Contacts of the strand formed by residues 142 - 146 (chain A) in PDB entry 3RR1
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 HIS 142 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A ARG* 3.6 36.3 + - - -
116A THR 4.0 9.5 - - - +
117A TYR* 3.4 32.1 - - + +
118A SER* 3.6 3.1 + - - -
140A PHE* 4.4 3.7 - - - +
141A ASP* 1.3 108.3 + - - +
143A PHE* 1.3 71.6 + - - +
179A GLU* 3.4 24.8 - - + +
206A LEU* 3.7 24.3 - - + +
308A LEU* 3.6 23.8 - - + +
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Residues in contact with PHE 143 (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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117A TYR* 4.1 9.2 - - - +
118A SER* 3.5 7.6 - - - +
120A VAL* 3.6 18.8 - - + -
132A MET* 3.6 45.1 - - + -
135A LEU* 3.7 29.4 - - + -
136A GLN* 4.8 0.4 - - - -
140A PHE* 3.9 27.4 - - + -
141A ASP* 3.9 9.2 - - - -
142A HIS* 1.3 78.0 - - - +
144A LYS* 1.3 61.9 + - - +
145A LEU* 4.2 11.7 - - + -
178A VAL* 3.9 24.9 - - + -
179A GLU 2.9 17.3 + - - +
180A PHE* 3.2 10.0 - - + -
181A GLY* 2.8 24.2 + - - -
206A LEU* 6.0 0.9 - - - +
207A PHE* 5.2 1.4 - - - -
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Residues in contact with LYS 144 (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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117A TYR* 3.6 30.1 + - + +
118A SER 3.0 7.5 + - - -
119A TRP* 3.2 24.8 - - + -
120A VAL 2.9 25.8 + - - -
143A PHE* 1.3 74.6 - - - +
145A LEU* 1.3 73.5 + - - +
181A GLY 3.6 9.0 - - - +
183A ASP* 3.5 26.3 + - + -
207A PHE* 4.5 5.4 - - + -
209A GLU* 3.4 31.0 + - - +
256A GLN* 5.0 1.0 - - - +
285A HIS* 4.5 9.7 + - - -
310A GLU* 3.6 30.4 + - + +
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Residues in contact with LEU 145 (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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119A TRP* 4.6 0.9 - - - -
120A VAL* 4.1 17.9 - - + +
128A VAL* 3.9 19.5 - - + -
132A MET* 3.9 12.1 - - - -
143A PHE* 4.2 9.0 - - + -
144A LYS* 1.3 84.0 - - - +
146A ASN* 1.3 70.9 + - - +
166A ARG* 4.5 7.0 - - - +
167A VAL* 5.9 0.2 - - + -
170A ILE* 3.9 33.9 - - + -
180A PHE* 3.7 36.1 - - + -
181A GLY 2.9 6.8 + - - +
182A LEU* 3.5 10.8 - - + -
183A ASP* 2.8 26.9 + - - +
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Residues in contact with ASN 146 (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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119A TRP* 3.3 39.3 + - - +
120A VAL 4.7 1.8 + - - -
121A GLY* 5.7 1.0 - - - -
145A LEU* 1.3 76.8 - - - +
147A GLY* 1.3 60.8 + - - +
148A CYS* 4.1 15.4 + - - +
166A ARG* 2.8 33.1 + - - +
182A LEU* 4.5 0.3 - - - +
183A ASP* 3.5 9.4 - - - +
185A HIS* 3.2 31.2 + - - +
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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