Contacts of the strand formed by residues 539 - 544 (chain B) in PDB entry 2C31
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 CYS 539 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472B VAL 2.8 9.6 + - - +
473B THR* 4.2 6.7 - - + +
474B VAL* 2.9 23.4 + - - +
509B MET* 3.4 10.3 - - - +
515B LYS* 3.1 26.0 - - - +
517B TYR* 4.0 10.1 - - + -
532B ALA* 3.7 38.1 - - + -
535B SER* 3.9 9.2 - - - -
537B LYS* 3.4 16.6 - - - +
538B PRO* 1.3 75.9 - - - +
540B LEU* 1.3 61.8 + - - +
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Residues in contact with LEU 540 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455B PHE* 4.4 0.7 - - + -
462B LEU* 3.8 34.5 - - + -
474B VAL* 3.1 17.7 - - + +
476B ILE* 3.4 30.5 - - + -
505B TYR* 3.8 12.8 - - + +
506B ASP* 3.7 23.8 - - - +
509B MET* 3.7 18.4 - - + -
515B LYS 2.9 5.3 + - - -
516B GLY* 3.4 2.3 - - - -
517B TYR* 2.8 26.2 + - - -
539B CYS* 1.3 77.4 - - - +
541B ILE* 1.3 75.3 + - - +
542B ASN* 3.8 3.1 - - - +
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Residues in contact with ILE 541 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473B THR* 3.9 22.7 - - + -
474B VAL 2.7 10.3 + - - +
475B ILE* 3.5 12.0 - - + +
476B ILE 3.0 26.3 + - - -
517B TYR* 3.8 26.0 - - + -
519B ALA* 4.1 17.3 - - + +
525B LEU* 3.9 23.1 - - + -
528B ALA* 3.8 8.1 - - + +
529B LEU* 3.6 42.4 - - + +
532B ALA* 4.5 0.7 - - + -
540B LEU* 1.3 76.2 - - - +
542B ASN* 1.3 60.8 + - - +
543B ALA* 3.2 5.0 + - + +
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Residues in contact with ASN 542 (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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476B ILE* 4.2 4.7 - - - +
478B ASN* 3.1 25.8 + - - +
503B GLY 3.0 24.6 + - - -
504B ARG* 3.8 3.6 - - - +
505B TYR* 3.6 14.1 - - - +
506B ASP* 3.3 22.6 + - - +
517B TYR 3.0 19.1 + - - +
518B VAL* 4.4 0.7 - - - -
519B ALA 3.0 17.9 + - - -
540B LEU* 3.8 9.5 - - + +
541B ILE* 1.3 70.9 - - - +
543B ALA* 1.3 58.0 + - - +
544B MET* 3.0 37.4 - - + +
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Residues in contact with ALA 543 (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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375B MET* 4.1 13.0 - - + -
380B SER* 5.7 0.2 - - - -
475B ILE* 4.3 18.2 - - + -
476B ILE 3.0 14.6 + - - +
477B MET* 4.7 4.7 - - - -
478B ASN* 3.0 26.7 + - - +
519B ALA* 3.7 12.8 - - + -
525B LEU* 4.7 10.1 - - + -
541B ILE 3.2 2.4 + - - +
542B ASN* 1.3 70.9 - - - +
544B MET* 1.3 64.6 + - - +
545B ILE* 3.3 11.2 + - + +
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Residues in contact with MET 544 (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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373B GLY* 3.8 10.2 - - - +
375B MET* 3.4 29.5 + - - +
478B ASN* 4.0 15.7 - - - -
502B ARG* 3.6 28.0 - - - +
504B ARG* 5.7 2.5 - - - -
518B VAL* 3.5 17.0 - - + -
519B ALA 2.9 9.7 + - - +
520B ASN* 3.0 32.3 - - - +
542B ASN* 3.0 54.1 - - + +
543B ALA* 1.3 68.7 - - - +
545B ILE* 1.3 61.3 + - - +
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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
------------------------------------------------------------
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