Contacts of the strand formed by residues 438 - 443 (chain B) 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 VAL 438 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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383B VAL* 3.5 13.0 - - + +
385B ILE* 3.9 26.7 - - + -
422B THR* 4.0 25.6 - - + +
425B ALA* 4.1 5.8 - - + +
426B ALA* 3.9 15.3 - - + -
429B ALA* 3.8 27.8 - - + -
436B LYS 4.1 1.8 + - - +
437B ARG* 1.3 78.7 - - - +
439B ILE* 1.3 63.1 + - - +
440B LEU 4.2 0.2 - - - -
463B LYS 5.4 1.0 + - - -
464B PRO* 3.3 15.7 - - + +
465B TYR* 2.9 27.1 + - - -
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Residues in contact with ILE 439 (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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377B PHE* 3.6 25.6 - - + -
378B LEU* 3.8 14.1 - - + -
382B ASP* 3.2 35.9 - - + +
383B VAL 2.8 13.2 + - - +
384B VAL* 3.4 8.4 - - + +
385B ILE* 2.8 34.3 + - - +
437B ARG* 3.8 9.4 - - + +
438B VAL* 1.3 79.0 - - - +
440B LEU* 1.3 57.4 + - - +
441B PHE* 3.8 28.0 - - + -
465B TYR* 3.7 18.4 - - + -
467B PHE* 4.1 12.6 - - + -
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Residues in contact with LEU 440 (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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385B ILE* 3.5 10.8 - - + +
418B THR* 3.4 35.9 - - - +
419B THR* 4.6 7.2 - - + +
422B THR* 3.5 28.3 - - + +
438B VAL 4.2 0.4 - - - -
439B ILE* 1.3 73.9 - - - +
441B PHE* 1.3 76.6 + - - +
442B ILE* 3.8 30.1 - - + -
447B LEU* 6.0 0.7 - - + -
465B TYR 2.9 14.0 + - - +
466B LEU* 3.8 24.5 - - + -
467B PHE* 2.8 36.7 + - - +
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Residues in contact with PHE 441 (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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370B MET* 4.4 8.5 - - + -
371B TRP* 3.6 28.9 - + + -
374B LEU* 3.7 40.4 - - + -
384B VAL* 5.2 5.2 - - + -
385B ILE 2.9 14.7 + - - +
386B ALA* 3.6 4.1 - - + -
387B GLU* 2.9 27.9 + - - +
391B SER* 3.5 16.3 + - - +
395B ILE* 5.2 1.1 - - + -
439B ILE* 3.8 24.5 - - + -
440B LEU* 1.3 76.1 - - - +
442B ILE* 1.3 61.3 + - - +
467B PHE* 3.4 38.8 - + + -
469B LEU* 4.0 13.5 - - + -
518B TRP* 3.9 13.7 - + - -
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Residues in contact with ILE 442 (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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387B GLU* 3.9 7.6 - - + +
391B SER* 4.3 3.8 - - - -
416B GLY* 5.0 0.2 - - - -
418B THR* 3.3 19.3 - - - +
419B THR* 3.2 28.0 - - - +
440B LEU* 3.8 24.2 - - + -
441B PHE* 1.3 75.4 - - - +
443B GLY* 1.3 72.2 + - - +
446B SER* 3.9 12.1 - - - +
447B LEU* 3.7 26.9 - - + +
450B THR* 5.0 0.2 - - - +
466B LEU* 5.7 0.9 - - + -
467B PHE 2.9 14.8 + - - +
468B VAL* 3.3 18.3 - - + -
469B LEU* 2.9 24.1 + - - +
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Residues in contact with GLY 443 (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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387B GLU* 4.3 5.9 - - - +
388B THR 5.8 0.2 + - - -
391B SER* 4.4 4.2 + - - -
442B ILE* 1.3 78.2 - - - +
444B ASP* 1.3 60.7 + - - -
445B GLY 3.2 2.5 - - - -
446B SER 3.3 1.0 + - - -
447B LEU* 2.9 30.2 + - - +
468B VAL* 4.7 0.7 - - - -
469B LEU* 4.0 9.4 - - - -
600B TPP 3.2 30.2 + - - -
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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