Contacts of the strand formed by residues 356 - 365 (chain A) in PDB entry 5OAQ
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 HIS 356 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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321A GLU* 3.3 43.8 + - + +
322A SER 3.4 15.0 - - - +
323A PRO* 4.6 5.4 - - + -
352A TYR* 3.8 2.8 - - - -
353A GLU* 2.5 73.6 + - + -
354A ASN* 3.1 21.0 + - + -
355A GLY* 1.3 77.5 - - - +
357A TYR* 1.3 72.2 + - - +
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Residues in contact with TYR 357 (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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321A GLU* 3.3 6.4 - - - +
322A SER 2.7 34.5 + - - +
323A PRO 3.5 19.3 - - - -
324A GLU 3.4 28.0 - - - +
325A ASN* 3.8 32.9 + - + +
350A ALA* 3.9 15.9 - - + -
351A ARG 3.3 4.9 - - - +
352A TYR* 3.7 48.1 - + + -
355A GLY 4.4 6.7 - - - -
356A HIS* 1.3 79.9 - - - +
358A SER* 1.3 60.3 - - - +
359A TYR* 4.0 3.9 - - + -
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Residues in contact with SER 358 (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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319A GLN* 4.5 12.3 - - - -
320A TYR 3.4 9.0 - - - -
321A GLU* 4.6 1.3 - - - +
349A TYR 4.0 1.0 - - - +
350A ALA* 3.5 4.7 - - - -
351A ARG* 2.8 55.6 + - - +
353A GLU* 3.9 32.5 + - - +
356A HIS* 5.1 0.2 - - - -
357A TYR* 1.3 73.6 - - - +
359A TYR* 1.3 64.7 + - - +
360A ARG* 6.3 0.4 - - - -
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Residues in contact with TYR 359 (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 LEU* 4.1 14.8 - - + -
319A GLN* 3.3 6.2 - - - +
320A TYR* 2.8 48.2 + - + +
322A SER* 3.9 22.0 - - - -
324A GLU 3.0 11.7 + - - -
326A MET* 2.7 55.6 + - + +
328A ILE* 3.7 34.3 - - + -
348A GLU* 4.0 8.3 - - + -
349A TYR 3.6 19.7 - - - -
350A ALA* 3.5 17.9 - - + +
357A TYR 4.0 9.9 - - - -
358A SER* 1.3 76.3 - - - +
360A ARG* 1.3 61.7 + - - +
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Residues in contact with ARG 360 (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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228A GLU* 2.9 29.8 + - - +
317A SER* 4.1 12.6 - - - -
318A SER 3.4 5.8 + - - +
319A GLN* 2.9 33.7 + - + +
348A GLU* 3.2 18.8 + - - +
349A TYR 5.3 1.0 + - - -
351A ARG* 6.1 2.5 - - - +
358A SER* 4.4 0.9 - - - -
359A TYR* 1.3 76.2 - - - +
361A ILE* 1.3 71.2 + - - +
362A HIS* 3.2 42.5 + - + +
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Residues in contact with ILE 361 (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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316A VAL 5.1 0.7 - - - +
317A SER* 3.2 8.9 - - - -
318A SER* 2.8 55.0 + - - +
320A TYR* 3.9 17.5 - - + +
328A ILE* 6.0 0.4 - - + -
330A CYS* 3.8 31.6 - - + -
346A GLU* 3.3 34.5 - - - +
348A GLU* 3.5 34.3 - - + +
360A ARG* 1.3 71.6 - - - +
362A HIS* 1.3 58.4 + - - +
363A ARG 3.8 0.2 + - - -
364A SER* 3.9 13.9 - - - -
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Residues in contact with HIS 362 (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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317A SER* 3.9 3.6 - - - -
360A ARG* 3.2 50.1 + - + +
361A ILE* 1.3 71.3 - - - +
363A ARG* 1.3 97.4 + - + +
364A SER* 3.2 3.8 + - - -
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Residues in contact with ARG 363 (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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232A PHE* 3.9 25.8 - - + -
234A GLU* 2.7 44.6 + - - -
244A LYS* 4.9 5.9 - - - +
313A PHE* 3.5 41.5 - - + +
316A VAL 3.5 3.7 + - - -
317A SER* 2.8 22.4 + - - +
362A HIS* 1.3 100.1 - - + +
364A SER* 1.3 66.1 + - - +
365A PRO* 3.3 6.8 - - - +
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Residues in contact with SER 364 (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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315A GLY* 3.3 2.6 - - - -
316A VAL* 2.8 41.0 + - - +
344A LYS* 3.0 28.5 + - - +
346A GLU* 2.5 29.7 + - - -
361A ILE* 3.9 11.4 - - - -
362A HIS 3.2 4.3 + - - -
363A ARG* 1.3 70.8 - - - +
365A PRO* 1.4 71.6 - - - +
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Residues in contact with PRO 365 (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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313A PHE* 4.0 19.1 - - + -
314A TYR 3.7 7.2 - - - +
344A LYS* 4.4 7.3 + - + +
363A ARG 3.3 6.7 - - - +
364A SER* 1.4 90.3 + - - +
366A LEU* 1.3 67.6 + - - +
367A CYS* 3.5 2.8 + - - -
502A MYR 4.4 4.3 - - - +
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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