Contacts of the strand formed by residues 358 - 365 (chain A) in PDB entry 3WSZ
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 GLN 358 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A TYR* 3.5 0.2 + - - -
353A ASP* 4.4 1.7 - - - +
355A SER* 2.9 28.7 + - - +
356A GLU 3.2 4.9 + - - +
357A ASP* 1.3 100.6 - - - +
359A VAL* 1.3 62.4 + - - +
360A PHE* 4.8 7.1 - - + -
374A ILE* 3.7 20.5 - - + +
375A SER 2.4 30.8 - - - +
376A GLU* 2.6 21.4 + - - +
446A LYS* 4.0 40.1 + - + +
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Residues in contact with VAL 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A TYR* 3.4 43.3 - - + -
308A PHE* 3.8 23.1 - - + -
351A ILE* 4.1 6.3 - - + -
353A ASP 3.8 11.0 - - - +
354A ALA* 5.0 2.0 - - - -
355A SER 4.4 0.2 - - - +
358A GLN* 1.3 77.9 - - - +
360A PHE* 1.3 66.8 + - - +
361A VAL* 3.8 21.1 - - + -
373A TYR 3.1 12.8 - - - +
374A ILE* 3.2 14.2 - - - +
375A SER* 3.4 21.7 + - - +
382A PHE* 3.8 7.0 - - + -
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Residues in contact with PHE 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A ILE* 3.6 2.1 - - - +
352A ALA* 2.7 42.8 + - + -
353A ASP* 3.1 20.6 + - - +
358A GLN* 4.8 7.9 - - + -
359A VAL* 1.3 78.3 - - - +
361A VAL* 1.3 59.4 + - - +
372A LEU* 3.5 35.7 - - + -
373A TYR 3.5 2.5 - - - -
374A ILE* 3.8 25.1 - - + -
414A PHE* 3.6 18.4 - + + -
424A TYR* 3.9 28.5 - + - -
446A LYS* 3.1 46.4 - - + -
447A GLY* 3.7 4.0 - - - -
450A TRP* 4.6 2.7 - + - -
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Residues in contact with VAL 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A PHE* 5.6 0.7 - - + -
326A LEU* 4.2 10.5 - - + -
340A PHE* 5.0 2.5 - - + -
349A TYR* 4.0 20.4 - - + -
350A TYR 3.3 14.8 - - - +
351A ILE* 3.8 13.0 - - + -
359A VAL* 3.8 19.5 - - + -
360A PHE* 1.3 79.3 - - - +
362A CYS* 1.3 73.8 + - - +
363A VAL* 3.7 6.1 + - + +
371A ASN 3.4 2.3 - - - +
372A LEU* 3.5 4.7 - - - +
373A TYR* 3.0 33.1 + - + +
382A PHE* 3.8 25.4 - - + -
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Residues in contact with CYS 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A GLU 3.8 0.5 - - - +
349A TYR* 3.8 3.5 - - - -
350A TYR* 2.8 40.8 + - + +
352A ALA* 4.8 7.5 - - - +
361A VAL* 1.3 78.6 - - - +
363A VAL* 1.3 60.1 + - - +
364A SER 4.1 0.7 - - - -
370A THR* 4.2 8.1 - - + -
371A ASN 3.2 7.9 - - - +
372A LEU* 4.5 12.5 - - - +
389A VAL* 4.6 16.8 - - - -
391A TYR* 3.9 23.9 - - + -
412A ALA* 4.3 22.4 - - - -
414A PHE* 5.7 3.1 - - - -
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Residues in contact with VAL 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A PHE* 4.0 7.4 - - + -
346A ILE* 3.6 21.8 - - + -
348A GLU 3.7 2.7 - - - -
349A TYR* 3.6 24.7 - - + -
361A VAL* 4.3 4.0 - - + +
362A CYS* 1.3 76.9 - - - +
364A SER* 1.3 61.0 + - - +
365A HIS* 3.6 32.2 + - + +
369A ARG 3.7 1.6 - - - +
370A THR* 3.2 4.0 - - - -
371A ASN* 2.7 36.9 + - + +
373A TYR* 3.5 35.9 - - + -
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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
----------------------------------------------------------
346A ILE* 4.4 0.2 - - - -
347A ASN* 3.1 26.2 + - - +
348A GLU* 2.9 36.0 + - - +
362A CYS 4.1 0.4 - - - -
363A VAL* 1.3 72.7 - - - +
365A HIS* 1.3 65.2 + - - +
368A ASN 5.6 0.7 - - - -
369A ARG 3.4 5.4 - - - -
370A THR* 3.8 20.8 - - - +
391A TYR* 4.1 16.7 - - - -
393A SER* 5.1 1.2 + - - -
397A ALA* 4.6 9.0 + - - +
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Residues in contact with HIS 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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342A THR* 4.0 13.4 - - + +
344A HIS* 3.4 27.8 + + + +
345A PRO 2.2 29.5 + - - +
346A ILE* 3.1 30.4 - - + -
347A ASN* 4.2 8.9 + - - +
363A VAL* 3.6 13.1 - - + +
364A SER* 1.3 77.2 + - - +
366A SER* 1.3 64.5 + - - +
367A ASN* 3.1 23.8 - - - +
368A ASN* 2.9 22.2 + - - +
369A ARG* 2.8 14.7 + - - -
371A ASN* 3.4 30.1 + - - -
373A TYR* 4.5 0.2 + - - -
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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