Contacts of the strand formed by residues 140 - 144 (chain F) in PDB entry 2RHB
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 140 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120F THR* 3.7 5.9 - - - +
121F VAL* 3.2 17.3 - - - -
123F PHE* 4.6 6.3 - - - -
134F PHE* 3.6 12.4 - - - -
137F ALA* 5.2 0.4 - - - -
139F ASN* 1.3 76.2 - - - +
141F VAL* 1.3 66.6 + - - +
180F LYS* 3.9 1.4 - - - +
181F LYS* 3.0 34.5 + - - +
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Residues in contact with VAL 141 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72F LEU* 5.6 0.7 - - + -
75F LEU* 3.9 33.4 - - + -
77F VAL* 3.9 22.0 - - + -
120F THR* 3.8 16.1 - - + +
121F VAL 2.7 10.6 + - - +
122F LEU* 3.4 9.7 - - + +
123F PHE* 2.7 33.1 + - - +
134F PHE* 3.9 3.3 - - - -
140F GLY* 1.3 78.2 - - - +
142F LEU* 1.3 63.8 + - - +
178F TYR* 4.2 10.3 - - + -
179F PHE 3.4 9.0 - - - +
180F LYS* 3.8 19.3 - - + -
189F LEU* 6.5 0.2 - - + -
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Residues in contact with LEU 142 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123F PHE* 3.4 29.6 - - + +
124F ASP 4.1 2.0 - - - -
125F GLY* 4.0 9.0 - - - +
131F VAL* 4.4 20.6 - - + -
134F PHE* 3.6 41.2 - - + -
141F VAL* 1.3 75.7 - - - +
143F ILE* 1.3 77.5 + - - +
144F THR* 3.9 13.5 - - + -
148F VAL* 4.6 6.3 - - + -
151F LEU* 5.6 0.4 - - + -
177F ASN 3.3 4.2 - - - +
178F TYR* 3.5 3.1 - - - -
179F PHE* 2.9 52.8 + - + +
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Residues in contact with ILE 143 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66F VAL* 5.8 0.9 - - + -
67F PRO* 3.9 26.7 - - + -
72F LEU* 5.9 0.2 - - + -
122F LEU* 4.0 15.5 - - + -
123F PHE 3.0 14.0 + - - +
124F ASP* 3.5 25.3 - - - +
125F GLY* 2.7 33.4 + - - -
126F ARG* 3.6 14.6 - - - +
141F VAL* 5.1 0.4 - - + -
142F LEU* 1.3 76.0 - - - +
144F THR* 1.3 57.0 + - - +
176F PHE* 4.0 18.8 - - + -
177F ASN 3.2 2.7 - - - +
178F TYR* 3.5 40.4 - - + +
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Residues in contact with THR 144 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124F ASP* 5.7 0.2 - - - -
125F GLY* 3.8 19.3 - - - -
131F VAL* 4.9 2.9 - - + -
142F LEU* 3.9 11.7 - - + -
143F ILE* 1.3 78.4 - - - +
145F GLU* 1.3 62.6 + - - +
146F GLY 3.5 12.9 + - - -
147F SER 4.8 1.1 - - - +
148F VAL* 3.7 26.2 - - + +
175F GLN 4.6 0.2 - - - +
176F PHE* 3.6 11.8 - - - -
177F ASN* 3.0 35.1 + - - +
179F PHE* 3.1 24.1 - - - -
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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