Contacts of the strand formed by residues 172 - 176 (chain B) in PDB entry 4RN1
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 ILE 172 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B ILE* 3.4 37.5 - - + +
165B LEU* 3.6 19.1 - - + -
166B ARG* 3.7 25.1 - - + +
169B PHE* 4.2 15.3 - - + +
171B ARG* 1.3 78.5 - - - +
173B LEU* 1.3 65.1 + - - +
174B TYR 4.8 0.7 - - - +
194B LYS 3.0 5.9 + - - -
195B VAL* 3.3 12.1 - - + +
196B MET 2.9 26.2 + - - +
255B PHE* 3.5 4.8 - - - -
259B ALA* 3.5 16.6 - - + +
261B VAL* 4.1 24.7 - - + -
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Residues in contact with LEU 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B ILE* 1.3 74.6 - - - +
174B TYR* 1.3 60.0 + - - +
175B VAL* 3.9 17.5 - - + -
196B MET* 3.4 22.2 - - + +
198B VAL* 3.9 15.0 - - + -
248B LEU* 4.7 2.2 - - + -
251B VAL* 3.6 33.2 - - + -
255B PHE* 4.6 2.2 - - + -
257B PRO* 3.6 25.4 - - + +
259B ALA 2.9 11.4 + - - +
260B VAL* 3.3 8.2 - - + +
261B VAL 2.8 27.0 + - - +
294B TRP* 3.7 35.4 - - + -
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Residues in contact with TYR 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B HIS* 3.5 16.8 - - - +
158B ALA* 4.0 19.0 - - + +
162B ILE* 3.9 22.2 - - + -
172B ILE 3.9 1.2 + - - -
173B LEU* 1.3 71.8 - - - +
175B VAL* 1.3 57.7 + - - +
176B ASP* 2.7 44.7 + - + -
182B GLY 5.1 2.2 - - - -
185B VAL* 3.5 31.3 - - + +
195B VAL* 4.9 2.0 - - + -
196B MET 2.8 15.2 + - - +
197B THR* 4.1 17.7 - - + -
198B VAL* 2.7 36.4 + - - +
199B SER* 6.0 0.4 - - - -
261B VAL* 3.4 30.3 - - + +
263B GLN* 3.6 18.5 - - + +
301B LEU* 5.2 0.2 - - + -
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Residues in contact with VAL 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B LEU* 3.9 23.6 - - + -
174B TYR* 1.3 78.5 - - - +
176B ASP* 1.3 61.3 + - - +
177B LEU* 3.7 20.4 - - + -
198B VAL* 3.4 11.0 - - + +
200B LEU* 5.6 0.4 - - + -
244B CYS* 5.5 0.2 - - - -
248B LEU* 3.9 28.7 - - + -
260B VAL* 4.6 6.5 - - + -
261B VAL 2.9 10.4 + - - +
262B LEU* 3.5 23.3 - - + +
263B GLN* 2.8 28.1 + - - +
291B ILE* 4.3 14.8 - - + -
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Residues in contact with ASP 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B HIS* 2.3 29.0 + - - -
174B TYR* 2.7 30.1 + - + -
175B VAL* 1.3 72.0 - - - +
177B LEU* 1.3 61.1 + - - +
178B ASP* 3.1 20.4 + - - +
182B GLY* 3.3 10.9 - - - +
198B VAL 2.7 14.1 + - - +
199B SER* 3.5 8.5 - - - +
200B LEU 3.0 19.2 + - - -
263B GLN* 3.5 6.4 - - - +
402B K 2.8 35.2 - - - -
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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