Contacts of the strand formed by residues 392 - 403 (chain A) in PDB entry 6ZGI
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 PHE 392 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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363A ALA* 4.6 11.2 - - + -
387A LEU* 3.6 46.4 - - + -
390A LEU* 3.7 25.8 - - + -
391A CYS* 1.3 74.3 - - - +
393A THR* 1.3 61.7 + - - +
394A ASN 4.3 0.3 + - - -
395A VAL* 3.6 20.6 - - + +
515A PHE* 3.9 26.0 - + + -
516A GLU 3.8 2.9 - - - -
517A LEU* 3.6 23.8 - - + -
522A ALA* 3.5 10.5 - - - +
523A THR* 3.7 10.7 + - - +
524A VAL* 3.7 30.6 + - + +
525A CYS 4.0 4.6 - - - +
526A GLY* 4.3 8.1 - - - -
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Residues in contact with THR 393 (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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391A CYS 5.0 0.9 + - - -
392A PHE* 1.3 71.8 - - - +
394A ASN* 1.3 91.2 + - - +
395A VAL 3.5 0.9 - - - -
515A PHE* 3.5 1.7 - - - -
516A GLU* 2.9 51.2 + - + +
518A LEU 5.1 4.3 + - - -
520A ALA* 3.5 35.0 + - + -
521A PRO 3.7 15.3 - - - +
522A ALA* 3.6 13.3 - - - +
523A THR* 6.3 0.2 - - - -
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Residues in contact with ASN 394 (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 ARG* 3.1 41.4 - - - +
392A PHE 4.3 0.8 + - - -
393A THR* 1.3 92.8 - - - +
395A VAL* 1.3 61.5 + - - +
396A TYR* 3.6 12.4 + - + -
514A SER* 3.2 11.8 + - - +
515A PHE* 3.8 2.6 - - - -
516A GLU* 3.3 18.4 - - - +
520A ALA* 5.7 0.3 - - - +
523A THR* 6.1 2.6 - - - +
200B TYR* 5.4 2.3 + - + +
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Residues in contact with VAL 395 (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 ARG* 3.8 5.9 - - - +
358A ILE* 3.0 64.2 + - + +
392A PHE* 3.6 35.2 - - + -
394A ASN* 1.3 72.8 - - - +
396A TYR* 1.3 69.9 + - - +
513A LEU* 5.3 6.5 - - + -
514A SER 3.3 7.4 - - - +
515A PHE* 3.8 16.4 - - + -
524A VAL* 3.8 17.5 - - + -
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Residues in contact with TYR 396 (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 ARG* 3.9 31.6 - - + +
356A LYS 3.4 16.6 - - - -
357A ARG* 3.5 52.6 + - + -
358A ILE* 4.7 0.7 - - - +
394A ASN* 3.8 15.3 - - + -
395A VAL* 1.3 75.0 - - - +
397A ALA* 1.3 59.3 + - - +
398A ASP* 4.3 2.9 - - - +
512A VAL 3.6 0.9 - - - +
513A LEU* 3.4 6.2 - - - +
514A SER* 2.9 38.8 + - - +
200B TYR* 4.0 30.2 - + - -
228B ASP 4.9 3.3 + - - -
230B PRO* 3.4 32.5 - - + +
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Residues in contact with ALA 397 (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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341A VAL* 4.4 19.1 - - + -
354A ASN* 3.7 1.4 + - - +
355A ARG* 3.5 2.1 - - - -
356A LYS* 2.9 43.7 + - + +
358A ILE* 3.9 16.1 - - + +
396A TYR* 1.3 73.4 - - - +
398A ASP* 1.3 63.5 + - - +
399A SER* 4.2 3.6 + - - +
511A VAL* 4.4 3.1 - - + -
512A VAL 3.4 4.3 - - - +
513A LEU* 3.8 19.7 - - + -
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Residues in contact with ASP 398 (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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353A TRP* 4.0 11.4 - - + -
354A ASN 3.0 7.0 - - - +
355A ARG* 3.3 42.8 + - - +
396A TYR* 4.7 1.6 - - - +
397A ALA* 1.3 76.6 + - - +
399A SER* 1.3 63.0 + - - +
400A PHE* 4.8 4.2 - - + -
423A TYR* 2.7 30.1 + - + +
464A PHE* 3.9 5.7 - - - -
510A VAL 3.6 0.5 - - - +
511A VAL* 3.1 8.3 - - - +
512A VAL* 2.9 45.5 + - + +
514A SER* 5.4 3.9 - - - -
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Residues in contact with SER 399 (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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341A VAL* 4.7 8.7 + - - +
347A PHE* 3.8 22.8 - - - -
348A ALA* 4.0 5.9 - - - +
353A TRP* 3.9 0.7 - - - -
354A ASN* 2.9 45.7 + - - +
397A ALA* 4.8 3.8 + - - +
398A ASP* 1.3 76.8 + - - +
400A PHE* 1.3 67.6 + - - +
510A VAL 3.4 4.0 - - - -
511A VAL* 3.9 14.6 - - - +
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Residues in contact with PHE 400 (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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347A PHE* 3.5 10.4 - - - -
348A ALA 3.6 11.2 - - - +
349A SER 4.2 2.9 - - - +
350A VAL* 3.7 36.6 - - + -
353A TRP* 3.9 14.4 - - + -
398A ASP* 4.9 3.4 - - + -
399A SER* 1.3 82.0 - - - +
401A VAL* 1.3 63.3 + - - +
402A ILE* 3.9 17.3 - - + -
410A ILE* 4.1 24.0 - - + -
423A TYR* 4.1 35.0 - + - -
510A VAL* 2.9 61.8 + - + +
512A VAL* 4.6 6.3 - - + -
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Residues in contact with VAL 401 (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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347A PHE* 3.5 27.4 - - + -
348A ALA 3.4 4.1 + - - +
350A VAL* 3.9 13.3 + - - +
400A PHE* 1.3 75.4 - - - +
402A ILE* 1.3 77.6 + - - +
442A ASP* 4.6 2.2 - - - +
451A TYR* 3.8 39.5 - - + +
495A TYR* 4.5 7.5 - - + -
497A PHE* 4.3 16.4 - - + -
507A PRO* 4.4 9.9 - - + -
508A TYR 3.3 8.1 - - - +
509A ARG* 3.7 22.9 - - + +
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Residues in contact with ILE 402 (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 VAL* 3.8 28.7 - - + -
400A PHE* 3.9 5.6 - - + -
401A VAL* 1.3 79.0 - - - +
403A ARG* 1.3 67.5 + - - +
406A GLU* 3.8 21.1 - - + +
407A VAL* 3.9 32.1 - - + -
410A ILE* 4.1 13.5 - - + -
418A ILE* 4.6 7.4 - - + -
495A TYR* 4.3 8.1 - - - +
497A PHE* 4.4 6.5 - - - -
507A PRO* 3.6 4.5 - - - +
508A TYR 2.9 29.2 + - - +
510A VAL* 3.8 29.2 - - + -
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Residues in contact with ARG 403 (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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402A ILE* 1.3 89.4 - - - +
404A GLY* 1.3 63.8 + - - +
405A ASP* 3.3 11.2 - - - +
406A GLU* 3.3 47.9 + - - +
407A VAL* 3.9 2.3 + - - +
417A LYS* 4.1 9.3 - - - +
453A TYR* 4.7 10.3 + - - -
495A TYR* 3.7 42.7 + - + +
496A GLY 5.7 1.4 - - - +
497A PHE* 4.5 5.1 - - + -
504A GLY 3.1 22.4 - - - +
505A TYR* 3.2 43.7 + - - +
506A GLN 3.8 4.3 - - - -
508A TYR* 4.7 0.4 - - - -
373B SER* 3.9 16.6 + - - -
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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