Contacts of the strand formed by residues 260 - 266 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182A MET* 3.5 12.2 - - - +
187A GLU* 5.3 0.2 - - - -
249A VAL* 3.5 4.9 - - - +
250A ASN* 2.8 55.1 + - - +
258A ARG 4.2 8.0 + - - +
259A TRP* 1.3 81.0 - - - +
261A ILE* 1.3 63.6 + - - +
262A GLN* 4.4 5.6 - - - +
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Residues in contact with ILE 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A MET* 3.9 6.9 - - + +
183A ILE* 5.1 1.3 - - + -
187A GLU* 3.5 43.0 + - + +
247A LEU* 4.4 18.4 - - + -
248A LEU 3.4 5.6 - - - +
249A VAL* 3.8 27.1 - - + -
260A THR* 1.3 76.4 - - - +
262A GLN* 1.3 59.7 + - - +
263A LYS 3.5 24.0 - - - +
264A VAL* 3.8 20.0 - - + -
272A ASP 4.5 7.6 - - - +
273A SER* 5.5 2.9 - - - -
274A LEU* 4.7 4.3 - - + +
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Residues in contact with GLN 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A ALA* 3.7 13.9 - - - +
248A LEU* 2.8 39.7 + - + +
250A ASN* 3.2 41.0 + - + +
260A THR* 3.8 4.9 + - - +
261A ILE* 1.3 74.0 - - - +
263A LYS* 1.3 71.1 + - - +
272A ASP* 4.3 7.1 - - - +
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Residues in contact with LYS 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A TRP* 3.7 18.2 - - + -
247A LEU* 3.7 0.7 - - - -
248A LEU* 3.0 35.9 + - + +
261A ILE* 3.5 8.6 - - - +
262A GLN* 1.3 85.6 + - - +
264A VAL* 1.3 74.4 + - - +
270A TYR* 4.1 27.6 - - + -
271A TYR 4.1 6.3 - - - +
272A ASP* 3.3 26.2 + - - +
553B TRP* 4.1 30.9 + - + +
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Residues in contact with VAL 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A TRP* 4.7 0.9 - - - -
245A LEU* 3.8 26.2 - - + -
246A GLU 3.7 2.9 - - - -
247A LEU* 3.9 11.9 - - + -
261A ILE* 3.8 15.0 - - + -
263A LYS* 1.3 80.8 - - - +
265A PHE* 1.3 66.8 + - - +
266A TYR 4.7 0.2 - - - +
270A TYR* 3.4 10.0 - - - -
271A TYR* 2.9 43.1 + - + +
273A SER* 3.7 7.0 - - - +
274A LEU* 3.7 26.5 - - + +
277A LEU* 3.8 18.8 - - + -
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Residues in contact with PHE 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A TRP* 4.3 5.2 - - + -
244A GLY 3.3 8.9 - - - +
245A LEU* 3.5 2.8 - - - +
246A GLU* 2.9 41.8 + - + +
264A VAL* 1.3 74.5 - - - +
266A TYR* 1.3 61.5 + - - +
268A GLY* 3.5 35.9 - - - -
269A ARG 3.2 17.5 - - - -
270A TYR* 3.4 48.2 - + + -
375A ASN 4.0 8.1 - - - -
376A SER* 3.6 21.8 - - - -
377A PRO* 3.6 24.5 - - + -
501A PHE* 3.9 14.6 - + - -
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Residues in contact with TYR 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A LEU* 4.0 26.6 - - + +
195A LEU* 5.5 0.7 - - + -
198A CYS* 3.2 32.3 - - - +
199A CYS* 4.5 0.7 - - - -
243A VAL* 4.0 13.7 - - + -
244A GLY 3.4 7.0 - - - -
245A LEU* 3.9 21.8 - - + -
265A PHE* 1.3 74.5 - - - +
267A GLN* 1.3 110.7 + - + +
268A GLY 3.0 3.4 + - - -
269A ARG* 2.8 23.9 + - - +
271A TYR* 4.0 10.5 + + + -
277A LEU* 3.8 33.4 - - + -
286A VAL* 4.4 15.5 - - + -
287A ASN 5.5 0.2 - - - -
288A VAL* 3.4 6.7 - - + +
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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