Contacts of the strand formed by residues 271 - 275 (chain B) in PDB entry 3RIG
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 271 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245B CYS* 3.2 13.7 - - + +
247B VAL* 4.0 10.5 - - + -
261B ALA* 3.8 17.0 - - + +
264B VAL* 3.6 23.8 - - + -
265B ALA* 3.6 17.3 - - + +
269B VAL 3.4 12.9 + - - +
270B PRO* 1.3 78.6 - - - +
272B ALA* 1.3 62.0 + - - +
285B PHE* 3.3 37.2 - - + +
286B ARG* 3.1 13.0 + - - +
287B PHE* 3.0 24.7 + - - -
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Residues in contact with ALA 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B PHE* 3.6 37.7 - - + -
244B LEU* 5.8 0.4 - - + +
245B CYS 2.9 9.2 + - - +
246B LEU* 3.3 3.6 - - + -
247B VAL* 2.8 26.4 + - - -
271B VAL* 1.3 72.7 - - - +
273B GLU* 1.3 61.0 + - - +
274B PHE* 3.6 17.4 - - + -
287B PHE* 3.8 17.0 - - + -
289B PHE* 4.5 1.6 - - + -
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Residues in contact with GLU 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B VAL* 3.2 24.5 - - + +
250B THR* 4.9 1.3 - - - +
271B VAL 4.1 1.0 - - - -
272B ALA* 1.3 73.9 - - - +
274B PHE* 1.3 64.1 + - - +
275B ASN* 4.2 14.1 - - + +
277B GLU 4.7 1.6 - - - -
279B THR* 2.3 39.0 + - - +
282B THR* 1.9 33.6 + - - +
285B PHE* 4.0 16.8 - - + -
287B PHE 3.1 14.2 + - - +
288B HIS* 3.4 16.5 + - - +
289B PHE* 3.3 25.3 + - - -
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Residues in contact with PHE 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B MET* 4.4 1.1 - - + -
43B PHE* 4.7 3.4 - + - -
246B LEU* 3.7 27.1 - - + -
247B VAL 2.8 10.7 + - - +
248B VAL* 4.1 16.6 - - + -
249B GLY 3.0 24.9 + - - -
272B ALA* 3.6 20.4 - - + -
273B GLU* 1.3 75.4 - - - +
275B ASN* 1.3 62.5 + - - +
289B PHE* 3.8 32.1 - + + -
293B CYS* 3.9 20.2 - - - -
296B THR* 3.4 33.0 - - - +
297B LEU* 4.2 11.0 - - + -
300B ALA* 3.6 33.2 - - + -
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Residues in contact with ASN 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247B VAL 5.3 0.2 + - - -
249B GLY* 3.1 33.8 - - - +
250B THR 3.1 15.5 + - - +
251B SER* 4.2 8.2 + - - -
273B GLU* 4.2 10.0 - - + +
274B PHE* 1.3 74.4 + - - +
276B THR* 1.3 61.2 + - - +
277B GLU* 2.9 34.4 + - - +
279B THR* 3.4 22.3 - - - +
288B HIS* 4.4 6.2 + - + -
289B PHE 3.1 18.1 + - - +
290B GLN* 3.5 2.1 - - - -
291B GLY 3.4 14.2 + - - +
293B CYS* 4.8 3.1 - - - -
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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
------------------------------------------------------------
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