Contacts of the strand formed by residues 266 - 271 (chain B) in PDB entry 3RC0
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 CYS 266 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B VAL* 3.7 22.2 - - + -
92B VAL 3.3 14.6 - - - +
93B PRO* 4.1 2.0 - - + -
94B ARG* 3.7 4.3 - - - +
263B SER* 2.9 35.5 + - - +
264B ALA 3.7 0.6 - - - -
265B ASN* 1.3 85.8 - - + +
267B LEU* 1.3 66.6 + - - +
268B ARG* 3.6 42.0 - - - -
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Residues in contact with LEU 267 (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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90B PHE 3.9 0.3 - - - +
91B VAL* 3.4 3.6 - - - +
92B VAL* 2.8 45.7 + - + +
94B ARG* 3.9 26.0 - - + +
97B LEU* 4.3 14.8 - - + -
244B VAL* 4.0 26.0 - - + -
260B LEU* 3.6 25.6 - - + -
261B GLU 3.3 6.3 - - - +
262B TYR* 3.4 41.7 - - + -
266B CYS* 1.3 82.4 - - - +
268B ARG* 1.3 62.3 + - - +
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Residues in contact with ARG 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B LEU* 3.6 29.3 - - + +
90B PHE 3.4 4.0 - - - -
91B VAL* 3.8 21.4 - - + +
259B ASN 3.7 0.7 - - - +
260B LEU* 3.3 5.6 - - - -
261B GLU* 2.6 55.3 + - + +
263B SER* 4.0 20.8 + - - +
266B CYS* 3.6 25.3 - - - -
267B LEU* 1.3 77.6 - - - +
269B MET* 1.3 59.9 + - - +
270B VAL* 3.8 7.2 + - + +
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Residues in contact with MET 269 (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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88B LEU* 3.6 1.9 - - - +
89B LEU* 2.8 43.0 + - + +
90B PHE* 2.9 47.0 + - + -
247B ALA* 3.8 23.1 - - + +
250B LEU* 3.9 25.1 - - + -
258B ALA* 4.3 1.8 - - + -
259B ASN* 3.5 30.5 - - - -
260B LEU* 3.6 25.2 - - + +
267B LEU 4.3 0.2 + - - -
268B ARG* 1.3 73.7 - - - +
270B VAL* 1.3 55.9 + - - +
283B ASN* 4.0 15.3 - - - +
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Residues in contact with VAL 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B GLY* 3.3 27.1 - - - +
87B GLU 3.4 5.6 - - - +
88B LEU* 3.9 18.4 - - + -
89B LEU* 3.8 4.0 - - - -
258B ALA* 3.2 1.4 - - - -
259B ASN* 2.9 36.9 + - - +
261B GLU* 3.7 33.7 - - - +
268B ARG* 4.1 8.5 - - + +
269B MET* 1.3 80.0 - - - +
271B ALA* 1.3 70.7 + - - +
272B THR* 3.5 4.0 + - + +
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Residues in contact with ALA 271 (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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83B VAL* 3.8 17.0 - - + -
84B GLN 3.8 18.6 - - - +
86B GLY* 2.7 30.4 + - - -
87B GLU 2.9 16.8 + - - +
89B LEU* 3.6 13.1 - - + +
257B ASN 3.3 10.5 - - - +
270B VAL* 1.3 75.1 - - - +
272B THR* 1.3 57.8 + - - +
273B GLN 3.6 7.9 - - - +
275B ILE* 4.2 4.7 - - + -
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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