Contacts of the helix formed by residues 540 - 547 (chain B) in PDB entry 2H3W
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 ASP 540 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50B TYR* 4.7 0.9 + - - -
62B GLU* 5.1 0.9 - - - +
65B HIS* 3.9 14.5 + - - -
66B THR* 2.5 41.6 + - - +
69B LEU* 3.7 19.2 - - + +
536B ASP 2.8 10.3 + - - +
537B ILE* 3.4 19.2 - - - +
538B PHE 3.3 1.1 - - - +
539B MET* 1.3 82.6 - - - +
541B THR* 1.3 82.1 + - - +
542B SER* 3.2 13.8 + - - +
543B TYR* 3.2 11.7 + - - +
544B ALA* 3.4 11.4 + - - +
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Residues in contact with THR 541 (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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62B GLU* 4.0 20.0 - - - +
539B MET 3.6 2.0 + - - -
540B ASP* 1.3 80.7 + - - +
542B SER* 1.3 60.6 + - - +
544B ALA* 3.2 8.7 + - + +
545B ILE* 3.0 40.0 + - + +
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Residues in contact with SER 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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50B TYR* 3.7 2.9 - - - -
54B LEU* 3.6 24.1 - - - +
58B VAL* 4.0 16.1 - - - +
62B GLU* 3.3 22.9 + - - +
66B THR* 2.5 29.6 + - - -
540B ASP* 3.2 5.5 + - - -
541B THR* 1.3 78.6 - - - +
543B TYR* 1.3 57.9 + - - +
545B ILE* 3.5 3.4 + - - +
546B ALA* 2.9 29.6 + - - +
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Residues in contact with TYR 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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50B TYR* 3.3 24.9 + + - +
517B ASP 4.9 1.2 + - - -
520B LEU* 4.1 32.0 - - + +
521B LEU* 4.2 14.4 + - - +
524B LYS* 4.6 18.7 + - + +
537B ILE* 3.5 23.6 - - + +
538B PHE* 3.7 41.6 - + - +
540B ASP* 3.2 9.3 + - - +
542B SER* 1.3 75.6 - - - +
544B ALA* 1.3 67.1 + - - +
546B ALA* 3.3 2.2 + - + +
547B MET* 2.9 70.8 + - + +
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Residues in contact with ALA 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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538B PHE 5.4 0.4 + - - -
540B ASP 3.4 7.8 + - - +
541B THR* 3.2 13.6 + - + +
543B TYR* 1.3 80.5 - - - +
545B ILE* 1.3 63.0 + - + +
547B MET* 3.4 4.4 + - - +
548B HIS* 3.2 25.0 + - - +
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Residues in contact with ILE 545 (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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57B ILE* 3.6 29.2 - - + +
58B VAL* 4.3 11.4 - - + -
62B GLU* 3.8 24.7 - - - +
450B ALA* 3.5 13.7 - - + +
541B THR* 3.0 31.2 + - + +
542B SER* 3.7 4.9 - - - +
544B ALA* 1.3 79.0 - - + +
546B ALA* 1.3 63.1 + - - +
548B HIS* 3.2 17.8 + - - +
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Residues in contact with ALA 546 (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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50B TYR* 4.3 8.3 - - + -
54B LEU* 3.7 20.0 - - + -
57B ILE* 4.0 10.5 - - + +
450B ALA* 3.6 2.3 - - - +
469B ARG* 2.8 44.3 + - - +
542B SER 2.9 19.2 + - - +
543B TYR* 3.3 7.4 + - + +
545B ILE* 1.3 77.3 - - - +
547B MET* 1.3 58.9 + - + +
549B PHE* 3.3 10.2 - - - -
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Residues in contact with MET 547 (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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469B ARG* 3.4 24.0 - - - -
517B ASP* 3.6 16.6 - - + +
518B ARG* 6.3 0.4 - - - +
521B LEU* 6.1 4.5 - - + -
543B TYR* 2.9 63.2 + - + +
544B ALA* 3.8 4.9 - - - +
546B ALA* 1.3 75.6 - - - +
548B HIS* 1.3 59.4 + - - +
549B PHE* 3.5 28.4 + - + -
570B VAL* 5.5 0.5 - - - +
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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