Contacts of the strand formed by residues 134 - 140 (chain A) in PDB entry 1RPJ
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 GLY 134 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129A LEU* 4.6 2.0 - - - -
132A GLU 3.4 1.7 + - - -
133A GLY* 1.3 75.3 - - - -
135A GLU* 1.3 66.4 + - - -
136A VAL* 3.8 3.2 + - - -
164A GLN 2.8 11.6 + - - -
165A ILE* 3.4 8.8 - - - +
166A LYS* 3.0 23.7 + - - -
195A LYS* 4.5 10.5 - - - -
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Residues in contact with GLU 135 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134A GLY* 1.3 75.1 - - - -
136A VAL* 1.3 64.6 + - - +
166A LYS* 3.3 25.8 + - + +
168A VAL* 3.7 18.6 - - + +
191A ASN* 3.0 38.3 + - - +
193A ASN* 4.1 16.2 + - - +
194A ILE* 3.6 20.9 + - - +
195A LYS* 2.8 30.9 + - - +
196A ALA 3.7 0.2 + - - -
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Residues in contact with VAL 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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125A ILE* 4.0 8.5 - - + -
129A LEU* 3.9 24.5 - - + -
134A GLY 4.0 5.8 - - - +
135A GLU* 1.3 80.6 - - - +
137A ALA* 1.3 61.1 + - - +
159A PHE* 3.6 34.5 - - + -
165A ILE* 3.6 25.6 - - + -
166A LYS 2.8 7.7 + - - -
167A LEU* 3.4 9.0 - - + -
168A VAL* 2.9 27.0 + - - +
194A ILE* 3.7 4.5 - - - -
196A ALA* 3.2 20.4 - - + +
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Residues in contact with ALA 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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136A VAL* 1.3 77.3 - - - +
138A ILE* 1.3 68.9 + - - +
139A ILE* 4.2 1.3 - - + -
159A PHE* 4.8 1.0 - - - -
167A LEU* 3.9 1.6 - - - -
169A ALA* 3.1 18.2 - - + +
187A VAL* 3.8 19.7 - - + -
194A ILE* 3.4 19.5 - - + -
196A ALA 3.0 7.1 + - - +
197A ILE* 3.2 12.2 - - + -
198A TYR* 2.9 24.3 + - - +
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Residues in contact with ILE 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 ALA* 1.3 79.6 - - - +
139A ILE* 1.3 72.6 + - - +
140A GLU* 3.9 20.9 - - + +
152A ARG* 4.0 12.1 - - + +
155A ALA* 3.9 11.4 - - + -
156A THR* 3.2 39.0 - - - +
159A PHE* 4.0 11.7 - - + -
167A LEU* 3.9 19.1 - - + -
169A ALA* 2.9 7.7 + - - +
170A SER* 3.3 14.2 - - - +
171A GLN 2.9 25.8 + - - -
198A TYR* 3.3 21.8 - - + +
200A ALA* 5.9 0.7 - - + -
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Residues in contact with ILE 139 (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 ALA* 5.3 2.0 - - + -
138A ILE* 1.3 78.4 - - - +
140A GLU* 1.3 61.0 + - - +
171A GLN* 3.3 2.9 - - + +
173A ALA* 3.4 30.7 - - + -
180A ALA* 4.3 3.4 - - + -
183A VAL* 3.4 29.6 - - + -
184A ALA* 4.3 12.8 - - + +
187A VAL* 4.5 10.8 - - + -
197A ILE* 3.5 24.2 - - + -
198A TYR 2.9 9.8 + - - +
199A CYS* 3.4 8.3 - - - -
200A ALA* 2.9 26.5 + - - +
204A MET* 3.8 8.5 - - + +
208A VAL* 4.1 19.5 - - + -
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Residues in contact with GLU 140 (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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138A ILE* 3.9 11.7 - - + -
139A ILE* 1.3 72.1 - - - +
141A GLY* 1.3 67.7 + - - +
143A ALA* 4.7 6.5 - - - +
148A GLY 5.4 3.4 - - - +
149A GLU* 4.5 9.5 - - - +
152A ARG* 3.1 29.8 - - + -
170A SER* 2.5 39.0 + - - +
171A GLN* 2.8 23.8 + - - +
172A PRO* 3.7 11.8 - - + +
173A ALA 2.8 20.4 + - - -
200A ALA* 4.1 5.4 - - - -
204A MET* 3.1 13.0 - - - +
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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