Contacts of the helix formed by residues 498 - 506 (chain B) in PDB entry 2W9M
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 498 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193B GLU* 4.0 5.4 - - - +
460B ARG* 3.1 31.4 + - - +
495B LEU 3.8 7.3 - - - +
496B ASP* 3.6 6.3 + - - +
497B LEU* 1.3 81.1 - - - +
499B TRP* 1.3 68.9 + - - +
500B ARG* 3.0 53.0 + - - +
501B GLU* 3.1 24.4 + - + +
502B ALA* 3.1 9.9 + - - +
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Residues in contact with TRP 499 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B GLU* 3.2 16.6 + - - -
305B GLU* 3.7 27.6 - - + -
307B GLU* 3.3 26.2 - - + -
308B HIS* 3.5 19.5 - + - -
488B ILE* 6.2 0.7 - - - -
495B LEU 4.9 0.6 + - - -
497B LEU 3.5 2.7 + - - -
498B ASP* 1.3 73.9 - - - +
500B ARG* 1.3 104.8 + - + +
502B ALA* 3.7 9.2 - - - +
503B LEU* 2.9 40.4 + - + +
532B GLN* 3.3 42.6 + - + +
535B LYS* 2.8 46.2 - - + +
536B ALA* 3.8 2.6 - - + +
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Residues in contact with ARG 500 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B LEU* 4.8 9.5 - - - +
193B GLU* 3.0 26.4 + - - -
305B GLU* 5.3 1.2 + - - -
307B GLU* 3.9 27.6 + - + -
460B ARG* 5.1 0.8 - - - +
498B ASP* 3.0 33.2 + - - +
499B TRP* 1.3 133.5 - - + +
501B GLU* 1.3 64.9 + - + +
503B LEU* 3.5 7.2 + - - +
504B ARG* 3.4 25.4 + - - +
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Residues in contact with GLU 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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472B LEU* 3.6 27.2 - - + +
473B ASP* 4.1 4.1 - - - +
476B LEU* 4.8 2.7 - - + -
497B LEU* 3.9 20.2 - - + -
498B ASP* 3.1 19.7 + - + +
500B ARG* 1.3 78.3 - - + +
502B ALA* 1.3 64.1 + - - +
504B ARG* 2.7 35.0 + - - +
505B TRP* 3.1 32.1 + - - +
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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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488B ILE* 4.4 14.1 - - + -
497B LEU* 4.0 10.7 - - + +
498B ASP 3.1 12.8 + - - +
499B TRP* 3.7 10.8 - - - +
501B GLU* 1.3 75.8 - - - +
503B LEU* 1.3 59.2 + - - +
505B TRP 3.6 0.3 - - - -
506B ARG* 2.9 34.3 + - - +
511B PHE* 4.0 23.4 - - + -
536B ALA* 3.7 16.3 - - + +
538B LEU* 5.0 0.7 - - + -
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Residues in contact with LEU 503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B GLU* 4.1 14.6 - - + +
308B HIS* 4.3 7.4 - - + -
311B LEU* 3.7 29.4 - - + -
315B LEU* 4.1 24.2 - - + -
499B TRP* 2.9 37.9 + - + +
500B ARG* 3.5 8.1 - - - +
502B ALA* 1.3 77.6 - - - +
504B ARG* 1.3 58.9 + - + +
506B ARG* 3.0 23.1 - - - +
535B LYS 4.1 3.4 - - - +
536B ALA* 3.4 32.6 - - - +
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Residues in contact with ARG 504 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473B ASP* 3.0 35.6 + - - -
500B ARG* 3.4 11.6 + - - +
501B GLU* 2.7 46.0 + - - +
502B ALA 3.2 0.4 - - - -
503B LEU* 1.3 80.7 - - + +
505B TRP* 1.3 69.2 + - + +
506B ARG* 3.6 0.8 + - - +
507B GLU* 5.2 3.1 + - - +
508B ARG* 5.6 3.3 + - - +
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Residues in contact with TRP 505 (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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473B ASP* 3.4 42.2 + - + -
476B LEU* 3.4 36.3 - - + +
477B GLY* 3.5 20.6 - - - -
480B GLU* 3.9 10.1 - - + -
501B GLU* 3.1 25.4 + - - +
502B ALA 3.2 2.4 + - - +
504B ARG* 1.3 95.5 - - + +
506B ARG* 1.3 57.5 + - - +
507B GLU 3.0 5.6 - - - -
508B ARG* 2.8 82.2 + - + +
509B LEU* 3.2 33.3 + - + -
511B PHE* 4.0 5.8 - - + -
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Residues in contact with ARG 506 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B THR* 4.8 11.3 + - - +
315B LEU* 3.8 20.2 - - - +
316B PRO* 3.6 21.6 - - - +
502B ALA 2.9 12.3 + - - +
503B LEU* 3.0 21.8 - - - +
504B ARG 3.6 1.0 - - - -
505B TRP* 1.3 76.7 - - - +
507B GLU* 1.3 89.8 + - + +
508B ARG 3.3 0.4 + - - -
509B LEU 4.0 4.1 - - - +
511B PHE* 4.0 9.6 - - - -
536B ALA 3.3 14.6 - - - +
537B GLY 2.7 31.3 + - - -
538B LEU* 3.8 17.5 - - + -
542B HIS* 3.1 41.0 + - - +
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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