Contacts of the strand formed by residues 438 - 443 (chain A) in PDB entry 3WSZ
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 MET 438 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390A LEU* 4.3 11.4 - - + -
427A THR* 4.1 7.9 - - + -
428A LEU 3.4 3.8 - - - -
429A ILE* 3.7 17.0 - - + -
437A ASN* 1.3 82.2 - - - +
439A ARG* 1.3 69.8 + - - +
482A SER* 3.4 30.5 - - - +
485A LEU* 3.6 36.8 - - + -
486A ASN* 5.1 9.6 - - - +
513A ASN* 3.1 22.3 + - - +
514A LEU* 3.3 35.4 + - + +
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Residues in contact with ARG 439 (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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427A THR* 3.4 5.7 - - - +
428A LEU* 2.7 46.0 + - + +
437A ASN 4.9 4.7 - - - +
438A MET* 1.3 82.6 - - - +
440A SER* 1.3 64.1 + - - +
441A VAL* 5.4 1.1 - - + -
452A PHE* 3.2 39.2 - - + -
472A GLY* 2.5 36.4 + - - -
476A HIS* 3.7 15.0 - - + -
512A LYS* 3.3 27.5 + - - +
514A LEU* 4.2 0.9 - - - -
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Residues in contact with SER 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A ILE* 5.0 4.6 - - - +
426A ALA 3.5 6.9 - - - -
427A THR* 4.2 5.5 + - - -
439A ARG* 1.3 75.5 + - - +
441A VAL* 1.3 68.6 + - - +
452A PHE* 4.2 3.8 - - - -
453A LEU* 3.3 29.6 + - - +
474A SER* 4.4 3.8 + - - -
475A LEU 3.8 13.1 - - - +
476A HIS* 3.3 8.1 + - - +
477A LEU* 2.8 42.7 + - - +
479A GLN* 5.9 0.3 + - - -
514A LEU* 4.4 1.9 - - - +
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Residues in contact with VAL 441 (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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386A LEU* 3.7 19.3 - - + -
425A ILE* 3.5 3.8 - - - +
426A ALA 3.0 37.6 + - - +
428A LEU* 3.6 28.9 - - + -
439A ARG* 5.4 0.9 - - + -
440A SER* 1.3 79.4 - - - +
442A ILE* 1.3 57.3 + - - +
450A TRP* 3.6 26.6 - - + -
451A GLU 3.1 19.7 - - - +
452A PHE* 3.9 20.4 - - + -
453A LEU* 3.4 5.6 - - - +
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Residues in contact with ILE 442 (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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423A VAL* 4.4 2.9 - - + -
424A TYR 3.3 13.7 - - - +
425A ILE* 3.7 20.2 - - + -
441A VAL* 1.3 75.0 - - - +
443A THR* 1.3 64.4 + - - +
444A PHE* 3.4 38.3 - - + -
450A TRP* 3.7 2.9 - - - -
451A GLU* 3.0 41.1 + - + +
453A LEU* 3.3 27.1 - - + +
454A GLN* 4.9 5.8 - - - +
526A ALA 3.6 17.0 - - - +
527A GLY* 3.9 15.9 - - - +
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Residues in contact with THR 443 (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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422A GLY 3.0 9.9 - - - +
423A VAL* 3.2 2.3 - - - +
424A TYR* 3.2 30.0 + - + +
442A ILE* 1.3 74.3 - - - +
444A PHE* 1.3 61.9 + - - +
445A ASP* 2.2 52.2 + - - +
447A GLY 3.5 5.3 + - - +
449A THR* 2.6 19.6 + - - -
450A TRP* 3.5 37.0 - - + -
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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