Contacts of the strand formed by residues 346 - 355 (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 ILE 346 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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340A PHE* 4.2 23.1 - - + -
342A THR* 4.4 9.0 - - + +
344A HIS 4.3 3.4 - - - +
345A PRO* 1.3 77.0 - - - +
347A ASN* 1.3 65.1 + - - +
348A GLU 4.1 9.2 - - - +
349A TYR* 3.3 42.2 - - + +
363A VAL* 3.6 27.8 - - + -
365A HIS* 3.1 21.3 - - + -
366A SER 5.4 0.2 - - - -
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Residues in contact with ASN 347 (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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298A ARG* 3.3 21.0 + - - -
345A PRO 4.2 0.6 + - - -
346A ILE* 1.3 75.3 - - - +
348A GLU* 1.3 64.9 + - - +
349A TYR* 6.3 0.2 - - - -
364A SER* 3.1 16.5 + - - +
365A HIS 4.2 16.6 + - - -
366A SER* 4.3 7.2 - - - +
368A ASN* 5.6 3.0 + - - -
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Residues in contact with GLU 348 (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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298A ARG* 3.5 25.3 + - - +
346A ILE* 3.9 2.9 - - - +
347A ASN* 1.3 82.8 - - + +
349A TYR* 1.3 74.0 + - - +
362A CYS 3.8 0.7 - - - +
363A VAL* 3.7 6.1 - - - -
364A SER* 2.9 42.7 + - - +
391A TYR* 3.0 27.1 - - + +
393A SER* 3.0 26.1 + - - +
394A PRO* 4.9 2.1 - - - +
395A GLY* 4.7 6.8 + - - -
410A PRO* 5.7 3.8 - - - -
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Residues in contact with TYR 349 (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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298A ARG* 5.0 2.8 - - - +
299A ASP* 5.5 2.6 - - - +
310A THR* 3.9 28.5 + - + +
326A LEU* 3.3 51.3 + - + -
340A PHE* 3.1 35.2 - + - -
346A ILE* 3.3 28.1 - - + +
347A ASN 6.3 0.2 - - - -
348A GLU* 1.3 91.9 + - - +
350A TYR* 1.3 63.8 + - - +
351A ILE* 5.7 1.8 - - + -
361A VAL* 4.0 4.5 - - + -
362A CYS 3.8 0.4 - - - -
363A VAL* 3.6 29.2 - - + -
391A TYR* 4.3 0.9 + - - -
410A PRO* 5.9 1.4 - - - +
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Residues in contact with TYR 350 (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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301A GLN* 6.1 2.5 - - - -
349A TYR* 1.3 78.6 - - - +
351A ILE* 1.3 84.4 + - - +
352A ALA* 3.4 14.4 + - + -
361A VAL* 3.3 5.6 - - - +
362A CYS* 2.8 45.2 + - + +
391A TYR* 3.5 32.5 - + + +
409A GLU* 5.8 2.7 - - - -
410A PRO* 3.5 32.6 + - + -
411A PHE* 3.6 19.2 - - - +
412A ALA* 4.2 18.2 + - + -
414A PHE* 6.3 0.4 - - + -
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Residues in contact with ILE 351 (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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301A GLN* 3.6 27.4 + - - +
303A ARG* 3.6 25.2 + - - +
308A PHE* 3.9 49.8 - - + -
326A LEU* 4.5 10.1 - - + -
349A TYR* 5.7 1.1 - - + -
350A TYR* 1.3 89.0 - - - +
352A ALA* 1.3 64.4 + - - +
353A ASP 4.4 7.9 - - - +
354A ALA* 4.5 0.4 - - + -
359A VAL* 4.1 10.8 - - + -
360A PHE 3.8 7.6 - - - +
361A VAL* 3.8 23.8 - - + -
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Residues in contact with ALA 352 (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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303A ARG* 4.2 5.1 + - - -
350A TYR* 3.4 21.5 + - + +
351A ILE* 1.3 73.6 - - - +
353A ASP* 1.3 61.3 + - - +
360A PHE* 2.7 22.8 + - + +
361A VAL 4.7 0.4 - - - +
362A CYS* 4.8 8.7 - - - +
372A LEU* 4.8 4.0 - - + -
412A ALA* 6.0 0.2 - - + -
414A PHE* 3.4 37.8 - - + +
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Residues in contact with ASP 353 (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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303A ARG* 3.7 7.8 + - - +
351A ILE* 3.5 2.4 - - - -
352A ALA* 1.3 83.1 - - - +
354A ALA* 1.3 85.9 + - - +
355A SER* 4.2 1.8 + - - -
358A GLN 4.4 1.3 - - - +
359A VAL* 3.8 6.8 - - - +
360A PHE* 3.1 30.0 + - + +
414A PHE* 4.2 5.8 - - + -
416A ARG* 3.4 25.8 + - + -
424A TYR* 2.3 50.9 + - + +
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Residues in contact with ALA 354 (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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303A ARG* 3.4 49.6 + - + +
304A ASP* 3.9 15.0 - - - +
306A TYR* 4.8 5.8 - - + -
308A PHE* 4.4 14.8 - - + -
351A ILE* 4.5 1.6 - - + -
353A ASP* 1.3 82.7 + - - +
355A SER* 1.3 61.5 + - - +
358A GLN 4.7 1.3 - - - -
359A VAL* 5.0 2.2 - - + -
416A ARG* 5.2 0.9 + - - -
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Residues in contact with SER 355 (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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304A ASP* 5.0 5.6 - - - -
306A TYR* 3.2 13.3 - - - -
353A ASP* 4.2 3.2 + - - -
354A ALA* 1.3 74.1 - - - +
356A GLU* 1.3 76.1 + - - +
358A GLN* 2.9 24.3 + - - +
416A ARG* 4.1 20.3 + - - -
421A GLN* 6.1 0.3 - - - -
424A TYR* 5.6 2.0 - - - -
446A LYS* 4.2 16.1 + - - -
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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