Contacts of the helix formed by residues 431 - 450 (chain A) in PDB entry 2W3S
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 SER 431 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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425A LEU 4.2 0.7 - - - -
426A SER* 3.5 7.6 - - - -
427A ASP 5.0 0.4 - - - -
430A ALA* 1.3 72.4 - - - +
432A ALA* 1.3 64.1 + - - +
433A ALA* 3.6 9.1 + - - +
434A TYR* 2.9 16.5 + - - +
435A ARG* 2.8 19.9 + - - +
764B GLU* 2.7 31.2 + - - -
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Residues in contact with ALA 432 (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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424A PRO* 3.6 22.8 - - + +
425A LEU 3.3 21.8 + - - +
426A SER* 2.5 21.8 + - - +
431A SER* 1.3 69.6 - - - +
433A ALA* 1.3 65.1 + - - +
435A ARG* 3.0 4.6 + - - +
436A MET* 2.9 25.8 + - - +
572F GLN* 4.4 17.7 - - - +
574F GLN* 5.3 1.1 - - - +
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Residues in contact with ALA 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A SER* 3.2 9.1 + - - +
432A ALA* 1.3 80.3 - - - +
434A TYR* 1.3 52.1 + - + +
436A MET* 3.3 5.5 + - - +
437A ASN* 2.7 36.7 + - - +
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Residues in contact with TYR 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A LEU* 3.2 39.8 - - + +
354A SER 6.0 0.2 - - - -
363A ALA* 4.9 3.8 - - + -
429A ARG 5.4 1.3 - - - -
430A ALA* 3.5 29.6 - - + -
431A SER* 2.9 7.4 + - - +
433A ALA* 1.3 78.3 - - - +
435A ARG* 1.3 59.9 + - - +
437A ASN* 3.6 6.0 - - - +
438A ALA* 2.7 38.0 + - + +
637B THR 3.0 28.7 + - - -
763B PRO* 3.6 11.2 - - + +
764B GLU* 3.5 49.4 - - + +
767B LEU* 3.5 22.7 - - + -
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Residues in contact with ARG 435 (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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291A ILE* 4.9 4.4 - - - +
362A SER 4.4 3.4 + - - -
363A ALA* 2.9 29.5 + - + +
364A VAL* 3.3 38.2 - - + +
386A GLY* 3.1 26.3 + - - -
387A MET* 3.5 7.3 - - - +
424A PRO* 4.1 13.2 - - + -
425A LEU* 3.4 24.5 + - - +
427A ASP* 2.8 34.7 + - - -
429A ARG* 3.9 8.3 - - - +
430A ALA* 3.4 24.4 + - + +
431A SER 2.8 10.4 + - - +
432A ALA* 3.5 7.9 - - - +
434A TYR* 1.3 78.6 - - - +
436A MET* 1.3 63.6 + - - +
439A ALA* 3.1 20.8 + - - +
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Residues in contact with MET 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A MET* 3.8 14.8 - - + -
418A LEU* 3.3 32.1 - - + +
419A ALA* 3.7 29.2 - - + +
422A PHE 4.8 2.7 - - - +
424A PRO* 3.9 15.5 - - + +
432A ALA 2.9 11.7 + - - +
433A ALA* 3.3 10.3 - - - +
435A ARG* 1.3 74.5 - - - +
437A ASN* 1.3 56.1 + - - +
439A ALA* 2.8 37.5 + - + +
440A GLN* 3.1 33.8 + - + +
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Residues in contact with ASN 437 (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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433A ALA 2.7 20.3 + - - +
434A TYR* 3.6 10.5 - - - +
436A MET* 1.3 73.8 - - - +
438A ALA* 1.3 51.4 + - - +
440A GLN* 3.4 16.3 + - - +
441A ALA* 2.8 33.3 + - - +
636B LEU 4.2 4.2 - - - +
767B LEU* 3.2 29.4 - - - +
771B ARG* 4.0 29.7 + - - +
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Residues in contact with ALA 438 (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* 3.2 35.0 - - + -
364A VAL* 4.5 4.3 - - + -
434A TYR* 2.7 29.5 + - + +
435A ARG 4.1 2.2 - - - +
437A ASN* 1.3 72.8 + - - +
439A ALA* 1.3 60.5 + - - +
441A ALA* 3.4 10.3 - - - +
442A MET* 3.0 35.6 + - + +
636B LEU 5.2 0.4 - - - -
637B THR* 4.5 7.2 - - + +
767B LEU* 5.5 0.2 - - + -
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Residues in contact with ALA 439 (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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364A VAL* 4.2 4.0 - - + +
384A PHE* 3.4 45.1 - - + -
387A MET* 3.7 20.4 - - + -
418A LEU* 4.2 6.4 - - + +
422A PHE* 5.7 0.9 - - + -
435A ARG 3.1 15.0 + - - +
436A MET* 2.8 19.1 + - + +
438A ALA* 1.3 78.5 - - - +
440A GLN* 1.3 58.4 + - - +
442A MET* 3.5 9.5 + - - +
443A ALA* 4.0 4.0 + - - +
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Residues in contact with GLN 440 (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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415A LEU* 3.8 49.3 + - + +
416A PRO* 4.1 9.9 + - - +
418A LEU* 3.8 15.7 - - + -
419A ALA* 4.9 2.2 - - - +
436A MET* 3.1 41.7 + - + +
437A ASN* 3.6 16.2 + - - +
439A ALA* 1.3 71.3 - - - +
441A ALA* 1.3 66.6 + - - +
442A MET 3.1 2.0 - - - -
443A ALA* 3.0 19.6 + - - +
444A LEU* 3.5 6.2 + - - +
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Residues in contact with ALA 441 (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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437A ASN* 2.8 20.3 + - - +
438A ALA* 3.2 14.3 + - - +
440A GLN* 1.3 72.7 - - - +
442A MET* 1.3 55.7 + - - +
444A LEU* 3.5 3.2 + - - +
445A ARG* 3.0 22.2 + - - +
636B LEU* 3.3 59.3 - - + +
637B THR* 4.4 5.4 - - + -
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Residues in contact with MET 442 (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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351A TYR* 3.5 49.1 - - + +
352A LYS 4.8 0.2 - - - -
353A LEU* 3.9 20.4 - - + -
364A VAL* 3.6 33.7 - - + +
366A GLY* 3.4 26.9 - - - -
368A LEU* 4.2 9.8 - - + +
384A PHE* 4.1 4.5 - - + -
438A ALA* 3.0 15.1 + - + +
439A ALA 3.7 7.6 - - - +
440A GLN 3.1 0.6 - - - -
441A ALA* 1.3 77.3 - - - +
443A ALA* 1.3 52.3 + - - +
445A ARG* 3.1 16.0 - - - +
446A TYR* 2.8 33.6 + - - +
637B THR* 5.2 6.1 - - + -
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Residues in contact with ALA 443 (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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368A LEU* 4.2 17.4 - - + +
397A PHE* 4.0 11.9 - - + -
411A ILE* 3.7 25.3 - - + +
415A LEU* 3.9 9.6 - - + -
418A LEU* 5.5 1.1 - - + -
439A ALA 4.0 4.8 + - - +
440A GLN* 3.0 12.2 + - - +
442A MET* 1.3 73.9 - - - +
444A LEU* 1.3 65.2 - - - +
445A ARG 3.1 1.1 - - - -
446A TYR* 3.2 3.5 + - - +
447A VAL* 3.2 29.2 + - - +
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Residues in contact with LEU 444 (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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408A GLU* 3.5 21.0 - - - +
411A ILE* 4.8 4.5 - - + -
412A ALA* 4.3 21.8 - - + +
415A LEU* 4.1 28.9 - - + -
440A GLN 3.5 3.5 + - - +
441A ALA* 3.5 8.4 + - - +
442A MET 3.5 0.2 - - - -
443A ALA* 1.3 78.9 - - - +
445A ARG* 1.3 59.9 + - - +
447A VAL* 3.8 5.2 + - - +
448A ARG* 2.9 55.6 + - - +
636B LEU* 3.9 19.3 - - + -
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Residues in contact with ARG 445 (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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351A TYR* 3.2 60.4 - - + +
352A LYS 5.5 2.6 + - - +
441A ALA 3.0 15.4 + - - +
442A MET* 3.1 13.7 - - - +
444A LEU* 1.3 74.4 - - - +
446A TYR* 1.3 58.8 + - - +
448A ARG* 2.9 7.8 + - - +
449A GLU* 2.7 32.1 + - - +
455A VAL* 3.4 30.5 + - + +
456A ALA* 5.4 5.1 - - - +
457A VAL* 5.4 1.2 - - - +
443B THR* 6.1 0.2 - - - +
634B ASP* 2.3 32.3 + - - -
636B LEU* 3.6 14.7 - - + +
637B THR* 3.6 13.0 + - - +
639B GLU* 3.0 24.4 + - - -
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Residues in contact with TYR 446 (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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347A GLY* 2.1 34.9 + - - -
349A ARG* 3.7 25.1 - - + -
351A TYR* 4.1 9.2 - + + -
368A LEU* 3.2 55.2 - - + -
369A ASN 4.1 0.2 - - - -
370A LEU* 3.2 26.6 + - + -
406A PHE* 4.0 20.6 - + - -
442A MET 2.8 15.9 + - - +
443A ALA 3.4 9.4 - - - +
445A ARG* 1.3 71.9 - - - +
447A VAL* 1.3 64.3 + - + +
449A GLU* 3.5 0.7 + - - +
450A LEU* 2.9 54.2 + - + +
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Residues in contact with VAL 447 (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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406A PHE* 4.0 26.0 - - + +
407A ARG* 3.9 9.9 - - - +
408A GLU* 3.8 34.8 - - + +
411A ILE* 3.5 32.1 - - + -
443A ALA 3.2 17.2 + - - +
444A LEU* 4.1 7.0 - - - +
446A TYR* 1.3 76.7 - - + +
448A ARG* 1.3 56.3 + - - +
450A LEU* 3.2 11.4 + - - +
451A SER* 2.8 28.3 + - - +
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Residues in contact with ARG 448 (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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408A GLU* 2.8 32.3 + - + +
444A LEU* 2.9 44.0 + - - +
445A ARG 2.9 3.9 + - - +
447A VAL* 1.3 72.8 - - - +
449A GLU* 1.3 66.1 + - - +
451A SER* 2.9 17.1 + - - -
453A GLU* 3.0 47.5 + - - +
455A VAL* 3.8 7.6 - - + -
442B ARG* 3.0 40.8 + - - +
443B THR* 3.2 22.7 + - - +
635B ARG* 6.1 0.6 - - - +
636B LEU* 4.6 16.0 - - - +
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Residues in contact with GLU 449 (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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349A ARG* 3.0 32.0 + - - +
351A TYR* 2.8 37.7 + - - +
445A ARG 2.7 19.1 + - - +
446A TYR 3.9 2.5 - - - +
448A ARG* 1.3 70.5 - - - +
450A LEU* 1.3 57.4 - - + +
451A SER 2.7 12.1 + - - -
452A GLY* 3.0 14.7 + - - -
453A GLU 4.0 5.9 + - - +
455A VAL* 3.7 27.1 - - + +
456A ALA* 4.9 4.3 - - - +
459A GLU* 4.8 9.1 - - - +
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Residues in contact with LEU 450 (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 PRO 5.8 0.4 - - - +
347A GLY* 5.2 7.4 - - - +
349A ARG* 3.4 45.3 - - + +
370A LEU 5.4 3.4 - - - +
372A LEU* 5.7 6.1 - - + -
406A PHE* 3.8 24.1 - - + -
446A TYR* 2.9 52.7 + - + +
447A VAL 3.2 4.7 + - - +
449A GLU* 1.3 75.6 - - - +
451A SER* 1.3 58.4 + - - +
452A GLY 3.7 0.4 - - - -
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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