Contacts of the helix formed by residues 406 - 413 (chain A) in PDB entry 2WTJ
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 ARG 406 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339A HIS* 3.3 53.2 + - + +
344A ILE* 3.6 26.6 - - + +
375A LEU* 3.7 14.3 - - - +
403A GLY 4.1 6.8 + - - -
404A TYR* 4.6 7.4 - - + -
405A ASN* 1.3 76.9 - - - +
407A ALA* 1.3 66.7 + - + +
408A VAL 3.1 0.2 - - - -
409A ASP* 3.1 13.9 + - - +
410A CYS* 3.8 1.4 + - - -
476A THR* 6.0 7.2 - - + -
1514A NO3 2.7 40.3 + - - +
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Residues in contact with ALA 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404A TYR* 3.0 20.0 + - + +
405A ASN 3.0 1.2 - - - -
406A ARG* 1.3 83.6 - - + +
408A VAL* 1.3 61.8 + - - +
410A CYS* 3.0 20.4 + - + +
411A TRP 3.0 5.2 + - - -
471A PRO* 3.6 27.4 - - + +
474A ARG* 2.9 32.9 + - + +
475A PHE 6.1 0.2 - - - +
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Residues in contact with VAL 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A ILE* 5.2 0.7 - - + -
346A ARG* 4.2 29.4 - - + +
404A TYR 5.6 0.4 - - - +
405A ASN* 3.1 21.0 + - - +
406A ARG* 3.1 2.0 - - - -
407A ALA* 1.3 78.1 - - - +
409A ASP* 1.3 69.4 + - - +
411A TRP* 3.3 7.2 + - - +
412A SER* 3.0 31.0 + - - +
474A ARG* 4.1 7.4 - - - +
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Residues in contact with ASP 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335A VAL* 3.8 13.1 - - + +
338A LEU* 5.0 0.9 - - - +
339A HIS* 3.0 26.0 + - - +
344A ILE* 3.5 4.7 - - - +
345A HIS* 2.9 26.7 + - - +
346A ARG* 2.9 29.2 + - - -
348A LEU* 3.9 17.3 - - + +
406A ARG 3.1 10.7 + - - +
408A VAL* 1.3 79.8 - - - +
410A CYS* 1.3 58.3 + - - +
412A SER* 3.3 5.5 + - - -
413A LEU* 2.9 32.8 + - - +
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Residues in contact with CYS 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332A LEU* 6.2 0.2 - - - -
339A HIS* 4.4 11.4 - - - -
406A ARG* 4.6 3.6 - - - -
407A ALA* 3.0 12.6 + - - +
409A ASP* 1.3 77.2 - - - +
411A TRP* 1.3 65.9 + - - +
413A LEU* 3.4 10.6 + - - +
414A GLY 3.1 17.0 + - - -
466A LEU* 3.7 18.4 - - + +
474A ARG* 4.1 7.6 - - - -
475A PHE 3.4 27.1 - - - +
476A THR* 3.9 3.8 - - - -
477A THR* 3.7 35.7 - - - -
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Residues in contact with TRP 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407A ALA 3.0 6.1 + - - -
408A VAL* 3.5 10.8 - - - +
410A CYS* 1.3 75.0 - - - +
412A SER* 1.3 68.3 + - - +
414A GLY* 3.0 11.4 + - - -
415A VAL* 3.0 25.6 + - + +
427A PHE* 3.5 36.2 - + - -
440A ILE* 4.1 35.9 - - + +
443A GLY* 4.7 4.7 - - - -
466A LEU 3.9 8.7 - - - -
467A LEU* 3.5 45.6 - - + +
468A VAL 3.7 21.5 - - - -
469A VAL* 4.3 5.2 - - + -
474A ARG* 3.6 24.7 - - - +
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Residues in contact with SER 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346A ARG 5.3 4.7 + - - -
347A ASP* 5.5 0.3 - - - -
348A LEU* 3.6 37.3 + - - +
408A VAL* 3.0 15.3 + - - +
409A ASP* 3.3 11.2 + - - -
411A TRP* 1.3 82.1 - - - +
413A LEU* 1.3 58.3 + - - +
415A VAL* 3.2 7.2 + - - +
416A ILE* 2.9 35.3 + - - +
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Residues in contact with LEU 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328A PHE* 3.2 29.7 - - + -
331A MET* 3.8 34.5 - - + -
332A LEU* 3.9 24.2 - - + -
335A VAL* 4.0 33.2 - - + -
348A LEU* 4.3 10.3 - - + -
366A ILE* 6.4 0.4 - - + -
409A ASP 2.9 21.1 + - - +
410A CYS* 3.6 12.8 - - - +
411A TRP 3.2 0.2 - - - -
412A SER* 1.3 75.8 - - - +
414A GLY* 1.3 57.9 + - - +
416A ILE* 3.4 7.8 + - + +
417A LEU* 2.8 24.8 + - - +
466A LEU* 4.9 2.9 - - + -
477A THR* 4.4 4.5 - - + -
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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