.4 - - + -
193A PHE* 3.0 13.3 + - - +
194A LEU* 3.7 17.0 - - + -
195A TYR* 2.9 26.3 + - - +
225A PHE* 4.1 13.7 - - + -
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Residues in contact with LEU 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* 4.2 2.9 + - + -
136A LEU* 1.3 76.0 - - - +
138A ASP* 1.3 74.1 + - - +
139A GLU* 4.1 13.5 - - + +
141A ALA* 4.5 7.4 - - + -
145A THR* 4.9 1.6 - - - +
146A LEU* 4.4 12.8 - - + -
149A LEU* 3.8 26.2 - - + -
156A ILE* 3.6 31.6 - - + -
157A ILE 3.3 6.1 + - - -
158A ASN* 3.3 4.8 - - - +
159A VAL* 2.8 25.6 + - - +
194A LEU* 3.9 5.4 - - - -
195A TYR* 3.2 35.4 - - + +
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Residues in contact with ASP 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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137A LEU* 1.3 74.7 - - - +
139A GLU* 1.3 60.0 + - - +
140A PRO* 3.2 15.2 - - - +
141A ALA* 3.5 12.6 - - - +
159A VAL* 3.4 18.1 - - + +
161A SER* 3.9 22.6 + - - -
165A GLY* 5.5 1.7 - - - -
166A ILE* 3.5 21.8 + - + +
195A TYR* 4.0 1.9 - - - +
196A THR* 2.7 34.2 + - - -
197A VAL 4.8 0.7 + - - +
201A ASN* 4.4 14.2 + - - +
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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