Contacts of the strand formed by residues 255 - 261 (chain A) in PDB entry 2QCU
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 255 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A ARG* 3.7 34.0 - - + +
96A ARG* 4.8 3.1 - - - +
247A ILE* 3.8 27.6 - - + -
248A LEU 3.2 10.8 - - - +
249A GLN* 4.4 13.9 - - + -
253A LYS 4.8 1.1 - - - +
254A ARG* 1.3 93.6 + - - +
256A VAL* 1.3 67.7 + - - +
257A PHE* 3.4 39.2 - - + -
270A THR 4.6 2.8 + - - +
801A BOG 4.0 21.8 - - - +
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Residues in contact with VAL 256 (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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247A ILE* 4.6 0.4 - - - -
248A LEU* 2.7 43.5 + - + +
250A ASN* 4.8 2.9 - - + +
254A ARG* 4.1 2.5 - - - +
255A ILE* 1.3 80.4 - - - +
257A PHE* 1.3 71.3 + - - +
268A ILE* 3.9 8.5 - - + -
269A GLY 3.6 10.8 - - - +
270A THR 3.8 17.0 - - - +
291A TYR* 3.9 22.7 - - + +
292A LEU* 3.8 14.1 - - + -
295A VAL* 3.7 34.3 - - + -
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Residues in contact with PHE 257 (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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46A SER* 4.6 14.8 - - - -
48A LEU* 3.7 32.5 - - + -
50A HIS* 4.7 16.8 - + - -
87A PHE* 4.2 15.5 - + - -
141A TYR* 4.7 2.7 - - - -
246A TYR 3.3 5.8 - - - -
247A ILE* 3.7 33.9 - - + -
255A ILE* 3.4 26.0 - - + -
256A VAL* 1.3 72.8 - - - +
258A VAL* 1.3 62.7 + - - +
259A ILE* 3.7 18.6 - - + -
267A ILE 3.5 0.6 - - - +
268A ILE* 3.2 10.6 - - - +
269A GLY 2.7 42.4 + - - +
270A THR* 5.2 2.0 - - + -
600A FAD 5.9 0.2 - - - -
804A PO4 5.7 4.0 - - - -
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Residues in contact with VAL 258 (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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239A VAL* 3.9 28.0 - - + -
240A HIS* 4.9 5.2 + - - +
244A GLN 4.5 0.9 - - - +
245A ALA* 3.3 4.3 - - - -
246A TYR* 2.9 39.1 + - + +
248A LEU* 3.7 29.6 - - + -
257A PHE* 1.3 78.0 - - - +
259A ILE* 1.3 61.4 + - - +
260A PRO* 4.0 1.3 - - - +
266A SER* 4.3 7.0 - - - +
267A ILE 3.4 3.4 - - - -
268A ILE* 4.2 20.2 - - + -
296A TYR* 4.1 12.3 - - + -
300A PHE* 4.1 15.0 - - + -
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Residues in contact with ILE 259 (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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46A SER* 3.6 28.0 - - - +
48A LEU* 4.0 15.3 - - + -
85A MET* 4.1 9.2 - - - -
87A PHE* 5.1 0.2 - - + -
145A TRP* 3.8 25.4 - - + +
233A HIS* 5.9 0.4 - - + -
245A ALA* 4.2 7.9 - - + -
257A PHE* 3.7 28.0 - - + -
258A VAL* 1.3 77.6 - - - +
260A PRO* 1.3 81.2 - - + +
261A TRP* 4.1 0.7 - - - +
266A SER* 3.3 4.0 - - - -
267A ILE* 2.9 52.7 + - + +
269A GLY 6.2 0.2 - - - +
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Residues in contact with PRO 260 (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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85A MET* 4.2 15.6 - - + +
145A TRP* 4.9 2.3 + - - -
238A ARG* 6.1 0.9 - - + -
240A HIS* 5.5 3.8 - - + -
242A GLN 4.2 9.9 - - - +
243A LYS* 3.5 28.7 - - - +
244A GLN 3.7 18.6 - - - +
245A ALA* 3.8 10.1 - - + +
258A VAL 4.0 1.3 - - - +
259A ILE* 1.3 100.6 - - + +
261A TRP* 1.3 59.3 + - - +
262A MET 4.3 0.2 - - - -
263A ASP* 5.4 2.7 - - - +
265A PHE 3.7 7.0 - - - +
266A SER* 4.5 3.4 - - - +
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Residues in contact with TRP 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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47A LYS* 4.9 5.5 - - - +
145A TRP* 3.7 34.8 - + - -
235A VAL* 3.8 36.1 - - + -
259A ILE 4.1 1.3 - - - +
260A PRO* 1.3 74.7 - - - +
262A MET* 1.3 113.7 + - + +
263A ASP* 3.2 2.3 - - - +
265A PHE* 2.8 42.9 + - + +
267A ILE* 3.5 36.0 - - + +
311A TRP* 3.7 23.3 - + - -
472A LYS* 3.6 28.6 - - + +
475A MET* 3.8 20.0 - - + -
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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