Contacts of the helix formed by residues 528 - 536 (chain B) in PDB entry 2WSC
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 HIS 528 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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422B LEU* 3.9 8.8 + - - +
425B ALA* 3.8 23.8 - - + +
426B SER* 3.6 11.2 + - - +
429B LEU* 4.0 14.8 - - + -
524B ALA 3.0 25.1 - - - +
525B LEU* 4.3 3.8 - - - -
526B GLY 2.9 1.9 + - - +
527B LEU* 1.3 73.6 + - - +
529B THR* 1.3 58.1 + - - +
531B THR* 3.3 16.0 + - - +
532B LEU* 2.8 33.6 + - - +
1755B CLA 5.4 0.2 - - - -
1768B CLA 4.1 4.6 - - - +
1769B CLA 2.8 80.1 + + - -
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Residues in contact with THR 529 (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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1813A CLA 3.8 42.8 - - + -
426B SER* 2.9 10.8 + - - +
525B LEU* 2.4 41.3 + - - +
526B GLY 3.1 2.1 + - - -
528B HIS* 1.3 75.5 - - - +
530B THR* 1.4 52.0 - - - +
531B THR 2.9 5.9 + - - -
532B LEU* 3.0 13.1 + - + +
533B ILE* 2.8 30.1 + - + +
582B TRP* 3.8 27.1 - - + -
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Residues in contact with THR 530 (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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384B THR* 5.3 0.2 - - + -
526B GLY 2.6 30.7 + - - -
529B THR* 1.4 71.7 - - - +
531B THR* 1.3 57.9 + - - +
533B ILE* 3.8 8.1 - - - +
534B LEU* 3.3 28.5 + - + +
579B ALA* 4.4 6.5 - - + +
582B TRP* 3.1 33.3 - - + +
583B MET* 4.1 12.3 - - + +
586B THR* 3.7 2.4 + - - -
1755B CLA 3.1 43.6 - - + +
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Residues in contact with THR 531 (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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387B PHE* 4.2 7.2 - - - -
422B LEU* 3.6 9.0 - - - +
527B LEU* 3.7 1.3 - - - -
528B HIS* 3.3 25.7 + - - +
529B THR 3.0 0.4 - - - -
530B THR* 1.3 78.5 - - - +
532B LEU* 1.3 54.7 + - - +
533B ILE 2.9 1.3 - - - -
534B LEU* 3.9 7.0 - - - +
535B VAL* 2.5 44.4 + - - +
1755B CLA 3.0 70.8 - - + +
1769B CLA 4.0 0.8 - - - +
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Residues in contact with LEU 532 (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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699A TYR* 4.6 7.2 - - - +
703A LEU* 3.8 27.1 - - + -
1813A CLA 3.8 28.0 - - + +
419B ILE* 3.6 18.9 - - + +
422B LEU* 4.1 17.9 - - + -
423B SER* 4.4 11.2 - - - +
426B SER* 4.1 8.5 - - - +
528B HIS 2.8 15.0 + - - +
529B THR* 3.0 30.9 + - + +
531B THR* 1.3 75.8 + - - +
533B ILE* 1.3 63.5 + - + +
535B VAL* 3.1 10.4 - - - +
536B LYS* 2.8 30.0 + - - +
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Residues in contact with ILE 533 (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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699A TYR* 3.3 29.4 - - + +
1813A CLA 3.8 22.7 - - + -
529B THR* 2.8 22.9 - - + +
530B THR* 3.8 8.1 - - - +
532B LEU* 1.3 80.2 - - + +
534B LEU* 1.3 53.4 + - - +
536B LYS* 3.5 1.9 - - - +
537B GLY* 2.3 36.7 + - - -
575B ASP* 2.8 49.5 - - + +
578B LEU* 4.0 5.8 - - + -
579B ALA* 3.8 17.9 - - + +
582B TRP* 5.6 2.7 - - + -
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Residues in contact with LEU 534 (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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384B THR* 3.6 35.0 - - + +
387B PHE* 3.4 52.6 - - + +
388B ALA* 5.6 0.7 - - + -
391B PRO* 6.3 0.7 - - + -
530B THR* 3.3 20.7 + - + +
531B THR* 3.4 1.8 + - - -
533B ILE* 1.3 71.6 - - - +
535B VAL* 1.4 57.9 + - - +
537B GLY* 3.4 2.4 - - - +
538B ALA* 2.7 38.1 + - - +
575B ASP 4.1 2.0 - - - +
576B PHE* 3.9 20.0 - - + +
579B ALA* 3.0 25.8 - - + -
1755B CLA 4.3 5.8 - - + -
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Residues in contact with VAL 535 (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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387B PHE* 4.2 15.2 - - + -
418B ILE* 3.6 15.0 - - + -
419B ILE* 4.5 3.6 - - + -
422B LEU* 3.2 35.9 - - + -
531B THR* 2.5 38.5 + - - +
532B LEU* 3.1 11.9 - - - +
534B LEU* 1.4 67.4 - - - +
536B LYS* 1.3 60.3 + - + +
538B ALA* 3.5 3.2 - - - +
539B LEU* 2.4 66.3 + - + +
1769B CLA 5.6 4.7 - - + -
1777B BCR 5.8 0.4 - - - -
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Residues in contact with LYS 536 (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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699A TYR* 2.6 67.0 + - + +
702A GLU* 3.2 34.8 - - - +
703A LEU* 3.0 24.9 - - + +
706A SER* 5.6 0.2 - - - +
419B ILE* 4.0 25.6 - - + -
532B LEU 2.8 19.1 + - - +
533B ILE 3.5 0.9 - - - +
535B VAL* 1.3 77.9 - - - +
537B GLY* 1.3 75.3 + - - +
538B ALA 3.2 0.5 - - - -
539B LEU* 2.8 13.6 + - - +
540B ASP* 3.3 20.0 - - - +
575B ASP* 5.4 1.1 - - - +
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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