Contacts of the helix formed by residues 381 - 388 (chain A) in PDB entry 2WWA
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 PHE 381 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A LEU* 4.4 15.0 - - + -
95A GLN* 3.8 34.7 - - + +
96A LEU* 5.0 7.0 - - + -
295A SER* 3.5 22.3 + - - +
298A PHE* 3.5 45.9 - + + -
299A SER* 3.9 4.7 - - - -
302A ILE* 4.3 19.7 - - + -
377A THR* 3.4 38.3 + - + +
380A TRP* 1.4 96.6 - + - +
382A ALA* 1.4 59.2 + - - +
383A ASP 3.4 0.4 - - - -
384A LYS* 3.8 7.9 - - + +
385A TRP* 3.2 25.3 + - - +
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Residues in contact with ALA 382 (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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295A SER* 3.4 11.1 + - - +
378A GLY 3.6 18.1 + - - +
379A ILE* 3.7 11.4 - - - +
380A TRP 3.3 0.6 - - - -
381A PHE* 1.4 78.5 - - - +
383A ASP* 1.4 55.9 + - - +
384A LYS 3.4 0.2 - - - -
385A TRP* 3.6 7.3 - - - +
386A GLN* 3.3 22.5 + - - +
427A ALA* 4.4 4.9 - - - +
428A VAL* 3.8 31.3 - - + +
431A ALA* 4.2 5.8 - - + -
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Residues in contact with ASP 383 (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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101A LYS* 5.5 2.4 + - - -
379A ILE 2.8 21.5 + - - +
380A TRP* 3.3 13.6 - - - +
382A ALA* 1.4 75.8 - - + +
384A LYS* 1.4 81.7 + - - +
385A TRP 3.3 0.7 - - - -
386A GLN* 3.9 19.2 - - - +
387A ALA* 3.2 23.6 + - - +
428A VAL* 5.2 6.5 - - + -
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Residues in contact with LYS 384 (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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95A GLN* 3.3 37.0 - - + +
96A LEU* 5.3 1.3 - - - -
99A GLY* 3.3 33.7 + - - +
100A LEU* 4.1 7.5 - - - +
380A TRP* 3.3 63.0 + - - +
381A PHE* 3.7 15.2 + - + +
382A ALA 3.4 0.4 - - - -
383A ASP* 1.4 90.5 + - - +
385A TRP* 1.4 59.6 + - - +
386A GLN 3.4 0.2 - - - -
387A ALA* 3.7 3.8 - - - +
388A ILE* 3.0 34.0 + - - +
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Residues in contact with TRP 385 (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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95A GLN* 3.4 18.1 + - - -
291A THR* 4.6 24.8 + - + +
294A LEU* 3.7 37.7 - - + -
295A SER* 5.5 7.0 - - - -
298A PHE* 4.0 27.6 - + - -
381A PHE 3.2 17.6 + - - +
382A ALA* 3.6 8.3 - - - +
384A LYS* 1.4 74.3 - - - +
386A GLN* 1.4 62.0 + - - +
388A ILE* 2.9 28.9 - - + +
389A SER 3.7 4.9 - - - +
390A GLY* 5.8 3.8 - - - -
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Residues in contact with GLN 386 (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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382A ALA 3.3 11.3 + - - +
383A ASP* 4.0 15.0 - - - +
384A LYS 3.4 0.2 - - - -
385A TRP* 1.4 80.9 - - - +
387A ALA* 1.4 61.2 + - - +
388A ILE 3.6 0.3 + - - -
389A SER 4.0 7.5 - - - +
392A SER* 3.9 18.3 + - - +
393A ALA* 3.8 27.9 - - + +
424A PRO* 4.1 18.4 + - - +
427A ALA* 5.8 4.6 - - + +
428A VAL* 4.2 22.2 - - - +
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Residues in contact with ALA 387 (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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98A ALA 5.8 0.2 - - - +
99A GLY* 4.9 4.0 - - - +
101A LYS* 4.0 30.1 - - - +
107A PHE* 5.6 1.4 - - - -
383A ASP 3.2 18.0 + - - +
384A LYS* 3.7 7.6 - - - +
385A TRP 3.4 0.2 - - - -
386A GLN* 1.4 80.3 - - - +
388A ILE* 1.4 61.8 + - + +
389A SER 3.4 5.4 + - - -
392A SER* 5.4 1.6 + - - -
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Residues in contact with ILE 388 (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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94A LEU 4.7 0.7 - - - +
95A GLN* 3.7 40.6 - - - +
98A ALA* 3.6 32.5 - - + +
99A GLY* 4.0 5.6 - - - +
107A PHE* 3.6 34.5 - - + -
116A PHE* 5.3 5.6 - - + -
384A LYS 3.0 18.0 + - - +
385A TRP* 2.9 22.6 - - + +
387A ALA* 1.4 78.5 - - + +
389A SER* 1.4 71.3 + - - +
390A GLY 3.7 0.7 + - - -
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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