Contacts of the helix formed by residues 390 - 407 (chain A) in PDB entry 2WHR
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 ASP 390 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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387A HIS* 3.2 32.5 + - + +
388A PRO 3.5 0.4 - - - -
389A GLU* 1.3 76.1 - - - +
391A PRO* 1.3 68.9 - - - +
392A THR* 3.4 11.5 + - - -
393A HIS* 3.0 30.9 + - + +
394A LEU* 3.0 30.6 + - - +
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Residues in contact with PRO 391 (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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353A LEU* 3.7 29.1 - - + -
354A ILE 3.0 30.5 + - - +
355A SER* 5.9 0.7 - - - -
389A GLU 3.2 9.8 - - - +
390A ASP* 1.3 93.6 - - - +
392A THR* 1.3 57.9 + - - +
394A LEU* 4.4 0.2 - - + -
395A ARG* 3.0 29.1 + - - +
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Residues in contact with THR 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A LEU* 3.4 24.6 - - + +
390A ASP* 3.3 11.4 + - - -
391A PRO* 1.3 76.1 - - - +
393A HIS* 1.3 66.9 + - - +
395A ARG* 3.3 23.9 + - - +
396A ASP* 3.1 30.0 + - - +
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Residues in contact with HIS 393 (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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382A TYR 3.0 26.3 + - - -
383A THR 4.6 0.2 - - - -
384A ASP* 3.2 40.3 + - + +
387A HIS* 4.7 6.1 - - + +
388A PRO* 6.0 0.4 - - + -
390A ASP* 3.0 25.1 + - + +
392A THR* 1.3 78.6 - - - +
394A LEU* 1.3 66.3 + - + +
396A ASP* 3.2 7.4 + - - +
397A ALA* 2.7 40.0 + - + +
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Residues in contact with LEU 394 (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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354A ILE* 3.7 21.9 - - + +
355A SER 3.8 2.7 - - - -
356A ARG* 3.5 38.6 - - - +
359A PHE* 3.6 34.7 - - + -
383A THR* 5.2 2.0 - - - +
388A PRO 3.7 15.3 - - - +
389A GLU 3.7 20.4 - - - +
390A ASP 3.0 21.0 + - - +
391A PRO 3.9 3.8 - - - +
393A HIS* 1.3 86.0 - - + +
395A ARG* 1.3 57.7 + - - +
397A ALA* 3.6 4.0 - - - +
398A MET* 2.9 30.1 + - - +
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Residues in contact with ARG 395 (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 PHE* 3.6 17.5 - - + -
351A GLU* 2.8 37.0 + - - +
352A SER* 3.2 26.7 - - - +
353A LEU* 3.6 20.6 - - - +
354A ILE* 3.7 9.1 - - + +
391A PRO 3.0 17.6 + - - +
392A THR* 3.6 15.5 - - - +
393A HIS 3.2 0.2 - - - -
394A LEU* 1.3 77.1 - - - +
396A ASP* 1.3 100.0 + - - +
398A MET* 3.3 4.0 + - - +
399A SER* 3.2 20.6 + - - -
442A TRP* 3.4 42.0 + - + +
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Residues in contact with ASP 396 (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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392A THR* 3.1 23.0 + - - +
393A HIS* 3.9 7.4 - - - +
395A ARG* 1.3 108.5 + - - +
397A ALA* 1.3 60.5 + - - +
399A SER* 3.5 8.5 + - - -
400A ALA* 3.1 26.3 + - - +
442A TRP 4.6 4.7 - - - +
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Residues in contact with ALA 397 (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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359A PHE* 4.0 17.3 - - + -
382A TYR* 4.0 26.5 - - + +
393A HIS* 2.7 29.1 + - + +
394A LEU* 3.6 5.8 - - + +
396A ASP* 1.3 75.4 - - - +
398A MET* 1.3 59.3 + - - +
400A ALA* 3.2 7.2 + - - +
401A VAL* 2.8 34.0 + - - +
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Residues in contact with MET 398 (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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339A LEU* 4.0 11.0 - - + -
343A VAL* 4.4 4.0 - - + -
346A PHE* 3.6 28.3 - - + -
354A ILE* 4.4 1.1 - - + -
359A PHE* 3.8 21.9 - - + +
362A GLY* 3.5 43.3 - - - +
363A VAL* 3.7 11.4 - - + +
366A GLY* 4.9 1.1 - - - -
394A LEU 2.9 17.4 + - - +
395A ARG 3.6 5.6 - - - +
397A ALA* 1.3 76.6 - - - +
399A SER* 1.3 63.2 + - - +
401A VAL* 4.0 14.4 - - + -
402A VAL* 3.3 43.7 + - + +
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Residues in contact with SER 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A ASP* 4.7 10.7 + - - +
335A GLY* 3.5 10.4 + - - -
336A SER* 3.2 28.6 + - - -
339A LEU* 3.6 19.6 - - - +
395A ARG* 3.2 10.6 + - - -
396A ASP* 3.5 11.9 - - - -
398A MET* 1.3 79.5 - - - +
400A ALA* 1.3 58.1 + - - +
402A VAL* 3.3 2.3 + - - +
403A GLY* 2.8 24.9 + - - -
442A TRP* 5.2 3.4 - - - -
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Residues in contact with ALA 400 (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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382A TYR* 3.8 17.3 - - + -
396A ASP 3.1 16.8 + - - +
397A ALA* 3.2 7.2 + - - +
399A SER* 1.3 74.1 - - - +
401A VAL* 1.3 56.1 + - - +
403A GLY* 4.3 1.6 - - - +
404A ASP* 2.7 47.2 + - - +
525A ARG* 5.0 9.2 - - - +
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Residues in contact with VAL 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A PHE* 4.4 10.8 - - + -
363A VAL* 4.6 2.5 - - + -
366A GLY 5.4 0.7 - - - -
367A VAL* 4.0 26.9 - - + -
378A VAL* 4.0 16.2 - - + -
382A TYR* 3.5 41.0 - - + -
397A ALA 2.8 25.6 + - - +
398A MET* 3.7 21.3 - - + +
400A ALA* 1.3 71.1 - - - +
402A VAL* 1.3 60.2 + - + +
405A HIS* 3.0 34.2 + - + +
532A TRP* 4.0 4.5 - - + -
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Residues in contact with VAL 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A ILE* 3.7 15.7 - - + -
295A PHE* 4.1 13.8 - - + -
335A GLY* 3.8 21.3 - - - +
338A PHE* 4.2 8.5 - - + -
339A LEU* 3.6 17.7 - - + -
366A GLY* 4.4 10.8 - - - -
398A MET* 3.3 25.8 + - + +
399A SER 3.3 7.1 + - - +
400A ALA 3.2 0.6 - - - -
401A VAL* 1.3 78.2 - - + +
403A GLY* 1.3 62.5 + - - +
405A HIS* 4.7 0.9 - - - -
406A ASN* 2.8 47.2 + - - +
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Residues in contact with GLY 403 (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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295A PHE* 6.0 0.4 - - - -
334A GLU* 3.8 9.9 - - - -
335A GLY 3.6 20.9 - - - -
399A SER 2.8 16.0 + - - -
400A ALA* 3.6 3.1 - - - -
402A VAL* 1.3 75.1 - - - +
404A ASP* 1.3 59.4 + - - +
406A ASN* 5.3 0.4 - - - -
407A VAL* 3.0 27.0 + - - +
408A VAL* 3.1 14.6 + - - +
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Residues in contact with ASP 404 (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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382A TYR* 2.5 37.7 + - - +
400A ALA* 2.7 25.8 + - - +
401A VAL 4.1 0.2 - - - +
403A GLY* 1.3 72.0 - - - +
405A HIS* 1.3 65.0 + - - +
408A VAL* 4.0 12.4 - - - +
409A CYS* 3.0 40.8 + - - +
410A PRO* 3.4 0.7 - - - +
525A ARG* 3.2 37.1 + - - -
528A THR* 3.7 9.6 - - - +
532A TRP* 3.7 7.0 - - - +
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Residues in contact with HIS 405 (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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235A PRO* 3.4 30.3 - - + +
296A ARG* 3.1 25.4 + - - -
366A GLY 3.6 22.7 - - - +
367A VAL* 4.2 5.3 - - + +
369A GLN* 3.5 19.0 + - - -
401A VAL* 3.0 20.1 + - + +
402A VAL* 4.1 2.2 - - - +
404A ASP* 1.3 78.4 - - - +
406A ASN* 1.3 67.1 + - - +
409A CYS* 5.2 0.6 - - - +
410A PRO* 3.4 13.3 - - - +
532A TRP* 3.4 42.9 - + + -
536A LEU* 6.0 2.9 - - + -
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Residues in contact with ASN 406 (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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230A GLY* 5.9 0.9 - - - -
231A THR* 4.9 1.6 + - - -
235A PRO* 3.9 6.0 - - - +
236A TRP* 3.1 31.5 + - + +
295A PHE* 3.4 48.1 - - + +
296A ARG* 3.0 27.3 + - - +
366A GLY* 4.6 4.4 + - - -
402A VAL* 2.8 34.1 + - - +
405A HIS* 1.3 89.9 - - - +
407A VAL* 1.3 61.2 + - + +
410A PRO* 3.4 14.0 - - - +
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Residues in contact with VAL 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A SER* 3.5 41.1 - - - +
230A GLY* 4.1 2.5 - - - +
231A THR* 5.9 0.4 - - - -
236A TRP* 5.0 1.6 - - + +
295A PHE* 3.8 27.1 - - + -
330A VAL* 4.0 8.1 - - + -
334A GLU* 3.5 34.5 - - + +
403A GLY 3.0 9.8 + - - +
406A ASN* 1.3 83.8 - - + +
408A VAL* 1.3 60.3 + - - +
409A CYS 3.3 2.0 - - - -
410A PRO* 3.2 4.2 - - - +
411A VAL* 2.9 35.6 + - + +
447A HIS* 4.3 0.7 - - + -
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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
------------------------------------------------------------
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