Contacts of the strand formed by residues 114 - 119 (chain A) in PDB entry 3RRA
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 MET 114 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111A ARG* 3.8 20.4 - - - -
113A LYS* 1.3 74.9 - - - +
115A ARG* 1.3 67.4 + - - +
116A THR 3.5 0.5 + - - -
297A LEU* 5.1 0.4 - - + -
300A ASP* 3.5 45.3 - - + +
301A PHE* 3.6 21.1 - - + -
306A ALA* 3.9 4.9 - - + +
307A THR 3.6 38.4 - - - +
308A LEU 3.6 17.3 - - - +
309A GLN* 4.0 6.3 - - + +
339A TYR* 3.3 4.2 - - - -
340A ILE* 2.8 47.8 + - + +
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Residues in contact with ARG 115 (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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113A LYS 4.4 0.2 + - - -
114A MET* 1.3 77.6 - - - +
116A THR* 1.3 65.2 + - - +
141A ASP* 4.7 8.3 + - - -
142A HIS* 3.8 33.7 + - + -
307A THR 3.5 14.3 + - - +
308A LEU* 3.5 31.7 - - + -
309A GLN* 2.8 26.3 + - - +
338A GLY 3.7 6.5 - - - +
339A TYR* 3.0 47.4 + - + +
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Residues in contact with THR 116 (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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114A MET 3.9 9.6 - - - +
115A ARG* 1.3 84.2 - - - +
117A TYR* 1.3 61.1 + - - +
140A PHE* 3.4 16.9 - - - -
142A HIS* 4.1 8.1 - - - +
293A LEU* 6.3 0.2 - - + -
309A GLN* 3.2 22.4 - - + +
311A GLN* 3.9 17.3 - - + -
335A LEU* 3.4 27.9 - - + +
338A GLY* 2.8 30.4 + - - +
340A ILE* 4.0 16.6 - - + -
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Residues in contact with TYR 117 (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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116A THR* 1.3 75.4 - - - +
118A SER* 1.3 60.9 + - - +
140A PHE* 4.8 0.2 - - - -
142A HIS* 3.4 32.3 - - + +
143A PHE 4.0 6.3 - - - +
144A LYS* 3.7 40.6 - - + +
206A LEU* 6.5 0.4 - - + -
207A PHE* 4.0 15.0 - + - -
256A GLN* 3.8 17.5 + - - +
283A ALA* 4.5 11.8 + - + +
285A HIS* 5.5 0.5 + - - -
308A LEU* 3.7 35.0 - - + -
309A GLN 3.0 14.2 + - - +
310A GLU* 3.2 45.3 + - + +
311A GLN* 3.1 27.5 + - - -
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Residues in contact with SER 118 (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* 1.3 73.7 - - - +
119A TRP* 1.3 63.6 + - - +
120A VAL* 3.7 1.2 + - - +
135A LEU* 3.9 23.0 - - - +
140A PHE* 3.3 22.9 - - - -
142A HIS 3.4 6.1 + - - -
143A PHE* 3.3 7.3 - - - +
144A LYS* 2.9 24.8 + - - -
310A GLU* 6.0 0.2 - - - -
311A GLN* 2.9 30.7 + - - -
313A MET 5.2 6.5 - - - -
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Residues in contact with TRP 119 (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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118A SER* 1.3 76.9 - - - +
120A VAL* 1.3 65.5 + - - +
121A GLY* 3.7 26.9 - - - -
135A LEU* 5.1 1.6 - - - +
144A LYS* 3.2 46.1 + - + +
145A LEU* 4.7 0.2 - - - -
146A ASN* 3.2 45.9 + - - +
310A GLU* 5.6 7.7 - - + +
311A GLN 3.7 9.9 + - - +
312A SER* 5.2 10.6 - - - +
313A MET 5.3 8.7 + - - +
385A ASN 5.4 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