Contacts of the helix formed by residues 539 - 544 (chain B) in PDB entry 2YA6
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 ILE 539 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417B ILE* 4.2 17.3 - - + -
521B LEU* 3.0 47.0 + - + +
522B TRP 4.4 3.8 - - - -
523B MET* 4.0 17.7 - - + -
537B GLN* 3.2 12.9 + - + +
538B ASP* 1.3 73.7 - - - +
540B THR* 1.3 66.7 + - - +
541B PRO* 3.3 3.8 - - - -
542B MET* 3.0 45.0 + - + +
543B VAL* 3.6 8.0 - - + +
592B ILE* 3.9 17.7 - - + -
601B TRP* 3.9 23.6 - - + +
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Residues in contact with THR 540 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438B TYR* 3.3 26.5 + - + +
518B ASP* 5.8 0.4 - - - +
519B SER 4.0 9.2 - - - +
520B TYR* 3.5 8.4 - - + +
521B LEU* 2.9 27.2 + - + +
538B ASP* 2.7 17.0 + - - -
539B ILE* 1.3 75.8 - - - +
541B PRO* 1.4 61.3 - - - +
543B VAL* 3.0 8.0 + - - -
544B LYS* 2.9 63.0 + - + +
551B LEU* 5.2 0.9 - - + -
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Residues in contact with PRO 541 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438B TYR* 3.8 42.6 - - + +
445B THR* 4.2 17.3 - - + -
538B ASP* 3.6 14.4 - - + +
539B ILE 3.3 6.3 - - - -
540B THR* 1.4 94.5 - - - +
542B MET* 1.3 61.6 + - + +
543B VAL 3.4 0.4 + - - -
544B LYS* 4.6 7.8 + - + +
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Residues in contact with MET 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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538B ASP 4.6 3.6 - - - +
539B ILE* 3.0 49.3 + - + +
541B PRO* 1.3 82.7 - - + +
543B VAL* 1.3 59.6 - - + +
599B LYS 4.3 7.2 - - - +
600B THR* 3.8 13.9 - - - -
601B TRP* 3.4 51.6 - - + +
602B HIS* 4.6 4.3 + - - -
603B ALA 4.8 0.7 + - - -
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Residues in contact with VAL 543 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521B LEU* 4.0 18.6 - - + -
539B ILE* 3.6 15.7 - - + +
540B THR* 3.6 4.7 - - - +
542B MET* 1.3 84.8 - - - +
544B LYS* 1.3 63.3 + - - +
545B ALA* 3.6 3.1 + - - +
548B MET* 4.1 7.8 - - - +
551B LEU* 3.8 19.3 - - + +
592B ILE* 3.7 28.0 - - + -
601B TRP* 3.8 22.2 - - + -
602B HIS 3.8 17.5 - - - -
603B ALA* 3.5 20.7 - - + +
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Residues in contact with LYS 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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434B LYS* 5.1 3.2 - - - +
518B ASP* 3.0 23.5 + - - +
519B SER* 3.3 21.3 - - - +
540B THR* 2.9 39.4 + - + +
541B PRO* 4.6 7.5 + - + +
543B VAL* 1.3 75.6 - - - +
545B ALA* 1.3 71.5 + - - +
546B ASP* 4.0 1.9 + - - +
548B MET* 3.0 26.5 + - + -
549B LYS 2.7 29.2 + - - -
551B LEU* 3.6 29.2 - - + -
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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