Contacts of the helix formed by residues 491 - 505 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9B HIS* 3.9 16.4 - - - -
487B GLU* 3.1 7.3 + - - -
489B GLY 3.1 5.9 + - - -
490B GLN* 1.3 78.6 - - - +
492B LEU* 1.3 65.2 + - - +
493B HIS 3.4 2.6 + - - -
494B ALA* 3.5 3.7 + - - -
495B LYS* 3.4 24.7 + - - +
659B LEU* 3.4 22.9 - - - +
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Residues in contact with LEU 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483B HIS* 3.8 9.2 - - + -
485B GLY* 3.7 33.0 - - - -
486B THR 3.8 8.7 - - - +
487B GLU* 2.8 7.4 + - - +
490B GLN* 3.3 34.8 - - + +
491B GLY* 1.3 75.8 - - - +
493B HIS* 1.3 60.9 + - - +
495B LYS* 3.0 11.8 + - - +
496B MET* 2.9 40.5 + - + +
527B THR* 4.1 3.6 - - + -
532B GLY* 4.0 4.3 - - - +
533B ALA* 3.6 35.9 - - + +
536B ASN* 4.9 0.4 - - + -
1778B MTE 3.8 6.3 - - - +
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Residues in contact with HIS 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ASP* 3.8 18.4 - - + +
222B ARG* 3.2 36.8 + - - -
483B HIS* 2.9 35.8 + + - -
485B GLY 4.0 9.6 - - - -
487B GLU* 2.9 37.1 + - + +
492B LEU* 1.3 76.9 - - + +
494B ALA* 1.3 56.2 + - - +
496B MET* 3.2 6.0 + - - +
497B VAL* 2.8 31.3 + - - +
513B ILE* 3.4 26.4 - - + +
514B THR 4.7 6.4 + - - -
516B THR* 4.5 9.2 + - - -
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Residues in contact with ALA 494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LEU* 6.0 0.4 - - + -
8B PRO 3.8 22.2 - - - +
9B HIS* 4.6 1.1 - - - -
10B ASP* 4.0 19.2 - - + +
491B GLY* 3.5 10.5 + - - +
492B LEU 3.3 0.6 - - - -
493B HIS* 1.3 73.9 - - - +
495B LYS* 1.3 61.2 + - - +
497B VAL* 3.1 9.7 + - - +
498B GLN* 2.7 40.1 + - + +
659B LEU* 4.0 13.0 - - + -
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Residues in contact with LYS 495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490B GLN 4.7 8.3 + - - -
491B GLY 3.4 17.0 + - - +
492B LEU* 3.0 9.0 + - - +
494B ALA* 1.3 74.2 - - - +
496B MET* 1.3 77.1 + - + +
498B GLN* 3.2 9.2 + - - +
499B VAL* 2.9 28.4 + - - +
533B ALA* 4.3 15.9 - - + +
655B LEU* 4.1 30.6 - - + +
656B ASN* 4.3 20.4 - - + +
659B LEU* 4.2 14.8 - - + -
660B ASP* 2.9 30.6 + - - -
663B GLN* 5.8 0.6 - - - +
726B LYS 5.7 1.4 + - - -
728B VAL* 4.1 11.1 - - - +
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Residues in contact with MET 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481B LEU* 3.5 16.6 - - + +
483B HIS* 3.2 42.4 - - + +
492B LEU* 2.9 25.9 + - + +
493B HIS 3.5 8.1 - - - +
495B LYS* 1.3 98.1 - - + +
497B VAL* 1.3 60.4 + - - +
499B VAL* 3.4 7.1 + - + +
500B ALA* 3.2 18.9 + - - +
533B ALA* 3.9 10.3 - - + +
536B ASN* 3.5 11.4 - - - +
537B GLY* 3.2 40.6 - - - +
540B VAL* 3.9 10.3 - - + +
655B LEU* 5.1 1.6 - - + -
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Residues in contact with VAL 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ASP* 5.7 3.8 - - + -
481B LEU* 3.7 17.5 - - + -
493B HIS 2.8 18.2 + - - +
494B ALA* 3.1 12.1 + - - +
496B MET* 1.3 77.1 - - - +
498B GLN* 1.3 59.3 + - + +
500B ALA* 3.3 2.8 + - - +
501B ALA* 2.9 27.7 + - - +
508B PRO* 4.0 37.9 - - + +
511B VAL* 4.0 21.0 - - + +
513B ILE* 4.6 15.9 - - + +
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Residues in contact with GLN 498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B SER* 3.0 39.5 + - - -
3B VAL* 3.8 13.5 - - + +
5B LYS 3.3 10.3 + - - -
7B LEU* 4.0 16.5 - - + +
494B ALA* 2.7 35.0 + - + +
495B LYS* 3.2 9.6 + - - +
497B VAL* 1.3 78.2 - - + +
499B VAL* 1.3 56.6 + - - +
501B ALA* 3.5 0.6 + - - +
502B ALA* 2.9 31.0 + - - +
508B PRO* 5.7 0.2 - - + -
655B LEU* 3.5 13.9 + - + +
656B ASN* 2.7 35.3 + - - +
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Residues in contact with VAL 499 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B VAL* 3.7 17.7 - - + -
495B LYS 2.9 21.0 + - - +
496B MET* 3.7 8.5 - - + +
498B GLN* 1.3 76.3 - - - +
500B ALA* 1.3 60.2 + - - +
502B ALA* 3.0 4.2 + - - +
503B VAL* 2.8 31.8 + - + +
537B GLY* 3.8 25.8 - - - +
540B VAL* 4.1 4.5 - - + -
541B LYS* 3.8 25.1 - - + +
655B LEU* 4.8 7.4 - - + -
722B ILE* 3.9 26.2 - - + -
723B PHE* 4.1 4.5 - - + -
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Residues in contact with ALA 500 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471B VAL* 5.9 0.2 - - + -
479B VAL* 5.8 1.8 - - + -
481B LEU* 4.3 13.2 - - + -
496B MET 3.2 13.1 + - - +
497B VAL 3.8 3.1 - - - +
499B VAL* 1.3 78.7 - - - +
501B ALA* 1.3 63.5 + - - +
503B VAL* 3.2 2.1 + - - +
504B LEU* 2.9 33.3 + - + +
511B VAL* 4.4 11.9 - - + -
540B VAL* 3.7 9.6 - - + -
544B CYS* 3.6 26.9 - - - -
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Residues in contact with ALA 501 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B SER* 4.2 6.5 - - - -
497B VAL 2.9 17.4 + - - +
498B GLN 3.7 4.0 - - - +
500B ALA* 1.3 74.8 - - - +
502B ALA* 1.3 58.0 + - - +
504B LEU 3.8 0.2 - - - -
505B GLY* 2.9 26.7 + - - -
506B ILE* 3.1 35.9 + - - +
507B ASP 4.2 1.1 - - - -
508B PRO* 3.7 28.7 - - + -
511B VAL* 4.4 5.2 - - + +
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Residues in contact with ALA 502 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B SER 3.2 25.0 - - - +
3B VAL* 3.8 16.6 - - + +
498B GLN 2.9 13.9 + - - +
499B VAL 3.0 4.5 + - - +
501B ALA* 1.3 77.5 - - - +
503B VAL* 1.3 60.1 + - - +
505B GLY* 3.7 8.2 + - - -
548B ARG* 5.3 0.7 + - - -
723B PHE* 4.4 11.7 - - + -
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Residues in contact with VAL 503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499B VAL* 2.8 24.5 + - + +
500B ALA 4.0 0.7 - - - +
502B ALA* 1.3 74.3 - - - +
504B LEU* 1.3 61.9 + - - +
505B GLY* 3.5 0.7 + - - -
541B LYS* 4.1 25.4 - - + -
544B CYS* 3.6 24.9 - - + +
545B GLU* 3.6 26.5 - - + +
548B ARG* 3.1 47.6 + - - +
568B PHE* 5.1 0.5 - - - +
723B PHE* 4.1 19.3 - - + -
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Residues in contact with LEU 504 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471B VAL* 5.1 2.0 - - + -
473B ILE* 4.5 11.7 - - + -
479B VAL* 3.8 36.3 - - + -
500B ALA* 2.9 21.6 + - + +
503B VAL* 1.3 75.4 - - - +
505B GLY* 1.3 63.6 + - - +
506B ILE* 3.8 23.2 - - + +
511B VAL* 5.2 0.7 - - + -
544B CYS* 3.8 37.2 - - - +
547B LEU* 4.3 9.9 - - + -
548B ARG* 4.2 17.0 - - + +
551B LEU* 5.6 0.9 - - + -
568B PHE* 3.3 26.5 - - - +
582B PHE* 4.0 13.5 - - + -
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Residues in contact with GLY 505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501B ALA 2.9 7.2 + - - -
502B ALA* 3.7 7.4 + - - -
503B VAL 3.3 3.4 - - - -
504B LEU* 1.3 80.2 - - - +
506B ILE* 1.3 62.1 + - - +
568B PHE* 3.6 19.9 - - - +
569B ASP* 3.4 8.2 + - - -
570B ALA 3.3 8.0 + - - -
571B GLY* 2.9 23.3 + - - -
572B GLN 4.4 0.9 + - - +
582B 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