Contacts of the strand formed by residues 152 - 157 (chain G) in PDB entry 2R9R
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 VAL 152 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110G ARG* 3.7 4.7 - - - +
115G ILE* 3.5 18.8 - - + +
117G THR* 3.7 24.9 - - + -
140G LEU* 4.1 7.9 - - + -
144G LEU* 3.7 17.0 - - + +
147G LEU* 3.9 15.0 - - + -
149G LEU* 5.1 0.2 - - + -
151G TYR* 1.3 80.6 - - - +
153G ASP* 1.3 58.4 + - - +
154G VAL 3.7 18.2 - - - +
155G VAL* 4.0 10.1 - - + -
181G MET 3.1 10.8 + - - +
182G ALA* 3.1 35.5 - - + -
183G MET 3.2 2.6 + - - -
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Residues in contact with ASP 153 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47G LEU* 4.6 12.4 - - + +
110G ARG* 2.9 31.3 + - - -
113G LEU 3.8 3.3 - - - +
114G VAL* 3.1 25.3 - - + +
115G ILE 2.7 38.5 + - - +
151G TYR* 4.3 3.3 - - - -
152G VAL* 1.3 73.0 - - - +
154G VAL* 1.3 60.8 + - + +
183G MET* 3.2 24.0 - - + +
184G TYR* 2.8 29.3 + - - -
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Residues in contact with VAL 154 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42G LEU* 4.2 11.7 - - + -
47G LEU* 3.7 26.5 - - + -
114G VAL* 5.0 0.2 - - + -
115G ILE 3.4 2.6 + - - -
116G THR* 3.2 43.7 - - + -
117G THR 3.2 5.0 + - - +
152G VAL* 3.7 6.5 - - - +
153G ASP* 1.3 84.7 - - + +
155G VAL* 1.3 63.3 + - - +
156G PHE* 3.6 24.2 + - + -
184G TYR* 3.3 16.2 - - + +
185G TRP 3.9 3.8 - - - +
186G GLY* 3.9 15.7 - - - +
211G ILE* 4.6 6.3 - - + -
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Residues in contact with VAL 155 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117G THR* 3.5 5.8 - - + +
119G ILE* 3.9 28.3 - - + -
136G ILE* 5.8 2.0 - - + -
140G LEU* 4.2 16.2 - - + -
152G VAL* 4.0 13.2 - - + +
154G VAL* 1.3 73.3 - - - +
156G PHE* 1.3 58.6 + - - +
173G MET* 4.1 18.9 - - + +
176G VAL* 4.2 10.3 - - + -
177G ILE* 5.4 0.7 - - + -
182G ALA* 3.7 19.5 - - + -
184G TYR 3.0 8.3 + - - +
185G TRP* 3.1 19.5 - - + +
186G GLY 2.8 27.1 + - - +
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Residues in contact with PHE 156 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116G THR* 3.8 20.2 - - + -
117G THR 2.9 16.0 + - - -
118G LYS* 3.7 19.3 - - + -
119G ILE* 2.8 33.6 + - - +
154G VAL* 3.6 22.2 - - + -
155G VAL* 1.3 76.4 - - - +
157G ALA* 1.3 65.0 + - - +
173G MET* 4.1 4.5 - - - -
186G GLY* 3.1 22.4 - - - -
187G THR 3.3 26.0 - - - -
188G SER* 4.6 0.7 - - - -
212G CYS* 3.9 27.1 - - - -
214G GLN* 3.3 39.0 - - + -
241G MET* 4.1 9.0 - - + -
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Residues in contact with ALA 157 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119G ILE 3.7 6.1 - - - -
131G LEU* 3.6 35.7 - - + -
156G PHE* 1.3 70.5 - - - +
158G ASN* 1.3 61.8 + - - +
159G ARG 3.1 1.4 + - - -
169G THR* 5.3 0.4 - - + -
173G MET* 3.8 14.7 - - + +
185G TRP* 4.9 1.8 - - + -
186G GLY 3.0 10.9 + - - +
188G SER* 3.0 25.8 + - - +
190G TRP* 3.7 20.2 - - + +
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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