Contacts of the helix formed by residues 366 - 374 (chain A) in PDB entry 2W93
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 LYS 366 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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364A PRO* 3.5 10.6 + - + +
365A LEU* 1.3 80.7 - - - +
367A GLN* 1.3 66.2 + - - +
368A GLU* 3.3 6.3 - - + +
369A TRP* 3.3 15.8 + - + +
370A MET* 3.0 21.1 + - - +
540A LEU* 4.2 4.9 - - - -
541A PRO* 4.4 10.4 - - + +
544A ASP* 3.3 28.7 + - - +
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Residues in contact with GLN 367 (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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366A LYS* 1.3 71.8 - - - +
368A GLU* 1.3 64.9 + - - +
370A MET* 3.0 16.8 + - + -
371A TRP* 2.8 46.6 + - + +
390A THR* 2.9 33.4 + - - +
469A LEU* 4.2 5.9 - - - +
471A ASN* 4.2 7.1 - - - +
540A LEU* 3.9 29.5 - - + +
544A ASP* 2.7 34.3 + - - +
545A ALA* 3.9 19.3 - - - -
546A PRO* 3.3 11.4 - - - +
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Residues in contact with GLU 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A ASN* 4.8 0.2 - - - +
366A LYS* 3.3 4.7 - - + +
367A GLN* 1.3 79.6 - - - +
369A TRP* 1.3 63.2 + - - +
371A TRP* 4.5 1.2 - - - +
372A ASN* 3.5 19.6 + - - +
397A GLN* 2.9 27.2 + - - +
544A ASP* 5.0 0.6 + - - -
545A ALA 4.6 5.4 + - - +
546A PRO* 3.5 2.0 - - + +
547A GLN* 2.8 41.4 + - - +
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Residues in contact with TRP 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A ASN* 2.9 50.3 + - + +
357A ALA 4.7 2.7 + - - -
359A VAL* 4.3 18.6 - - + +
363A THR* 6.3 0.9 - - + -
365A LEU* 3.5 30.1 - - + -
366A LYS* 3.3 17.4 + - + +
367A GLN 3.2 0.4 - - - -
368A GLU* 1.3 78.3 - - - +
370A MET* 1.3 65.1 + - - +
372A ASN 3.4 1.4 + - - -
373A GLN* 2.9 60.7 + - + -
515A THR* 3.5 33.6 + - - -
518A TRP* 3.7 18.8 - + - -
519A ASP* 3.7 13.7 - - - -
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Residues in contact with MET 370 (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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365A LEU* 5.1 4.0 - - + -
366A LYS 3.0 17.5 + - - +
367A GLN* 3.0 5.6 + - + +
369A TRP* 1.3 90.4 - - + +
371A TRP* 1.3 105.7 + - + +
373A GLN* 3.2 2.1 + - - +
374A LEU* 2.9 28.2 + - + +
441A PHE* 4.4 2.7 - - + -
469A LEU* 4.1 17.9 - - + -
518A TRP* 3.6 41.3 - - + -
538A VAL* 3.9 21.1 - - - -
540A LEU* 4.6 9.4 - - + -
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Residues in contact with TRP 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A GLN* 2.8 52.5 + - + +
368A GLU 4.6 1.8 - - - +
370A MET* 1.3 94.4 - - + +
372A ASN* 1.3 62.3 + - - +
374A LEU* 3.6 20.6 + - + +
391A SER* 3.6 33.9 - - - -
394A GLY* 3.3 39.0 - - - +
395A ILE* 4.0 12.1 - - + -
397A GLN* 4.3 11.0 - - + +
398A THR* 2.7 42.0 + - - +
441A PHE* 3.7 37.0 - + + -
469A LEU* 3.9 8.7 - - + -
546A PRO* 4.4 8.3 - - + +
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Residues in contact with ASN 372 (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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352A ARG* 5.7 2.6 + - - -
353A THR* 3.5 29.2 - - - +
354A PRO 3.0 24.7 + - - +
355A ALA* 3.8 2.2 - - - +
356A ASN* 3.0 31.4 + - - +
368A GLU 3.5 16.3 + - - +
369A TRP 3.4 4.2 + - - +
371A TRP* 1.3 79.3 - - - +
373A GLN* 1.3 61.8 + - - +
374A LEU 3.4 0.3 + - - -
375A GLY* 3.8 7.8 + - - -
376A ASN* 5.0 2.6 - - - +
397A GLN* 4.4 12.0 + - + +
398A THR* 5.3 0.2 - - - +
399A THR* 5.6 2.3 + - - -
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Residues in contact with GLN 373 (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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356A ASN* 2.8 29.6 + - - +
369A TRP* 2.9 48.8 + - + +
370A MET 3.7 3.4 - - - +
372A ASN* 1.3 76.7 - - - +
374A LEU* 1.3 66.6 + - - +
376A ASN* 2.9 47.7 + - + +
377A PHE 4.2 0.7 + - - -
518A TRP* 3.9 11.1 + - - +
519A ASP* 2.9 34.0 + - - +
523A GLN* 5.1 1.4 - - - +
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Residues in contact with LEU 374 (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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370A MET* 2.9 16.8 + - + +
371A TRP* 3.7 17.3 - - + +
372A ASN 3.3 1.0 - - - -
373A GLN* 1.3 76.8 - - - +
375A GLY* 1.3 57.9 + - - +
377A PHE* 2.9 39.9 + - + +
378A LEU* 3.3 19.8 + - + +
384A VAL* 5.2 0.7 - - + -
395A ILE* 3.7 27.4 - - + -
398A THR* 3.9 11.0 - - + +
441A PHE* 3.6 43.5 - - + -
467A PHE* 5.5 0.2 - - + -
518A TRP* 4.0 18.4 - - + +
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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