Contacts of the strand formed by residues 260 - 267 (chain A) in PDB entry 4ZPK
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 ARG 260 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259A SER* 1.3 81.8 + - - +
261A ARG* 1.3 67.7 + - - +
309A THR* 5.3 0.2 - - - -
310A GLY* 3.2 13.5 + - - +
311A TYR* 3.5 26.9 - - + +
312A ILE* 4.5 0.2 - - - -
93B LYS 2.7 27.9 + - - -
94B ALA* 3.0 21.6 + - - +
95B LEU 3.1 13.7 + - - -
96B GLU* 3.4 38.9 + - - +
117B LYS* 3.6 27.4 - - - +
118B PHE* 5.4 1.4 - - - -
236B ASP 5.2 1.0 - - - +
237B ILE* 4.1 12.9 - - + +
238B PRO* 3.8 15.6 - - - +
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Residues in contact with ARG 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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223A GLU 4.4 3.8 + - - -
224A GLN* 3.3 50.1 + - - +
225A LEU* 4.8 1.8 - - - +
226A SER* 2.6 35.6 + - - +
227A THR* 4.5 5.1 - - - +
259A SER 4.6 14.3 - - - +
260A ARG* 1.3 82.2 - - - +
262A SER* 1.3 62.3 + - - +
263A PHE* 4.6 9.7 - - + -
309A THR* 5.0 0.2 - - - +
310A GLY* 2.9 36.8 + - - +
311A TYR* 4.2 0.6 - - - +
312A ILE* 3.4 30.1 - - + +
337A LEU* 4.3 9.0 - - + -
96B GLU* 5.1 0.6 - - - +
237B ILE* 5.4 1.1 - - - -
238B PRO* 4.0 26.9 - - + +
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Residues in contact with SER 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 GLN* 3.9 8.3 + - - +
261A ARG* 1.3 78.2 - - - +
263A PHE* 1.3 67.9 + - - +
308A CYS 2.8 20.6 + - - -
309A THR* 3.6 14.9 + - - +
96B GLU* 4.4 14.4 - - - -
237B ILE* 4.4 22.9 - - - +
238B PRO* 5.7 0.4 - - - +
342B TYR* 4.7 6.4 + - - -
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Residues in contact with PHE 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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177A PHE* 6.4 1.8 - + - -
209A LEU* 5.8 2.7 - - + -
220A LYS* 3.9 15.9 - - + +
221A LEU* 4.2 25.4 - - + -
224A GLN* 3.3 55.6 - - + +
225A LEU* 5.8 3.1 - - + -
261A ARG* 4.6 8.1 - - + -
262A SER* 1.3 81.8 + - - +
264A ILE* 1.3 75.0 + - + +
265A CYS* 4.8 7.6 - - + -
307A HIS* 3.8 3.3 + - - +
308A CYS* 2.8 52.9 + - + +
337A LEU* 5.6 7.4 - - + -
342B TYR* 4.8 10.5 - - + -
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Residues in contact with ILE 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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217A ASP* 5.7 0.2 - - - -
220A LYS* 3.6 28.9 + - - +
263A PHE* 1.3 85.2 - - - +
265A CYS* 1.3 64.9 + - - +
305A VAL* 3.6 26.9 - - + -
306A VAL 3.2 29.4 - - - +
307A HIS* 3.6 23.8 - - + +
306B GLN* 6.2 0.4 - - + -
320B GLU* 6.0 4.3 - - + +
342B TYR* 4.1 24.0 - - + -
343B VAL 4.8 0.2 - - - +
344B LEU* 4.0 35.0 - - + -
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Residues in contact with CYS 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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213A VAL* 4.4 14.1 - - + -
217A ASP* 4.2 13.2 - - + +
220A LYS* 6.0 0.9 - - + -
221A LEU* 5.8 2.9 - - + -
263A PHE* 4.8 11.4 - - + -
264A ILE* 1.3 80.0 - - - +
266A ARG* 1.3 65.6 + - - +
267A MET* 3.5 38.6 - - - -
305A VAL* 3.8 3.5 - - - +
306A VAL* 2.8 41.2 + - - +
308A CYS* 4.2 9.6 - - - -
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Residues in contact with ARG 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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213A VAL* 3.2 8.1 - - - +
214A HIS* 2.9 69.9 + - + -
217A ASP* 3.3 18.0 + - - +
265A CYS* 1.3 77.3 - - - +
267A MET* 1.3 63.3 + - - +
303A PHE* 4.6 9.6 - - + -
304A VAL 3.4 10.1 - - - +
305A VAL* 4.6 16.8 - - + -
318B TRP* 5.5 3.1 - - - -
344B LEU* 3.4 25.6 + - + +
345B SER* 3.4 24.2 - - - +
346B GLU* 3.0 26.9 + - - -
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Residues in contact with MET 267 (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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175A PHE* 4.6 6.3 - - - -
177A PHE* 4.6 11.2 - - + -
197A LEU* 3.8 16.8 - - + -
204A TRP* 3.8 22.4 - - + -
209A LEU* 4.0 26.7 - - + -
212A GLN 3.7 11.9 - - - +
213A VAL* 4.6 2.2 - - + +
265A CYS* 3.5 25.8 - - - -
266A ARG* 1.3 79.9 - - - +
268A ARG* 1.3 65.1 + - - +
303A PHE* 3.3 10.2 - - - -
304A VAL* 2.9 32.5 + - + +
306A VAL* 4.0 26.2 - - + -
308A CYS* 4.3 14.8 - - - -
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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