Contacts of the helix formed by residues 491 - 505 (chain D) 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 GLY 491 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9D HIS* 3.9 19.1 - - - -
487D GLU* 3.6 4.4 + - - -
489D GLY 3.1 5.7 - - - -
490D GLN* 1.3 79.6 - - - +
492D LEU* 1.3 67.0 + - - +
493D HIS 3.4 2.0 - - - -
494D ALA* 3.4 5.3 + - - -
495D LYS* 3.3 20.6 + - - +
659D LEU* 3.4 25.0 - - - +
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Residues in contact with LEU 492 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483D HIS* 3.9 10.3 - - + +
485D GLY* 3.8 30.7 - - - -
486D THR 3.8 8.1 - - - +
487D GLU* 3.0 7.4 + - - +
490D GLN* 3.4 33.2 - - + +
491D GLY* 1.3 76.0 - - - +
493D HIS* 1.3 65.4 + - - +
495D LYS* 3.1 10.2 + - - +
496D MET* 3.0 37.7 + - + +
527D THR* 4.2 5.6 - - + -
532D GLY 3.8 8.3 - - - +
533D ALA* 3.7 35.2 - - + +
1778D MTE 3.9 7.4 - - - +
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Residues in contact with HIS 493 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D ASP* 3.7 19.7 - - + +
222D ARG* 3.2 34.8 + - - -
483D HIS* 2.8 42.6 + + - -
485D GLY 3.7 11.9 + - - -
486D THR 5.1 0.2 - - - -
487D GLU* 3.1 32.0 + - + +
492D LEU* 1.3 78.6 - - - +
494D ALA* 1.3 60.6 + - - +
496D MET* 3.3 5.4 + - - +
497D VAL* 3.1 27.4 + - - +
513D ILE* 3.2 26.8 - - + +
514D THR 4.5 7.4 + - - -
516D THR* 4.5 6.9 + - - -
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Residues in contact with ALA 494 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D LEU* 5.7 1.6 - - + -
8D PRO 3.8 22.2 - - - +
9D HIS* 4.4 0.9 - - - -
10D ASP* 3.9 21.1 + - + +
491D GLY* 3.4 3.9 + - - +
492D LEU 3.3 1.0 - - - -
493D HIS* 1.3 76.5 - - - +
495D LYS* 1.3 58.2 + - - +
497D VAL* 3.1 8.8 + - - +
498D GLN* 2.8 38.7 + - + +
656D ASN* 5.0 0.7 - - - +
659D LEU* 4.0 19.5 - - + -
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Residues in contact with LYS 495 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490D GLN* 4.5 10.2 + - - +
491D GLY 3.3 13.0 + - - +
492D LEU* 3.1 10.4 + - - +
494D ALA* 1.3 77.3 - - - +
496D MET* 1.3 69.9 + - + +
498D GLN* 3.5 9.7 + - - +
499D VAL* 3.1 30.5 + - - +
533D ALA* 4.4 14.0 - - + +
655D LEU* 4.2 32.6 - - + +
656D ASN* 4.3 9.9 - - + -
659D LEU* 4.1 25.4 - - + +
660D ASP* 3.1 27.4 + - - -
663D GLN* 5.5 1.0 - - - +
728D VAL* 4.1 13.7 - - - +
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Residues in contact with MET 496 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481D LEU* 3.4 25.1 - - + +
483D HIS* 3.5 25.8 - - + +
492D LEU* 3.0 30.9 + - + +
493D HIS 3.7 5.4 - - - +
494D ALA 3.1 0.4 - - - -
495D LYS* 1.3 93.6 - - + +
497D VAL* 1.3 67.0 + - - +
499D VAL* 3.5 8.7 + - + +
500D ALA* 3.1 18.7 + - - +
513D ILE* 4.9 0.2 - - + -
533D ALA* 4.0 10.5 - - + +
536D ASN* 3.8 11.4 - - - +
537D GLY* 3.4 40.2 - - - +
540D VAL* 4.0 8.8 - - + +
655D LEU* 4.6 2.7 - - + -
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Residues in contact with VAL 497 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D ASP* 5.6 4.5 - - + -
481D LEU* 4.0 10.3 - - + -
493D HIS 3.1 18.9 + - - +
494D ALA* 3.4 11.0 - - - +
496D MET* 1.3 75.5 - - - +
498D GLN* 1.3 59.1 + - + +
500D ALA* 3.1 4.5 + - - +
501D ALA* 2.8 28.1 + - - +
508D PRO* 3.6 37.9 - - + +
511D VAL* 3.9 28.4 - - + +
513D ILE* 4.6 15.9 - - + +
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Residues in contact with GLN 498 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D SER* 3.1 39.5 + - - +
3D VAL* 3.5 16.9 + - + +
5D LYS 3.1 26.5 + - - +
7D LEU* 3.9 20.4 - - + +
494D ALA* 2.8 29.1 + - + +
495D LYS* 3.7 8.1 - - - +
496D MET 3.4 0.2 - - - -
497D VAL* 1.3 76.9 - - + +
499D VAL* 1.3 56.1 + - - +
501D ALA* 4.5 0.7 - - - -
502D ALA* 3.1 29.5 + - - +
508D PRO* 5.5 0.4 - - + -
655D LEU* 3.5 13.4 + - + +
656D ASN* 2.8 26.8 + - - +
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Residues in contact with VAL 499 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D VAL* 3.8 17.0 - - + -
495D LYS 3.1 17.1 + - - +
496D MET* 3.7 20.6 - - + +
498D GLN* 1.3 71.5 - - - +
500D ALA* 1.3 57.7 + - - +
502D ALA* 3.0 3.5 + - - +
503D VAL* 2.7 42.1 + - + +
537D GLY 3.5 21.3 - - - +
540D VAL* 4.0 8.3 - - + -
541D LYS* 3.9 17.9 - - + +
655D LEU* 4.6 6.7 - - + -
722D ILE* 4.0 22.2 - - + -
723D PHE* 4.2 2.0 - - + -
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Residues in contact with ALA 500 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471D VAL* 6.0 0.2 - - + -
479D VAL* 5.6 1.8 - - + -
481D LEU* 4.4 7.2 - - + -
496D MET 3.1 10.5 + - - +
497D VAL 3.1 8.2 + - - +
499D VAL* 1.3 78.0 - - - +
501D ALA* 1.3 57.4 + - - +
503D VAL* 3.4 1.5 + - - +
504D LEU* 2.9 39.7 + - + +
511D VAL* 4.3 20.6 - - + -
540D VAL* 4.0 7.4 - - + +
544D CYS* 3.7 25.8 - - - -
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Residues in contact with ALA 501 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D SER* 4.2 6.1 - - - -
497D VAL 2.8 19.3 + - - +
498D GLN 4.0 3.8 - - - +
500D ALA* 1.3 73.0 - - - +
502D ALA* 1.3 53.6 + - - +
504D LEU 3.6 0.3 - - - -
505D GLY* 2.7 30.7 + - - -
506D ILE* 3.0 38.0 + - - +
507D ASP 4.3 0.9 - - - -
508D PRO* 3.6 28.5 - - + -
511D VAL* 4.3 5.8 - - + +
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Residues in contact with ALA 502 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D SER 3.3 23.5 - - - +
3D VAL* 4.0 13.9 - - + -
498D GLN 3.1 19.3 + - - +
499D VAL 3.0 4.2 + - - +
501D ALA* 1.3 76.6 - - - +
503D VAL* 1.3 65.6 + - - +
505D GLY* 3.0 14.8 + - - -
548D ARG* 5.1 0.5 + - - -
568D PHE 5.5 0.2 - - - +
723D PHE* 4.5 11.0 - - + -
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Residues in contact with VAL 503 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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499D VAL* 2.7 27.6 + - + +
500D ALA 4.0 0.2 - - - +
502D ALA* 1.3 72.1 - - - +
504D LEU* 1.3 57.3 + - - +
505D GLY* 4.8 0.2 - - - -
541D LYS* 3.9 34.3 - - + -
544D CYS* 3.4 30.1 - - + +
545D GLU* 3.7 29.4 - - + +
548D ARG* 2.9 42.2 + - - +
568D PHE* 5.4 0.3 - - - +
723D PHE* 4.4 10.8 - - + -
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Residues in contact with LEU 504 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471D VAL* 5.1 2.7 - - + -
473D ILE* 4.5 15.0 - - + -
479D VAL* 4.1 32.5 - - + -
500D ALA* 2.9 21.0 + - + +
501D ALA 4.1 1.3 - - - +
503D VAL* 1.3 77.2 - - - +
505D GLY* 1.3 62.7 + - - +
506D ILE* 3.5 22.1 - - + +
511D VAL* 5.5 0.2 - - + -
544D CYS* 3.8 38.1 - - - +
547D LEU* 4.5 3.1 - - + -
548D ARG* 4.2 18.4 - - + +
551D LEU* 5.1 0.4 - - + -
568D PHE* 3.6 18.3 - - - +
582D PHE* 3.8 23.4 - - + -
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Residues in contact with GLY 505 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501D ALA 2.7 10.2 + - - -
502D ALA 3.0 10.7 + - - -
503D VAL 3.7 0.4 + - - -
504D LEU* 1.3 80.9 - - - +
506D ILE* 1.3 58.1 + - - +
568D PHE* 3.8 19.4 - - - +
569D ASP* 3.4 7.4 + - - -
570D ALA 3.1 10.5 + - - -
571D GLY* 3.0 21.5 + - - -
572D GLN 4.8 0.3 - - - +
582D PHE* 5.5 0.3 - - - -
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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