Contacts of the strand formed by residues 322 - 329 (chain A) in PDB entry 3OP3
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 322 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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291A ALA* 3.9 16.6 - - + -
292A LEU* 3.4 32.3 - - + -
313A LEU* 4.4 7.6 - - + -
318A PHE* 2.8 41.5 + - + +
319A GLN* 4.2 10.2 + - - +
320A GLY 5.0 1.1 - - - -
321A LEU* 1.4 83.7 - - + +
323A GLU* 1.3 61.1 + - - +
324A LYS 3.4 25.8 - - - +
325A PHE* 4.2 7.9 - - + -
369A LYS* 4.5 0.7 - - - -
370A ARG* 3.6 11.4 - - + +
372A ILE* 4.1 20.6 - - + -
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Residues in contact with GLU 323 (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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320A GLY 5.9 1.3 - - - +
322A ILE* 1.3 75.5 - - - +
324A LYS* 1.4 82.1 + - + +
325A PHE* 5.6 1.8 - - - -
364A PRO* 3.4 15.0 - - + +
365A LEU* 2.8 43.6 + - - +
366A ASP* 2.8 21.1 + - + +
369A LYS* 3.8 16.6 - - + +
370A ARG 2.8 13.7 + - - +
371A ILE* 5.2 0.4 - - + -
465A SO4 5.1 1.2 + - - -
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Residues in contact with LYS 324 (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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322A ILE* 3.4 8.6 - - - +
323A GLU* 1.4 97.0 + - + +
325A PHE* 1.3 62.1 + - - +
326A TYR* 3.7 19.7 - - + +
362A ILE* 3.8 22.3 - - + +
363A VAL 4.5 6.1 + - - -
370A ARG 3.4 3.2 + - - -
371A ILE* 3.4 23.0 - - + -
372A ILE 3.0 22.2 + - - -
465A SO4 3.4 38.1 - - - +
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Residues in contact with PHE 325 (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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310A VAL* 6.2 0.2 - - + -
313A LEU* 3.5 62.1 - - + -
314A LEU* 4.0 29.2 - - + -
322A ILE* 4.2 3.8 - - + -
323A GLU 5.6 1.3 - - - -
324A LYS* 1.3 79.0 - - - +
326A TYR* 1.3 70.9 + - - +
327A VAL* 4.4 17.7 - - + -
372A ILE* 3.3 26.9 - - + -
374A VAL* 5.9 0.4 - - + -
465A SO4 3.6 12.4 + - - -
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Residues in contact with TYR 326 (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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324A LYS* 3.7 22.2 - - + +
325A PHE* 1.3 77.9 - - - +
327A VAL* 1.3 59.4 + - - +
328A ILE* 3.8 17.2 + - + -
345A LEU* 4.0 11.0 - - + -
356A PHE* 3.9 26.5 - + - -
357A PHE* 3.8 22.2 - + + -
362A ILE* 3.8 22.9 - - + +
371A ILE* 4.2 18.8 - - + -
372A ILE* 3.0 17.8 + - - +
373A ILE* 3.5 6.2 - - + +
374A VAL* 2.8 34.0 + - - +
465A SO4 3.6 30.6 + - - -
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Residues in contact with VAL 327 (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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310A VAL* 4.5 18.6 - - + -
313A LEU* 6.0 0.7 - - + -
314A LEU* 5.4 3.1 - - + -
325A PHE* 4.4 22.6 - - + -
326A TYR* 1.3 74.1 - - - +
328A ILE* 1.3 64.7 + - - +
329A ASP 4.0 0.2 - - - -
341A ILE* 3.9 20.0 - - + -
342A GLN 5.6 0.7 - - - +
343A GLY 5.4 2.7 + - - -
344A ALA* 3.3 26.6 - - + +
345A LEU* 2.8 27.1 + - - +
374A VAL* 3.3 19.1 - - + +
376A HIS* 3.8 23.1 - - + -
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Residues in contact with ILE 328 (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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326A TYR* 3.9 5.2 - - + +
327A VAL* 1.3 80.0 - - - +
329A ASP* 1.4 61.5 + - - +
330A CYS* 3.5 3.8 + - - -
345A LEU* 3.5 27.4 - - + +
347A LEU* 3.7 38.4 - - + +
353A LEU* 4.1 2.9 - - + -
357A PHE* 3.6 27.1 - - + -
373A ILE* 3.8 24.9 - - + -
374A VAL 2.8 10.1 + - - +
375A PHE* 3.5 26.2 - - + -
376A HIS* 3.0 29.1 + - - +
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Residues in contact with ASP 329 (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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327A VAL 4.0 1.6 - - - -
328A ILE* 1.4 67.9 - - - +
330A CYS* 1.4 57.6 + - - +
331A ARG* 2.7 56.1 + - - +
336A TYR* 3.4 31.7 - - + -
340A HIS* 3.7 5.7 - - - +
344A ALA* 4.5 4.5 - - + -
345A LEU 2.8 14.5 + - - +
346A ASN* 3.1 16.6 + - - -
347A LEU 3.3 14.6 + - - +
376A HIS* 3.3 27.0 + - - +
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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