Contacts of the strand formed by residues 260 - 266 (chain B) in PDB entry 2C10
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 THR 260 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182B MET* 3.5 12.3 - - - +
187B GLU* 5.6 0.4 - - - -
249B VAL* 3.6 5.0 - - - +
250B ASN* 3.0 45.4 + - - +
258B ARG 3.6 11.3 + - - +
259B TRP* 1.3 81.7 - - - +
261B ILE* 1.3 66.1 + - - +
262B GLN* 4.5 3.8 - - - +
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Residues in contact with ILE 261 (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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182B MET* 3.7 15.9 - - + -
183B ILE* 4.9 2.5 - - + -
187B GLU* 3.3 40.3 + - + +
247B LEU* 4.3 17.7 - - + -
248B LEU 3.3 6.7 - - - +
249B VAL* 3.8 24.0 - - + -
260B THR* 1.3 78.0 - - - +
262B GLN* 1.3 59.9 + - - +
263B LYS 3.3 26.4 + - - +
264B VAL* 3.9 16.6 - - + -
272B ASP 4.5 8.1 - - - +
273B SER* 6.0 2.2 - - - -
274B LEU* 5.0 3.6 - - + +
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Residues in contact with GLN 262 (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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224B ALA* 3.7 14.9 - - - +
248B LEU* 2.9 35.3 + - + +
250B ASN* 3.2 43.7 - - + +
260B THR* 3.9 5.1 - - - +
261B ILE* 1.3 73.2 - - - +
263B LYS* 1.3 70.4 + - - +
272B ASP* 4.4 6.5 - - - +
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Residues in contact with LYS 263 (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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553A TRP* 4.3 24.9 + - + +
226B TRP* 3.8 23.3 - - + -
247B LEU* 3.8 0.7 - - - -
248B LEU* 3.0 36.6 + - + -
261B ILE* 3.3 10.2 + - - +
262B GLN* 1.3 85.8 - - - +
264B VAL* 1.3 66.7 + - - +
270B TYR* 4.2 30.2 - - + +
271B TYR 3.8 13.9 - - - +
272B ASP* 3.3 25.9 + - - +
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Residues in contact with VAL 264 (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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226B TRP* 4.6 2.9 - - - -
245B LEU* 3.8 26.5 - - + -
246B GLU 3.7 3.6 - - - -
247B LEU* 3.9 17.7 - - + -
261B ILE* 3.9 10.5 - - + -
263B LYS* 1.3 80.9 - - - +
265B PHE* 1.3 63.2 + - - +
270B TYR* 3.4 8.1 - - - +
271B TYR* 2.8 45.3 + - + +
273B SER* 3.8 26.9 - - - +
274B LEU* 4.0 6.7 - - + +
277B LEU* 4.0 17.5 - - + -
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Residues in contact with PHE 265 (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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226B TRP* 4.3 4.7 - - + -
244B GLY* 3.5 7.1 - - - +
245B LEU* 3.4 5.7 - - - +
246B GLU* 3.0 45.8 + - + +
264B VAL* 1.3 76.1 - - - +
266B TYR* 1.3 61.3 + - - +
267B GLN* 4.7 1.6 - - - -
268B GLY* 3.3 46.7 - - - -
269B ARG 3.2 12.1 - - - -
270B TYR* 3.9 24.9 - + + -
375B ASN 4.1 4.7 - - - -
376B SER* 3.3 22.0 - - - -
377B PRO* 3.5 39.5 - - + -
499B PHE* 6.4 0.4 - + - -
501B PHE* 3.9 15.7 - + - -
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Residues in contact with TYR 266 (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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194B LEU* 3.9 27.2 - - + +
195B LEU* 5.7 1.3 - - + -
198B CYS* 3.2 32.2 - - - +
199B CYS* 4.6 1.3 - - - -
243B VAL 4.0 12.1 - - - -
244B GLY 3.2 10.8 - - - -
245B LEU* 3.7 22.2 - - + -
265B PHE* 1.3 74.9 - - - +
267B GLN* 1.3 107.2 + - + +
268B GLY 3.2 1.8 - - - -
269B ARG* 2.8 26.7 + - - +
271B TYR* 4.0 9.1 + + + -
277B LEU* 3.9 33.0 - - + -
286B VAL* 4.2 17.7 - - + -
288B VAL* 3.6 8.1 - - + +
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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