Contacts of the strand formed by residues 256 - 263 (chain A) in PDB entry 1ORZ
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 VAL 256 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226A TYR* 3.8 22.4 - - + +
253A LEU 4.7 2.9 - - - +
254A GLU 3.0 13.7 + - - +
255A PHE* 1.3 74.4 - - - +
257A GLN* 1.3 73.2 + - - +
258A PHE* 3.6 28.9 - - + -
369A VAL* 4.4 13.7 - - + -
370A HIS 5.7 0.2 - - - -
371A TYR 3.7 11.9 - - - +
372A ASN* 2.9 25.8 - - + +
373A MET* 3.9 0.7 - - - -
492A ARG* 4.6 3.6 + - - +
543A THR* 4.8 5.6 - - + +
556A ALA* 2.8 23.1 - - - +
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Residues in contact with GLN 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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256A VAL* 1.3 74.0 - - - +
258A PHE* 1.3 67.7 + - - +
259A HIS* 4.7 2.5 + - - +
303A ARG* 2.8 41.9 + - + -
304A ASP* 5.5 1.1 - - - +
370A HIS* 2.8 30.1 + - + +
371A TYR* 2.9 18.3 + - - +
373A MET* 3.3 19.1 - - + +
415A ASN* 3.2 3.1 + - - +
416A ARG* 2.9 67.4 + - - +
556A ALA* 4.4 5.4 - - + -
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Residues in contact with PHE 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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226A TYR* 4.2 14.8 - + - -
256A VAL* 3.6 25.1 - - + -
257A GLN* 1.3 78.5 - - - +
259A HIS* 1.3 62.8 + - - +
260A PRO* 3.2 8.8 - - - +
303A ARG 4.6 2.4 - - - +
304A ASP* 5.7 0.3 - - - -
307A SER* 4.0 24.6 - - - +
367A PRO* 4.4 2.5 - - + -
368A THR* 3.2 14.8 - - - +
369A VAL* 2.9 42.2 - - + -
485A GLN* 5.3 6.1 - - - -
488A VAL 4.1 16.6 - - - -
489A SER* 4.1 8.3 - - - -
490A VAL* 3.9 31.2 - - + -
492A ARG* 4.2 11.2 - - - -
556A ALA* 5.4 4.9 - - + +
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Residues in contact with HIS 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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143A TYR* 4.5 4.3 - - - -
257A GLN* 4.8 2.6 + - - -
258A PHE* 1.3 68.6 - - - +
260A PRO* 1.3 65.9 - - - +
261A SER* 3.0 45.3 + - - -
262A GLY 3.8 0.5 + - - -
269A LEU* 3.0 31.3 - - + +
270A ILE 3.3 10.2 + - - -
272A GLU* 4.0 13.3 + - + -
303A ARG* 2.9 39.3 + - - -
366A ILE 3.7 0.5 - - - +
367A PRO* 2.8 4.2 - - - +
368A THR* 2.6 39.9 + - + +
370A HIS* 3.5 35.0 + + + +
416A ARG* 5.9 0.8 + - - -
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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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258A PHE 3.2 8.3 - - - +
259A HIS* 1.3 88.8 - - + +
261A SER* 1.4 54.7 + - - -
275A ARG* 3.0 21.5 - - - +
303A ARG* 3.2 34.3 - - - +
306A VAL* 3.0 41.5 - - + +
307A SER* 3.9 8.3 - - - +
310A ILE* 3.4 9.6 - - + +
365A ILE* 3.0 14.9 - - - +
366A ILE 3.2 13.2 - - - -
367A PRO* 3.4 9.6 - - + -
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Residues in contact with SER 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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259A HIS* 3.0 23.3 + - - -
260A PRO* 1.4 73.4 - - - +
262A GLY* 1.3 68.0 + - - +
269A LEU* 4.7 0.2 - - - -
270A ILE* 2.8 40.7 + - - +
271A THR 4.5 4.7 + - - -
272A GLU* 4.7 0.7 - - - -
275A ARG* 2.8 27.7 + - - +
329A LEU* 4.2 10.0 - - - +
365A ILE* 2.8 14.7 - - - +
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Residues in contact with GLY 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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259A HIS* 3.8 5.3 + - - -
260A PRO 3.4 0.6 - - - -
261A SER* 1.3 78.0 - - - +
263A ILE* 1.4 59.9 + - - -
268A CYS 4.0 5.4 - - - -
269A LEU* 4.7 5.8 - - - -
365A ILE* 3.0 3.6 - - - -
366A ILE* 2.6 47.0 + - - -
368A THR* 3.5 22.9 - - - -
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Residues in contact with ILE 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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261A SER 4.6 4.0 - - - +
262A GLY* 1.4 74.0 - - - -
264A TYR* 1.3 72.4 + - - +
265A GLY 3.2 0.5 + - - -
266A SER* 2.8 24.9 - - - +
267A GLY* 2.8 29.9 + - - +
268A CYS* 2.9 27.4 + - + +
269A LEU 4.5 2.7 - - - +
270A ILE* 4.7 6.1 - - + -
324A LYS* 4.8 4.7 - - + +
349A THR* 3.9 40.4 - - + +
350A ALA* 4.9 5.2 - - - -
353A PHE* 4.6 2.9 - - + -
354A ALA* 4.6 17.5 - - + -
363A ILE* 4.6 11.9 - - + -
364A PRO* 3.6 11.9 - - + +
365A ILE* 4.6 1.3 - - + -
366A ILE* 4.0 2.9 - - - +
368A THR* 5.9 0.3 - - - -
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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