Contacts of the helix formed by residues 478 - 494 (chain A) in PDB entry 1ZVR
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 PRO 478 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359A MET* 4.0 13.2 - - + +
360A ARG* 3.9 17.3 - - - +
363A LEU* 3.8 20.0 - - + -
388A TRP* 4.0 14.4 - - + -
477A SER* 1.3 87.6 - - - +
479A VAL* 1.3 62.4 + - - +
481A LEU* 3.8 25.8 - - + -
482A GLN* 3.0 23.9 + - + +
513A TYR* 5.3 0.2 - - - +
1878A EDO 3.4 13.7 - - - +
1880A EDO 4.2 13.4 - - - +
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Residues in contact with VAL 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A ILE* 4.1 13.7 - - + -
359A MET* 6.0 2.5 - - + -
422A ASP* 3.4 36.6 - - + +
423A ARG* 4.7 0.7 - - + +
426A GLN* 3.0 45.5 + - + +
453A TRP* 4.0 2.5 - - + -
458A HIS* 3.6 23.6 - - + -
463A ARG* 4.3 1.8 - - - -
477A SER* 3.0 26.0 + - - +
478A PRO* 1.3 70.1 - - - +
480A PHE* 1.3 62.3 + - - +
482A GLN* 3.3 5.0 + - - +
483A PHE* 3.2 10.7 + - - +
1878A EDO 3.6 0.7 - - - +
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Residues in contact with PHE 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A VAL* 4.2 13.0 - - + -
453A TRP* 3.6 43.9 - + + -
460A PHE* 3.6 23.3 - + + -
479A VAL* 1.3 70.6 - - - +
481A LEU* 1.3 66.2 + - - +
483A PHE* 3.2 20.7 + + - +
484A ILE* 3.0 49.5 + - + +
508A ILE* 3.7 18.8 - - + -
509A LEU* 4.6 1.6 - - + -
512A LEU* 4.0 18.2 - - + -
520A PHE* 3.9 22.9 - + - -
1878A EDO 2.8 23.6 + - - +
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Residues in contact with LEU 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A LYS 6.1 0.2 - - - +
158A ILE* 5.2 2.0 - - + -
363A LEU* 4.0 17.7 - - + -
388A TRP* 4.4 3.4 - - + -
478A PRO* 3.6 28.9 - - + +
479A VAL 3.3 0.4 - - - -
480A PHE* 1.3 78.0 - - - +
482A GLN* 1.3 57.4 + - - +
484A ILE* 3.2 2.6 + - - -
485A ASP* 2.8 27.5 + - - +
509A LEU* 3.5 39.3 - - + -
512A LEU* 4.9 1.1 - - + +
513A TYR* 4.5 14.1 - - - +
576A TRP* 5.1 2.0 - - + -
579A TYR* 3.8 21.8 - - + +
580A TYR* 4.0 27.4 - - + +
1878A EDO 3.2 9.8 + - - +
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Residues in contact with GLN 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A MET* 3.2 48.0 - - - +
388A TRP* 3.6 28.3 - - + -
391A HIS* 3.7 17.0 - - - +
392A ILE* 3.9 7.8 - - + +
395A ILE* 3.3 16.2 - - + +
426A GLN* 3.0 26.3 + - - +
478A PRO 3.0 19.1 + - - +
479A VAL* 3.5 4.4 - - - +
481A LEU* 1.3 75.8 - - - +
483A PHE* 1.3 57.4 + - - +
485A ASP* 3.1 10.1 + - - +
486A CYS* 2.8 34.7 + - - -
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Residues in contact with PHE 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A GLN* 4.1 9.1 - - + +
429A SER* 3.1 33.0 - - - -
430A LEU* 3.6 26.2 - - + -
433A LEU* 4.2 4.9 - - + -
445A PHE* 3.9 18.4 - + - -
448A LEU* 4.4 4.0 - - + -
449A VAL* 4.8 2.7 - - + -
453A TRP* 3.5 35.4 - + + -
479A VAL 3.2 3.4 + - - +
480A PHE* 3.3 24.5 - + - +
481A LEU 3.2 0.2 - - - -
482A GLN* 1.3 79.0 - - - +
484A ILE* 1.3 80.8 + - + +
486A CYS* 3.0 10.6 + - - +
487A VAL* 2.8 50.0 + - + +
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Residues in contact with ILE 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A PHE* 4.0 20.0 - - + -
480A PHE* 3.0 44.6 + - + +
481A LEU 3.7 6.5 - - - +
483A PHE* 1.3 95.0 - - + +
485A ASP* 1.3 56.7 + - - +
487A VAL* 3.1 4.4 + - - +
488A TRP* 2.8 28.1 + - - +
505A LEU* 3.8 28.0 - - + +
508A ILE* 4.3 7.2 - - + -
509A LEU* 3.8 34.8 - - + -
576A TRP* 3.9 2.9 - - + -
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Residues in contact with ASP 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A TRP* 3.2 10.2 + - - -
389A LEU* 5.6 1.2 - - - +
392A ILE* 3.6 16.9 - - + +
481A LEU 2.8 14.5 + - - +
482A GLN* 3.2 10.1 - - - +
484A ILE* 1.3 76.6 - - - +
486A CYS* 1.3 57.1 + - - +
488A TRP* 3.2 6.1 + - - +
489A GLN* 3.0 46.0 + - - +
576A TRP* 3.9 19.1 + - + +
580A TYR* 2.6 40.5 + - - +
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Residues in contact with CYS 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A ILE* 3.7 30.3 - - - -
395A ILE* 3.8 23.8 - - - -
396A LEU* 3.8 18.1 - - + +
430A LEU* 3.7 19.1 - - + -
482A GLN 2.8 17.4 + - - -
483A PHE 3.0 7.8 + - - +
485A ASP* 1.3 73.8 - - - +
487A VAL* 1.3 66.5 + - - +
489A GLN* 3.3 12.6 + - - +
490A MET* 3.3 24.6 + - - +
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Residues in contact with VAL 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A LEU* 4.0 2.0 - - + -
433A LEU* 3.7 14.4 - - + -
445A PHE* 3.9 12.8 - - + -
483A PHE* 2.8 54.4 + - + +
484A ILE* 3.4 9.0 - - - +
486A CYS* 1.3 76.3 - - - +
488A TRP* 1.3 64.8 + - - +
490A MET* 3.0 20.7 + - - +
491A THR* 3.1 11.6 + - + +
498A PHE* 4.8 4.0 - - + -
500A PHE* 3.8 33.4 - - + -
505A LEU* 4.2 5.6 - - + -
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Residues in contact with TRP 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A ILE 2.8 13.5 + - - +
485A ASP 3.4 7.6 - - - +
487A VAL* 1.3 77.7 - - - +
489A GLN* 1.3 92.6 + - - +
491A THR* 2.5 36.2 + - - -
492A ARG* 3.0 44.2 + - + +
502A GLU* 3.5 23.7 + - + +
505A LEU* 3.7 15.5 - - + +
574A GLU* 4.0 16.4 - - + -
575A LEU 4.4 4.0 - - - -
576A TRP* 3.3 80.6 - + + +
577A VAL 4.9 1.1 - - - -
578A GLY 5.6 0.4 - - - -
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Residues in contact with GLN 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A LEU* 4.3 6.2 - - - +
392A ILE* 4.1 7.8 - - + +
396A LEU* 4.0 6.3 - - + -
485A ASP* 3.0 37.2 + - - +
486A CYS* 3.5 12.3 - - - +
487A VAL 3.2 0.2 - - - -
488A TRP* 1.3 89.3 - - - +
490A MET* 1.3 62.2 + - - +
492A ARG* 3.2 7.8 + - - +
493A GLN* 3.0 27.8 + - - +
566A PRO* 6.0 0.7 - - + -
572A HIS 4.6 1.6 + - - -
573A LEU* 3.4 32.9 - - + +
574A GLU* 2.9 46.1 + - - +
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Residues in contact with MET 490 (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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396A LEU* 4.2 4.5 - - + -
430A LEU* 3.5 33.2 - - + +
433A LEU* 3.9 27.6 - - + -
434A MET* 4.1 32.5 - - - -
486A CYS 3.3 11.2 + - - +
487A VAL* 3.0 10.5 + - - +
489A GLN* 1.3 76.2 - - + +
491A THR* 1.3 61.7 + - - +
493A GLN* 3.3 5.1 + - - +
494A PHE* 2.8 38.1 + - + +
498A PHE* 3.8 20.2 - - + -
564A LEU* 5.1 5.2 - - + -
566A PRO* 4.0 22.9 - - + -
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Residues in contact with THR 491 (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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487A VAL 3.1 12.7 + - - +
488A TRP* 2.5 38.5 + - - -
490A MET* 1.3 76.5 - - - +
492A ARG* 1.3 63.2 + - - +
494A PHE 3.2 18.5 - - - +
495A PRO* 3.2 10.7 - - - +
498A PHE* 3.7 33.7 - - + -
500A PHE* 3.9 23.1 - - + +
501A ASN 6.0 2.2 - - - -
502A GLU* 5.9 2.0 - - - -
505A LEU* 4.5 3.6 - - + -
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Residues in contact with ARG 492 (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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488A TRP* 3.0 55.7 + - + +
489A GLN* 3.4 10.8 - - - +
490A MET 3.2 0.2 - - - -
491A THR* 1.3 85.8 + - - +
493A GLN* 1.3 63.4 + - + +
494A PHE 3.4 0.2 + - - -
495A PRO* 3.6 11.0 - - - +
574A GLU* 3.8 31.7 + - - +
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Residues in contact with GLN 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A LEU* 6.0 0.2 - - - +
489A GLN* 3.0 18.4 + - - +
490A MET* 3.3 2.0 + - - +
492A ARG* 1.3 79.1 - - + +
494A PHE* 1.3 82.8 + - + +
495A PRO* 3.8 5.1 - - - +
566A PRO* 3.2 14.6 - - - +
567A VAL* 2.9 51.9 + - - +
572A HIS* 3.6 28.6 + - + +
573A LEU* 4.1 10.5 - - - +
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Residues in contact with PHE 494 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490A MET* 2.8 19.7 + - + +
491A THR* 3.2 7.5 - - - +
493A GLN* 1.3 93.8 - - + +
495A PRO* 1.4 68.8 - - - +
496A THR 3.1 4.6 + - - -
497A ALA* 3.2 27.6 + - + +
498A PHE* 3.8 10.2 - - - -
559A TYR* 3.6 32.8 - + + -
564A LEU* 3.5 21.5 - - + -
565A TYR 3.5 29.8 - - - -
566A PRO* 3.6 28.5 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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