Contacts of the strand formed by residues 438 - 443 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383C VAL* 3.5 14.4 - - + +
385C ILE* 4.0 26.2 - - + -
422C THR* 4.0 25.1 - - + +
425C ALA* 4.1 3.6 - - + +
426C ALA* 3.7 28.0 - - + +
429C ALA* 4.1 16.6 - - + -
436C LYS 4.2 1.7 + - - +
437C ARG* 1.3 79.2 - - - +
439C ILE* 1.3 64.1 + - - +
463C LYS 5.3 1.0 + - - -
464C PRO* 3.3 14.1 - - + +
465C TYR* 2.9 27.6 + - - -
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Residues in contact with ILE 439 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377C PHE* 3.6 26.5 - - + -
378C LEU* 3.8 14.4 - - + -
382C ASP* 3.2 37.7 - - + +
383C VAL 2.8 12.1 + - - +
384C VAL* 3.4 7.7 - - + +
385C ILE* 2.8 29.2 + - - +
437C ARG* 3.8 8.5 - - + +
438C VAL* 1.3 80.3 - - - +
440C LEU* 1.3 60.6 + - - +
441C PHE* 3.7 29.2 - - + -
465C TYR* 3.7 15.7 - - + -
467C PHE* 4.1 12.3 - - + -
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Residues in contact with LEU 440 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385C ILE* 3.5 10.3 - - + +
418C THR* 3.4 37.5 - - - +
419C THR* 4.6 7.4 - - + +
422C THR* 3.5 27.8 - - + +
438C VAL 4.2 0.2 - - - -
439C ILE* 1.3 74.4 - - - +
441C PHE* 1.3 74.1 + - - +
442C ILE* 3.9 29.4 - - + +
447C LEU* 6.0 1.3 - - + -
465C TYR 2.9 12.1 + - - +
466C LEU* 3.8 25.6 - - + -
467C PHE* 2.8 35.2 + - - +
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Residues in contact with PHE 441 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370C MET* 4.2 9.9 - - + -
371C TRP* 3.6 28.0 - + + -
374C LEU* 3.6 40.6 - - + -
384C VAL* 5.1 5.6 - - + -
385C ILE 2.8 15.3 + - - +
386C ALA* 3.5 4.0 - - + -
387C GLU* 2.9 27.4 + - - +
391C SER* 3.7 16.6 - - - +
395C ILE* 5.3 0.7 - - + -
439C ILE* 3.7 24.9 - - + -
440C LEU* 1.3 75.7 - - - +
442C ILE* 1.3 61.2 + - - +
467C PHE* 3.5 37.5 - + + -
469C LEU* 4.0 12.1 - - + -
518C TRP* 4.0 13.0 - + - -
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Residues in contact with ILE 442 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387C GLU* 3.9 7.9 - - + +
391C SER* 4.2 4.9 + - - -
418C THR* 3.4 21.8 - - - +
419C THR* 3.1 29.2 - - - +
440C LEU* 3.9 18.2 - - + -
441C PHE* 1.3 75.6 - - - +
443C GLY* 1.3 71.8 + - - +
446C SER* 3.9 10.1 - - - +
447C LEU* 3.6 30.1 - - + +
450C THR* 4.9 0.4 - - - +
466C LEU* 5.8 0.9 - - + -
467C PHE 3.0 15.1 + - - +
468C VAL* 3.3 17.6 - - + -
469C LEU* 2.9 23.1 + - - +
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Residues in contact with GLY 443 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387C GLU* 4.4 5.7 - - - +
388C THR 5.7 0.4 + - - -
391C SER* 4.6 4.1 + - - -
442C ILE* 1.3 79.9 - - - +
444C ASP* 1.3 67.1 + - - -
445C GLY 3.2 2.6 + - - -
446C SER 3.3 0.7 + - - -
447C LEU* 3.0 23.2 + - - +
468C VAL* 4.6 1.1 - - - -
469C LEU* 3.9 12.6 - - - -
600C TPP 3.4 27.0 + - - -
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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