Contacts of the strand formed by residues 340 - 349 (chain A) in PDB entry 2WXH
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 LYS 340 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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339A MET* 1.3 81.3 - - - +
341A LEU* 1.3 59.8 + - - +
342A VAL 4.2 0.2 + - - -
362A GLU* 4.2 32.0 + - + +
363A VAL* 3.5 27.8 - - - +
364A ASN* 3.4 24.8 + - + +
365A VAL* 4.0 5.4 - - - -
396A ALA* 3.2 5.4 - - - -
397A VAL* 3.0 37.6 + - + +
398A VAL 5.1 9.2 - - - -
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Residues in contact with LEU 341 (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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332A LYS* 3.0 48.2 - - + +
340A LYS* 1.3 72.4 - - - +
342A VAL* 1.3 66.8 + - - +
361A SER 4.1 0.9 - - - +
362A GLU* 3.4 1.6 - - - -
363A VAL* 2.7 36.0 + - - +
364A ASN 4.1 12.1 - - - +
365A VAL* 3.9 14.8 - - + +
366A CYS 5.0 1.1 - - - +
369A PRO* 3.9 26.7 - - + -
371A TRP* 4.1 15.4 - - + -
394A LEU* 3.8 14.8 - - + -
395A TYR 3.5 4.3 - - - +
396A ALA* 4.9 0.2 - - + -
418A ILE* 3.6 18.6 - - + -
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Residues in contact with VAL 342 (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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341A LEU* 1.3 82.3 - - - +
343A VAL* 1.3 72.5 + - - +
344A GLN 4.0 0.2 + - - -
359A SER* 4.5 6.3 - - - -
360A SER* 3.8 25.4 - - - +
361A SER 4.8 0.4 - - - -
362A GLU* 3.6 30.3 - - + +
371A TRP* 4.9 1.1 - - - -
393A ALA 3.7 1.2 - - - +
394A LEU* 3.6 3.5 - - - +
395A TYR* 3.0 60.7 + - + +
397A VAL* 4.3 15.3 - - + -
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Residues in contact with VAL 343 (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 LEU* 4.0 13.5 - - + -
342A VAL* 1.3 79.2 - - - +
344A GLN* 1.3 64.6 + - - +
345A ALA* 3.9 2.3 + - + +
359A SER* 3.5 1.2 - - - -
360A SER* 2.7 45.3 + - - +
371A TRP* 3.7 18.8 - - + -
375A LEU* 5.5 3.1 - - + +
392A PHE* 3.9 30.1 - - + -
393A ALA 3.4 6.3 - - - +
394A LEU* 3.7 28.5 - - + -
471A LEU* 4.0 16.8 - - + -
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Residues in contact with GLN 344 (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 VAL 4.0 1.2 - - - -
343A VAL* 1.3 74.5 - - - +
345A ALA* 1.3 61.8 + - - +
357A THR* 3.3 30.6 + - - +
359A SER* 3.5 18.4 + - - +
392A PHE* 3.4 3.1 - - - -
393A ALA 2.8 33.8 + - - +
395A TYR* 3.6 26.3 + - + +
452A LEU* 3.9 20.4 - - - +
453A LEU* 3.4 29.5 - - + +
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Residues in contact with ALA 345 (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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343A VAL* 3.9 1.3 + - + +
344A GLN* 1.3 74.7 - - - +
346A GLY* 1.3 57.2 - - - +
357A THR* 3.3 16.3 - - - -
358A VAL 3.0 26.4 + - - +
375A LEU* 4.4 11.4 - - + -
377A PHE* 4.1 21.2 - - + -
390A LEU* 4.6 1.1 - - + -
391A CYS 3.2 6.5 - - - +
392A PHE* 3.8 28.5 - - + -
453A LEU* 4.4 4.7 - - - -
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Residues in contact with GLY 346 (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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345A ALA* 1.3 76.2 - - - +
347A LEU* 1.3 61.3 + - - -
348A PHE* 3.7 5.1 - - - -
353A MET* 6.1 0.2 - - - -
355A CYS 5.8 0.2 - - - -
356A LYS 5.1 0.4 - - - -
357A THR* 4.1 12.3 - - - -
377A PHE* 4.3 5.6 - - - -
390A LEU* 3.9 1.1 - - - +
391A CYS* 2.8 39.8 + - - +
453A LEU* 3.9 15.4 - - - +
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Residues in contact with LEU 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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323A PHE* 3.8 13.5 - - + -
346A GLY* 1.3 73.0 - - - -
348A PHE* 1.3 61.8 + - - +
353A MET* 3.6 6.9 - - - +
354A LEU* 3.0 37.4 + - + -
355A CYS* 4.4 10.6 + - - +
356A LYS 5.5 0.2 + - - -
377A PHE* 3.8 29.3 - - + -
379A ILE* 3.8 28.9 - - + -
384A LEU* 4.1 9.6 - - + -
388A ALA* 5.5 0.9 - - + -
389A ARG 3.4 4.0 - - - +
390A LEU* 3.6 35.0 - - + -
425A LEU* 3.7 20.2 - - + -
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Residues in contact with PHE 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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346A GLY* 3.7 16.4 - - - -
347A LEU* 1.3 77.4 - - - +
349A HIS* 1.3 60.3 + - - +
350A GLY 3.8 10.1 - - - +
351A ASN 3.7 15.9 - - - -
352A GLU 3.4 15.3 - - - -
353A MET* 3.6 30.7 - - + -
354A LEU* 3.5 8.9 - - - +
388A ALA* 3.9 0.7 - - - -
389A ARG* 2.8 40.6 + - + +
391A CYS* 3.7 16.8 - - + -
453A LEU* 3.5 38.4 - - + -
455A PRO* 3.7 32.5 - - + -
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Residues in contact with HIS 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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348A PHE* 1.3 74.5 - - - +
350A GLY* 1.3 61.0 + - - +
351A ASN 3.6 0.2 + - - -
352A GLU* 2.8 27.1 + - + +
354A LEU* 3.6 22.9 - - + +
385A PRO* 3.5 27.8 - - + +
387A MET* 4.0 27.8 + - + -
388A ALA 4.5 0.2 + - - -
555A TRP* 3.5 48.1 - + + -
586A SER 5.6 0.3 - - - +
588A PRO* 3.2 36.2 - - + +
589A ASP* 4.2 10.3 + - + -
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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