Contacts of the strand formed by residues 438 - 443 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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383D VAL* 3.5 12.6 - - + -
385D ILE* 3.9 26.9 - - + -
422D THR* 4.0 23.8 - - + +
425D ALA* 4.0 5.8 - - + +
426D ALA* 3.9 16.8 - - + -
429D ALA* 3.8 25.8 - - + -
436D LYS 4.1 1.8 + - - +
437D ARG* 1.3 80.0 - - - +
439D ILE* 1.3 59.0 + - - +
440D LEU 4.2 0.2 - - - -
463D LYS 5.4 1.0 + - - -
464D PRO* 3.3 14.9 - - + +
465D TYR* 2.8 33.8 + - - +
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Residues in contact with ILE 439 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377D PHE* 3.7 22.9 - - + -
378D LEU* 3.8 14.4 - - + -
382D ASP* 3.2 38.4 - - + +
383D VAL 2.8 11.1 + - - +
384D VAL* 3.5 6.5 - - + +
385D ILE* 2.9 28.3 + - - +
437D ARG* 3.9 7.4 - - + +
438D VAL* 1.3 78.9 - - - +
440D LEU* 1.3 63.3 + - - +
441D PHE* 3.7 28.5 - - + -
465D TYR* 3.7 19.7 - - + -
467D PHE* 4.0 14.1 - - + -
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Residues in contact with LEU 440 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385D ILE* 3.5 11.9 - - + +
418D THR* 3.4 34.1 - - - +
419D THR* 4.6 7.4 - - + +
422D THR* 3.3 31.4 - - + +
438D VAL 4.2 0.2 - - - -
439D ILE* 1.3 74.9 - - - +
441D PHE* 1.3 70.6 - - - +
442D ILE* 3.9 29.8 - - + -
447D LEU* 5.9 0.7 - - + -
465D TYR 2.8 13.9 + - - +
466D LEU* 3.8 24.7 - - + -
467D PHE* 2.8 36.6 + - - +
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Residues in contact with PHE 441 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370D MET* 4.4 7.6 - - + -
371D TRP* 3.9 24.2 - + + -
374D LEU* 3.6 42.8 - - + -
384D VAL* 5.2 2.5 - - + -
385D ILE 2.9 15.4 + - - +
386D ALA* 3.5 3.6 - - + -
387D GLU* 2.9 28.4 + - - +
391D SER* 3.4 19.4 + - - +
395D ILE* 5.2 4.5 - - + -
439D ILE* 3.7 25.6 - - + -
440D LEU* 1.3 73.7 - - - +
442D ILE* 1.3 60.6 + - - +
467D PHE* 3.5 39.7 - + + -
469D LEU* 4.0 12.8 - - + -
518D TRP* 4.0 13.0 - + - -
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Residues in contact with ILE 442 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387D GLU* 3.8 9.4 - - + +
391D SER* 3.9 4.0 + - - -
418D THR* 3.3 23.3 - - - +
419D THR* 3.1 29.2 - - - +
440D LEU* 3.9 18.8 - - + -
441D PHE* 1.3 74.1 - - - +
443D GLY* 1.3 73.0 + - - +
446D SER* 3.8 11.2 - - - +
447D LEU* 3.7 27.1 - - + +
450D THR* 4.9 0.4 - - - +
466D LEU* 5.7 0.9 - - + -
467D PHE 3.0 16.1 + - - +
468D VAL* 3.3 17.8 - - + -
469D LEU* 3.0 22.8 + - - +
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Residues in contact with GLY 443 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387D GLU* 4.3 5.7 - - - +
388D THR 5.7 0.2 + - - -
391D SER* 4.4 3.6 + - - -
442D ILE* 1.3 80.3 - - - +
444D ASP* 1.3 67.3 + - - -
445D GLY 3.2 2.0 - - - -
446D SER 3.3 0.7 + - - -
447D LEU* 3.0 25.1 + - - +
468D VAL* 4.6 0.4 - - - -
469D LEU* 4.0 9.2 - - - -
600D TPP 3.3 31.5 + - - -
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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