Contacts of the helix formed by residues 485 - 506 (chain A) in PDB entry 2WSK
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 485 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484A GLY* 1.3 76.4 - - - +
486A LEU* 1.3 65.2 + - - +
487A ASP* 3.7 10.5 + - - +
488A LEU* 3.0 22.0 + - - +
489A VAL* 3.0 19.2 + - - +
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Residues in contact with LEU 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A GLY 3.8 0.6 + - - -
485A SER* 1.3 74.3 - - - +
487A ASP* 1.3 60.4 + - - +
489A VAL* 3.2 13.4 + - + +
490A GLU* 2.9 75.1 + - + +
493A ARG* 5.7 1.3 - - - +
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Residues in contact with ASP 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A SER* 3.0 10.3 + - - +
486A LEU* 1.3 81.3 - - - +
488A LEU* 1.3 58.0 + - - +
490A GLU* 3.1 3.0 + - - +
491A ARG* 2.7 81.4 + - - +
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Residues in contact with LEU 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A ASN 3.8 4.3 - - - +
477A HIS* 3.2 47.8 - - + +
478A GLY* 4.3 0.9 - - - +
479A LYS* 3.6 28.3 - - + +
483A GLY 3.5 24.5 - - - +
484A GLY* 4.0 6.3 - - - -
485A SER* 3.0 19.8 + - - +
487A ASP* 1.3 80.0 + - - +
489A VAL* 1.3 59.2 + - - +
491A ARG* 3.6 5.0 + - + +
492A ARG* 2.8 47.1 + - - +
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Residues in contact with VAL 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A GLY* 5.0 7.6 - - - -
484A GLY 4.1 17.0 - - - +
485A SER 3.0 13.9 + - - +
486A LEU* 3.5 17.5 - - + +
488A LEU* 1.3 79.7 - - + +
490A GLU* 1.3 60.5 + - + +
492A ARG* 3.7 9.6 + - - +
493A ARG* 3.2 31.7 + - + +
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Residues in contact with GLU 490 (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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486A LEU* 2.9 55.0 + - + +
487A ASP* 3.8 3.3 - - - +
489A VAL* 1.3 75.7 - - + +
491A ARG* 1.3 85.7 + - - +
493A ARG* 3.2 44.0 + - - +
494A ASP* 3.2 27.0 + - - +
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Residues in contact with ARG 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A HIS* 3.8 14.6 - - + +
487A ASP* 2.7 74.2 + - - +
488A LEU* 4.0 5.8 - - + +
490A GLU* 1.3 93.6 + - - +
492A ARG* 1.3 60.3 + - - +
493A ARG* 5.7 0.6 - - - +
494A ASP* 3.1 29.9 + - - +
495A SER 3.6 0.9 + - - -
648A PRO* 5.8 2.4 - - - +
649A ALA* 5.8 5.7 + - - +
650A HIS* 2.9 38.5 - - + +
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Residues in contact with ARG 492 (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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451A VAL* 3.1 39.5 + - + -
452A CYS* 3.3 25.1 - - - +
476A ASN 3.0 24.5 + - - -
477A HIS* 3.6 24.2 + - + +
479A LYS 3.8 3.8 + - - -
481A GLY 2.9 23.8 + - - -
483A GLY 3.0 31.7 + - - +
488A LEU* 2.8 38.5 + - - +
489A VAL* 4.0 9.7 - - - +
491A ARG* 1.3 74.6 - - - +
493A ARG* 1.3 59.1 - - - +
494A ASP 3.1 1.6 - - - -
495A SER* 3.3 1.8 + - - -
496A ILE* 2.8 35.1 + - + +
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Residues in contact with ARG 493 (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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486A LEU* 5.7 1.4 - - - +
489A VAL* 3.2 24.2 + - + +
490A GLU* 3.2 51.4 + - - +
491A ARG* 5.7 0.6 - - - +
492A ARG* 1.3 79.9 - - - +
494A ASP* 1.3 67.4 + - - +
496A ILE* 3.9 8.5 - - - +
497A HIS* 3.0 60.1 + - + +
547A LEU* 6.1 0.2 - - + -
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Residues in contact with ASP 494 (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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490A GLU 3.2 9.6 + - - +
491A ARG* 3.1 38.9 + - - +
492A ARG 3.1 0.4 - - - -
493A ARG* 1.3 86.6 + - - +
495A SER* 1.3 59.2 + - - +
497A HIS* 3.5 9.3 + - - +
498A ALA* 3.0 27.4 + - - +
648A PRO* 4.5 21.6 - - - +
649A ALA 4.5 3.7 - - - +
650A HIS* 3.9 16.6 - - + +
651A GLY* 4.4 6.8 - - - -
652A LEU* 5.3 0.5 - - - +
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Residues in contact with SER 495 (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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404A TRP* 4.5 3.2 + - - +
405A LEU* 4.1 18.4 - - - +
451A VAL* 4.2 4.5 - - - -
477A HIS* 2.9 37.0 - - - -
491A ARG 3.6 1.2 + - - -
492A ARG 3.3 5.0 + - - -
494A ASP* 1.3 77.0 - - - +
496A ILE* 1.3 59.7 + - - +
498A ALA* 3.1 4.7 + - - +
499A LEU* 2.7 35.5 + - - +
650A HIS* 3.0 25.0 + - - +
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Residues in contact with ILE 496 (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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447A LEU* 3.8 17.0 - - + +
448A ARG* 4.3 21.5 - - + -
451A VAL* 3.9 27.8 - - + -
492A ARG* 2.8 24.3 + - + +
493A ARG* 3.9 8.1 - - - +
495A SER* 1.3 76.7 - - - +
497A HIS* 1.3 57.3 + - + +
499A LEU* 3.9 7.1 - - - +
500A LEU* 2.9 47.6 + - + +
516A ASP 5.2 0.2 - - - +
519A GLY* 6.1 1.3 - - - -
547A LEU* 4.2 24.5 - - + -
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Residues in contact with HIS 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493A ARG* 3.0 51.0 + - + +
494A ASP* 3.7 10.4 + - - +
496A ILE* 1.3 76.3 - - + +
498A ALA* 1.3 55.8 + - - +
500A LEU* 3.8 1.0 - - - +
501A THR* 2.8 37.9 + - - -
547A LEU* 3.8 22.6 - - + +
550A PHE* 3.4 48.6 - + + +
633A PHE* 4.9 7.4 - - + -
652A LEU* 4.2 2.7 - - + -
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Residues in contact with ALA 498 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A TRP* 3.6 42.2 - - + -
494A ASP 3.0 19.3 + - - +
495A SER* 3.1 5.6 + - - +
497A HIS* 1.3 75.1 - - - +
499A LEU* 1.3 55.0 + - - +
501A THR* 3.4 2.1 + - - -
502A THR* 2.6 37.3 + - - -
650A HIS 4.2 1.6 - - - +
651A GLY* 4.5 0.9 - - - -
652A LEU* 3.4 17.6 - - + +
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Residues in contact with LEU 499 (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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400A ALA* 3.9 29.4 - - + +
401A ARG* 4.3 6.7 - - + -
404A TRP* 4.2 13.9 - - + -
405A LEU* 3.9 32.8 - - + -
439A VAL* 3.9 29.2 - - + +
447A LEU* 3.9 26.7 - - + -
450A CYS* 5.3 0.4 - - + -
451A VAL* 4.4 7.6 - - + -
495A SER 2.7 25.2 + - - +
496A ILE* 4.0 3.8 - - - +
498A ALA* 1.3 69.8 - - - +
500A LEU* 1.3 64.8 + - - +
502A THR* 3.4 6.3 + - - -
503A LEU* 3.1 23.6 + - - +
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Residues in contact with LEU 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A LEU* 3.5 19.3 - - + -
496A ILE* 2.9 36.7 + - + +
497A HIS 3.8 4.3 - - - +
499A LEU* 1.3 76.4 - - - +
501A THR* 1.3 57.7 + - - +
503A LEU* 3.4 7.8 + - + +
504A LEU* 3.0 44.4 + - + +
512A LEU* 4.1 26.2 - - + -
516A ASP* 4.0 10.3 - - + +
547A LEU* 3.9 14.8 - - + -
550A PHE* 4.3 4.0 - - + -
551A THR* 3.8 23.1 - - + +
554A LEU* 3.8 10.3 - - + -
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Residues in contact with THR 501 (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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418A PHE* 5.4 0.2 - - - -
497A HIS 2.8 22.6 + - - -
498A ALA 3.8 0.4 - - - -
500A LEU* 1.3 74.1 - - - +
502A THR* 1.3 64.1 + - - +
505A LEU* 2.9 56.5 + - + +
550A PHE* 4.1 0.3 - - - -
554A LEU* 3.6 16.7 - - + +
609A ILE* 4.9 3.4 - - + -
633A PHE* 3.4 19.0 - - + -
652A LEU* 3.5 29.4 - - + -
654A VAL* 4.3 9.2 - - + -
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Residues in contact with THR 502 (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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396A PHE* 3.9 13.9 - - + -
400A ALA* 4.4 14.4 - - + -
404A TRP* 2.8 24.4 + - - +
414A PHE* 3.7 28.3 - - + -
418A PHE* 5.2 4.9 - - + -
439A VAL* 5.5 0.2 - - - -
498A ALA 2.6 22.5 + - - -
499A LEU* 3.5 7.9 - - - -
501A THR* 1.3 76.6 - - - +
503A LEU* 1.3 59.4 + - - +
505A LEU 4.0 0.2 - - - -
506A SER* 2.6 43.6 + - - +
652A LEU* 4.8 2.6 - - - +
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Residues in contact with LEU 503 (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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396A PHE* 4.4 8.4 - - + -
437A ASN* 3.4 32.6 - - + +
438A LEU* 3.8 12.8 - - - +
439A VAL* 3.9 17.2 - - + +
499A LEU 3.1 14.3 + - - +
500A LEU* 3.5 9.4 - - + +
501A THR 3.2 0.2 - - - -
502A THR* 1.3 82.6 - - - +
504A LEU* 1.3 86.5 + - + +
505A LEU 3.4 0.2 + - - -
506A SER* 3.7 9.5 + - - +
510A PRO* 3.8 12.2 - - + +
511A MET 3.7 23.1 - - - +
512A LEU* 4.1 17.0 - - + -
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Residues in contact with LEU 504 (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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152A ILE* 5.0 5.4 - - + -
500A LEU* 3.0 43.2 + - + +
503A LEU* 1.3 99.8 - - + +
505A LEU* 1.3 67.0 + - + +
510A PRO* 4.1 16.6 - - + -
512A LEU* 4.6 10.5 - - + -
551A THR* 4.3 12.6 - - + -
554A LEU* 4.1 26.7 - - + -
555A ILE* 3.8 31.0 - - + -
558A ARG* 3.3 29.1 + - - +
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Residues in contact with LEU 505 (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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418A PHE* 3.1 18.5 - - + -
501A THR* 2.9 38.4 + - + +
504A LEU* 1.3 87.5 - - - +
506A SER* 1.3 64.4 + - - +
554A LEU* 3.9 31.0 - - + +
557A LEU* 4.6 14.1 - - + -
558A ARG* 4.4 12.6 - - + +
561A ILE* 4.7 6.5 - - + -
564A LEU* 3.2 25.5 - - + +
603A LEU* 4.7 0.3 - - - +
609A ILE* 3.6 27.4 - - + -
654A VAL* 3.9 13.5 - - + -
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Residues in contact with SER 506 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A PHE* 3.5 30.5 - - - -
418A PHE* 3.0 30.8 - - - +
437A ASN* 4.1 6.8 - - - +
502A THR* 2.6 25.3 + - - +
503A LEU 3.7 7.0 + - - +
504A LEU 3.6 0.6 - - - -
505A LEU* 1.3 79.4 - - - +
507A GLN* 1.3 64.8 + - - +
508A GLY 4.1 0.7 - - - +
510A PRO* 4.7 1.2 - - - +
558A ARG* 3.3 19.6 + - - -
564A LEU* 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