Contacts of the strand formed by residues 355 - 363 (chain A) in PDB entry 6X70
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 THR 355 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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353A LYS 3.6 4.4 + - - -
354A ASP* 1.3 74.7 - - - +
356A TYR* 1.3 67.8 + - - +
357A ILE* 6.3 0.4 - - + -
474A ILE* 3.5 5.7 - - - +
475A ILE* 2.8 49.8 + - + +
477A ASP* 4.2 18.4 + - - -
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Residues in contact with TYR 356 (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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350A ILE* 3.9 19.7 - - + -
354A ASP 3.6 17.5 - - - -
355A THR* 1.3 82.3 - - - +
357A ILE* 1.3 65.7 + - - +
358A ILE* 3.8 24.5 - - + -
472A VAL* 3.9 17.0 - - + -
473A ARG 3.2 12.8 - - - +
474A ILE* 4.5 5.8 - - + -
475A ILE* 4.4 1.6 - - - +
512A ASP* 4.1 31.8 + - - +
513A SER* 5.2 1.8 - - - -
514A LEU 5.7 0.2 - - - -
603A ASP* 4.9 2.9 + - - -
608A LEU* 3.6 26.3 - - - +
611A LEU* 3.6 18.6 - - + +
612A TYR* 4.1 17.0 + - - -
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Residues in contact with ILE 357 (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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355A THR* 6.3 0.4 - - + -
356A TYR* 1.3 78.6 - - - +
358A ILE* 1.3 66.6 + - - +
359A PHE* 3.6 14.3 + - + -
471A CYS 3.9 0.7 - - - +
472A VAL* 3.7 3.5 - - - +
473A ARG* 2.8 36.8 + - + +
475A ILE* 3.5 25.4 - - + -
481A ASN* 3.1 35.0 - - - +
486A ASN* 3.6 14.4 - - - +
510A CYS* 3.6 27.8 - - - -
511A SER 3.4 11.7 - - - +
533A PHE* 4.0 14.6 - - + -
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Residues in contact with ILE 358 (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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356A TYR* 3.8 29.6 - - + -
357A ILE* 1.3 73.7 - - - +
359A PHE* 1.3 67.8 + - - +
360A HIS* 4.2 2.7 - - + +
470A VAL* 3.9 21.3 - - + -
471A CYS 3.8 1.3 - - - +
472A VAL* 4.2 16.2 - - + -
509A GLY 3.6 0.7 - - - +
510A CYS* 3.1 9.0 - - - +
511A SER 2.8 37.4 + - - +
513A SER 4.0 19.5 - - - +
514A LEU* 4.0 21.8 - - + +
517A ALA* 3.4 24.5 - - + -
611A LEU* 4.3 7.0 - - + -
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Residues in contact with PHE 359 (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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357A ILE* 3.6 25.1 - - + -
358A ILE* 1.3 75.2 - - - +
360A HIS* 1.3 61.9 + - - +
361A ILE* 3.8 8.0 + - + +
458A PHE* 3.9 26.9 - + + -
469A ALA 3.9 0.2 - - - +
471A CYS* 2.8 44.8 + - - +
473A ARG* 4.3 17.9 - - + -
486A ASN* 3.8 21.1 - - + -
489A LEU* 4.0 21.8 - - + -
490A CYS* 3.7 25.1 - - - -
493A ILE* 3.9 15.3 - - + -
508A ILE* 4.2 7.2 - - + -
509A GLY 3.6 2.7 - - - -
510A CYS* 3.7 21.1 - - - -
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Residues in contact with HIS 360 (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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358A ILE* 3.9 4.5 - - + +
359A PHE* 1.3 69.7 - - - +
361A ILE* 1.3 63.3 + - - +
464A ILE* 4.6 2.0 - - + +
468A GLU* 2.6 35.8 + - + +
469A ALA 3.7 10.1 - - - -
470A VAL* 3.5 25.4 - - + +
508A ILE* 3.4 4.4 - - - +
509A GLY 2.7 37.5 + - - +
514A LEU* 4.8 4.0 + - - +
517A ALA* 3.9 20.1 - - + +
518A ARG* 4.0 35.1 + - + +
521A LEU* 3.6 21.7 - - + +
12P G 5.4 0.9 - - - -
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Residues in contact with ILE 361 (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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359A PHE* 3.9 11.0 - - + +
360A HIS* 1.3 77.0 - - - +
362A ASP* 1.3 64.5 + - - +
448A PHE* 3.7 27.4 - - + -
452A LEU* 3.7 25.6 - - + -
458A PHE* 4.3 10.1 - - + -
468A GLU* 3.2 8.1 - - - +
469A ALA 2.9 34.8 + - - +
471A CYS* 4.1 13.9 - - - -
493A ILE* 3.8 17.7 - - + -
497A ILE* 4.2 1.6 - - + -
506A VAL* 3.9 23.6 - - + -
507A SER 3.6 5.4 - - - +
508A ILE* 4.0 13.9 - - + -
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Residues in contact with ASP 362 (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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361A ILE* 1.3 77.7 - - - +
363A PHE* 1.3 76.4 + - - +
467A ASP* 2.9 29.0 - - - +
468A GLU* 3.4 23.0 - - + +
506A VAL* 4.0 4.5 - - - -
507A SER* 2.9 32.1 + - - -
521A LEU* 3.8 23.6 - - + +
525A LYS* 3.3 26.7 + - - -
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Residues in contact with PHE 363 (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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362A ASP* 1.3 89.0 + - - +
364A ASP* 1.3 63.8 + - - +
365A CYS 3.6 2.4 + - - -
366A PHE* 3.4 43.9 + + + -
369A THR* 5.9 1.1 - - + -
444A LYS* 4.0 11.2 - - + -
445A SER* 5.3 0.2 - - - -
448A PHE* 3.4 50.0 - + + -
466A ILE 4.8 1.1 - - - -
467A ASP* 3.1 35.7 + - + +
497A ILE* 4.6 0.4 - - + -
501A THR* 4.1 10.3 - - + -
504A CYS* 3.5 37.7 - - + -
505A THR 3.4 10.5 - - - -
506A VAL* 3.8 10.5 - - + -
525A LYS* 5.3 2.0 + - - -
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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