Contacts of the helix formed by residues 378 - 394 (chain A) in PDB entry 2W3C
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 PRO 378 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A ALA* 6.1 5.4 - - + -
376A ARG 3.8 3.5 - - - +
377A GLN* 1.4 99.8 - - + +
379A PHE* 1.3 65.2 + - - +
380A VAL* 4.3 17.5 - - + -
381A LEU* 2.9 23.7 + - + +
382A ARG* 3.2 10.0 + - - +
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Residues in contact with PHE 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A GLN 3.7 1.6 + - - -
378A PRO* 1.3 71.9 - - - +
380A VAL* 1.3 65.5 + - + +
382A ARG* 3.3 13.0 + - + +
383A CYS* 3.2 46.6 + - - -
435A LEU* 4.1 13.7 - - + -
601A PHE* 3.7 32.5 - + + -
602A PRO 5.0 1.3 - - - -
603A SER* 3.5 21.5 - - - -
604A PRO* 3.7 41.1 - - + -
607A MET* 3.5 28.7 - - + -
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Residues in contact with VAL 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A THR* 3.5 31.4 - - + +
332A GLU* 5.2 4.9 - - - +
378A PRO* 3.2 14.1 - - + +
379A PHE* 1.3 83.8 - - + +
381A LEU* 1.3 62.8 + - + +
383A CYS* 3.7 7.7 + - + +
384A ALA* 3.4 14.6 + - - +
1631A PEG 6.5 1.1 - - - -
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Residues in contact with LEU 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A LEU* 4.5 14.4 - - + -
331A THR* 3.9 22.2 - - + +
334A ILE* 3.5 30.5 - - + -
371A SER* 3.7 30.1 - - - +
377A GLN* 3.8 22.9 - - + +
378A PRO* 2.9 23.1 + - + +
380A VAL* 1.3 79.1 - - + +
382A ARG* 1.3 66.2 + - - +
383A CYS 3.2 0.2 - - - -
384A ALA* 3.2 4.2 + - - +
385A VAL* 3.0 24.2 + - + +
1630A PEG 4.5 4.9 - - - +
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Residues in contact with ARG 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A SER 3.5 9.2 - - - +
372A MET* 3.0 33.8 + - + +
373A VAL 4.1 1.8 - - - -
374A ASN 3.4 24.2 + - - -
375A GLU* 3.8 10.7 + - - +
377A GLN* 3.9 13.5 + - + +
378A PRO 3.2 15.2 + - - +
379A PHE* 3.3 13.0 + - + +
381A LEU* 1.3 76.2 - - - +
383A CYS* 1.3 57.7 + - - +
385A VAL* 3.1 12.7 - - - +
386A LEU* 3.0 29.2 + - - +
433A ASP* 3.1 18.6 + - - -
435A LEU* 3.1 42.5 - - - +
436A SER* 3.4 22.0 + - - +
439A CYS* 5.4 8.0 - - - -
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Residues in contact with CYS 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A PHE* 3.2 53.2 + - - +
380A VAL* 3.7 8.5 - - - +
381A LEU 3.2 0.2 - - - -
382A ARG* 1.3 79.2 - - - +
384A ALA* 1.3 55.6 + - - +
386A LEU* 3.4 9.9 + - - +
387A TYR* 3.0 29.5 + - - +
439A CYS* 6.2 0.7 - - - -
599A PRO* 3.8 23.4 - - + +
601A PHE* 4.1 19.7 - - - -
607A MET* 5.4 3.4 - - - -
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Residues in contact with ALA 384 (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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331A THR* 3.7 34.1 - - + +
334A ILE* 3.1 23.3 - - + +
335A ASN* 3.3 26.4 - - - +
338A SER* 4.0 0.5 + - - -
380A VAL 3.4 2.7 + - - +
381A LEU* 3.2 9.3 + - - +
383A CYS* 1.3 77.8 - - - +
385A VAL* 1.3 58.1 + - - +
387A TYR* 3.9 2.5 - - - +
388A CYS 3.1 19.4 + - - -
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Residues in contact with VAL 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A ILE* 4.3 14.4 - - + -
368A LEU* 3.5 51.8 - - + +
371A SER* 4.2 6.3 - - - +
372A MET* 3.6 21.9 - - + +
381A LEU* 3.0 30.1 + - + +
382A ARG* 3.1 17.7 - - - +
384A ALA* 1.3 74.8 - - - +
386A LEU* 1.3 65.2 + - - +
387A TYR 3.3 0.4 - - - -
388A CYS* 3.5 2.1 + - - +
389A PHE* 3.1 23.2 + - - +
1630A PEG 4.9 4.9 - - - -
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Residues in contact with LEU 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A MET* 4.0 26.0 - - + -
382A ARG 3.0 15.3 + - - +
383A CYS* 3.4 11.0 - - - +
385A VAL* 1.3 77.1 - - - +
387A TYR* 1.3 55.6 + - - +
389A PHE* 3.0 7.9 + - + +
390A GLN* 2.9 65.6 + - + +
438A TRP* 3.8 29.4 - - + -
439A CYS* 4.4 12.8 - - - +
442A VAL* 3.8 15.5 - - + -
443A ALA* 4.5 8.1 - - + +
599A PRO* 4.4 14.8 - - + -
601A PHE* 5.5 0.9 - - + -
607A MET* 5.6 0.4 - - - -
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Residues in contact with TYR 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A ARG* 4.4 0.9 - - - -
293A PRO* 4.2 10.7 - - - +
335A ASN* 3.7 20.9 - - - -
338A SER* 3.7 21.3 - - - -
339A GLU* 3.1 34.3 + - + +
342A ARG* 4.7 1.8 - - - -
383A CYS 3.0 17.5 + - - +
384A ALA* 3.9 4.7 - - - +
386A LEU* 1.3 74.0 - - - +
388A CYS* 1.3 65.0 + - - +
390A GLN* 3.8 16.4 - - + -
391A CYS* 2.9 47.5 + - - +
597A PRO* 3.9 15.1 - - + +
598A GLN* 3.8 37.5 + - + +
599A PRO* 3.6 20.4 - - + -
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Residues in contact with CYS 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A LEU* 5.7 0.7 - - - -
334A ILE* 3.8 12.1 - - + -
337A VAL* 4.4 5.2 - - - -
338A SER* 3.2 30.3 + - - +
341A ILE* 4.3 3.4 - - - +
351A PHE* 3.6 36.6 - - - -
368A LEU* 3.7 19.3 - - + -
384A ALA 3.1 17.8 + - - +
385A VAL 3.8 0.7 - - - +
386A LEU 3.4 0.2 - - - -
387A TYR* 1.3 74.9 - - - +
389A PHE* 1.3 57.2 + - - +
391A CYS* 3.3 2.4 + - - +
392A PHE* 2.8 28.9 + - - +
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Residues in contact with PHE 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A ILE* 4.0 12.1 - - + -
368A LEU* 3.9 17.9 - - + +
369A LEU* 3.9 39.0 - - + -
372A MET* 5.3 0.7 - - - -
385A VAL 3.1 13.8 + - - +
386A LEU* 3.0 13.0 + - + +
388A CYS* 1.3 73.7 - - - +
390A GLN* 1.3 64.0 + - + +
392A PHE* 3.3 10.2 + + - +
393A LEU* 3.2 48.7 + - + +
403A ILE* 3.9 37.0 - - + -
425A LEU* 4.7 3.1 - - + -
443A ALA* 3.6 38.8 - - + -
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Residues in contact with GLN 390 (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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386A LEU* 2.9 49.6 + - + +
387A TYR* 3.8 25.5 - - + +
389A PHE* 1.3 70.0 - - + +
391A CYS* 1.3 61.6 + - - +
393A LEU* 3.2 5.1 + - - +
394A TYR* 2.8 31.8 + - - +
442A VAL* 4.5 1.8 - - - +
443A ALA* 5.7 0.2 - - - -
446A HIS* 3.4 44.0 + - + +
597A PRO 4.1 9.2 - - - +
599A PRO* 4.3 5.0 - - - +
610A ASP* 3.2 24.2 + - - +
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Residues in contact with CYS 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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338A SER* 3.1 40.8 - - - +
339A GLU 4.3 0.2 - - - -
341A ILE* 4.2 3.6 - - + -
342A ARG* 3.6 24.8 - - + -
348A GLN* 2.7 29.1 + - - -
387A TYR* 2.9 49.3 + - - +
388A CYS 3.4 4.7 - - - +
390A GLN* 1.3 77.3 - - - +
392A PHE* 1.3 51.6 + - - +
394A TYR* 3.3 14.0 + - - +
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Residues in contact with PHE 392 (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 ILE* 4.0 11.1 - - + +
348A GLN* 3.0 45.2 + - + +
349A ASP* 5.4 0.7 - - - -
351A PHE* 4.5 11.0 - + + -
352A ALA* 3.5 22.7 - - + -
365A ILE* 3.9 28.5 - - + -
368A LEU* 5.5 0.4 - - + -
388A CYS 2.8 17.9 + - - +
389A PHE* 3.3 15.9 - + - +
390A GLN 3.2 0.2 - - - -
391A CYS* 1.3 72.0 - - - +
393A LEU* 1.3 64.7 + - + +
396A ASN* 2.8 44.5 + - - -
399A GLY* 4.0 29.8 - - - -
402A GLU* 4.2 8.7 - - + -
403A ILE* 4.7 4.7 - - + -
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Residues in contact with LEU 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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389A PHE* 3.2 42.4 + - + +
390A GLN* 3.2 4.5 + - - +
392A PHE* 1.3 86.5 - - + +
394A TYR* 1.3 59.2 + - - +
395A LYS 3.1 1.2 + - - -
396A ASN* 2.8 27.9 + - - +
399A GLY 3.7 24.9 - - - +
400A GLN* 3.8 25.2 + - + +
403A ILE* 3.9 13.0 - - + -
443A ALA 3.8 0.2 - - - +
446A HIS* 3.6 41.7 - - + +
447A ALA* 3.7 6.7 - - + +
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Residues in contact with TYR 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A ARG* 3.7 56.7 + - + +
343A GLY* 3.4 17.3 - - - -
348A GLN* 3.0 21.5 + - - +
390A GLN 2.8 16.7 + - - +
391A CYS* 3.3 11.4 + - - +
393A LEU* 1.3 73.6 - - - +
395A LYS* 1.3 101.1 + - + +
446A HIS* 5.9 3.4 - + - -
449A GLN* 5.3 7.4 - - - -
612A GLU* 4.2 23.3 + - + -
615A LYS* 4.8 6.9 + - - -
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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