Contacts of the helix formed by residues 484 - 502 (chain A) in PDB entry 5ZR1
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 GLY 484 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A LEU* 5.7 0.2 - - - +
452A ARG* 4.8 1.9 - - - +
482A GLY 3.4 0.8 + - - -
483A VAL* 1.3 73.9 - - - +
485A LYS* 1.3 56.0 + - - +
487A LEU* 3.9 3.0 - - - +
488A THR* 3.1 30.5 + - - +
624A PHE* 4.0 3.3 - - - -
627A TYR* 3.6 2.6 + - - -
2001A AGS 2.7 53.6 + - - -
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Residues in contact with LYS 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A VAL* 4.2 10.1 - - + -
478A ALA 4.0 17.5 - - - +
479A GLY 3.4 10.1 + - - +
480A THR 3.2 23.8 + - - -
483A VAL* 3.6 6.3 - - + +
484A GLY* 1.3 76.2 - - - +
486A THR* 1.3 67.1 + - - +
487A LEU 3.2 1.3 - - - -
488A THR* 3.9 0.2 - - - +
489A VAL* 3.2 29.3 + - - +
598A VAL* 3.7 20.9 - - + +
599A ALA 3.3 25.1 - - - -
624A PHE* 3.5 25.1 - - + -
2001A AGS 3.1 43.3 + - - +
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Residues in contact with THR 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A LYS* 1.3 79.8 - - - +
487A LEU* 1.3 61.8 + - - +
489A VAL* 4.4 2.9 - - - +
490A ARG* 3.3 51.5 + - + +
564A LEU* 5.2 5.6 - - + +
566A ASP* 3.3 29.0 + - - +
598A VAL* 4.7 5.8 - - - +
2001A AGS 2.4 16.4 + - - -
2002A MG 2.1 32.5 - - - -
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Residues in contact with LEU 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A SER 5.9 0.4 - - - +
449A LEU* 4.1 21.3 - - + -
484A GLY* 3.9 6.3 - - - +
485A LYS 3.2 0.4 - - - -
486A THR* 1.3 78.3 - - - +
488A THR* 1.3 57.1 - - - +
490A ARG* 3.4 10.4 + - + +
491A GLU* 3.0 28.6 + - - +
639A ARG* 5.5 0.7 - - - +
2001A AGS 2.8 78.4 + - + +
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Residues in contact with THR 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A LEU* 3.8 27.6 - - - +
452A ARG* 4.4 5.5 + - + -
456A PHE* 3.9 22.0 - - - +
459A ILE* 4.7 5.8 - - + -
484A GLY 3.1 22.5 + - - +
485A LYS 3.9 2.7 - - - +
486A THR 3.5 0.2 - - - -
487A LEU* 1.3 74.5 - - - +
489A VAL* 1.3 63.8 + - - +
491A GLU* 3.6 7.0 - - - -
492A VAL* 2.9 29.0 + - - +
624A PHE* 3.5 30.5 - - + -
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Residues in contact with VAL 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A ILE* 4.0 22.0 - - + -
477A VAL* 4.5 11.0 - - + -
485A LYS* 3.2 20.3 + - - +
486A THR* 4.4 3.1 - - - +
488A THR* 1.3 75.9 - - + +
490A ARG* 1.3 58.9 + - - +
492A VAL* 3.1 9.2 + - - +
493A VAL* 3.0 31.1 + - + +
510A TYR* 5.2 0.7 - - + +
564A LEU* 3.7 35.2 - - + -
596A ILE* 3.7 34.3 - - + -
598A VAL* 5.4 2.5 - - + -
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Residues in contact with ARG 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A THR* 3.3 39.0 + - - +
487A LEU* 3.4 9.5 + - + +
488A THR 3.4 0.4 - - - -
489A VAL* 1.3 76.9 - - - +
491A GLU* 1.3 57.8 + - - +
493A VAL* 3.5 11.7 - - + +
494A LYS* 3.2 26.5 + - - +
510A TYR* 4.0 5.6 - - + +
512A GLU* 3.3 38.6 + - - +
514A ASN* 6.2 0.2 - - - +
517A LYS* 5.3 8.9 - - - +
564A LEU* 4.8 3.6 - - + +
566A ASP* 5.0 2.4 + - - -
240D HIS* 5.5 9.9 + - - -
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Residues in contact with GLU 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A TYR 3.5 25.0 + - - +
449A LEU* 4.0 19.3 - - + +
456A PHE* 3.3 21.1 - - + -
487A LEU* 3.0 20.9 + - - +
488A THR* 3.7 10.1 - - - +
489A VAL 3.1 0.4 - - - -
490A ARG* 1.3 74.7 - - - +
492A VAL* 1.3 64.8 + - - +
494A LYS* 3.9 19.6 + - - +
495A GLU* 3.2 17.7 + - - +
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Residues in contact with VAL 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A PHE* 3.6 32.1 - - + +
459A ILE* 3.8 41.7 - - + +
460A TYR* 3.8 12.9 - - + +
463A ALA* 4.9 2.0 - - + -
488A THR 2.9 19.2 + - - +
489A VAL 3.1 8.0 + - - +
491A GLU* 1.3 75.9 - - - +
493A VAL* 1.3 63.6 + - + +
495A GLU* 3.1 18.4 + - - +
496A LEU* 3.1 31.8 + - + +
596A ILE* 5.3 1.6 - - + -
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Residues in contact with VAL 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489A VAL* 3.0 14.5 + - + +
490A ARG* 3.5 17.0 - - - +
492A VAL* 1.3 79.4 - - + +
494A LYS* 1.3 60.1 + - + +
496A LEU* 3.8 14.3 - - + -
497A LEU* 3.0 36.2 + - + +
508A PHE* 4.0 4.4 - - + -
510A TYR* 3.7 47.1 - - + -
562A VAL* 4.2 17.5 - - + -
596A ILE* 4.3 12.8 - - + -
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Residues in contact with LYS 494 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490A ARG 3.2 19.1 + - - +
491A GLU* 4.1 23.1 + - - +
492A VAL 3.2 0.2 - - - -
493A VAL* 1.3 77.7 - - + +
495A GLU* 1.3 62.7 + - - +
497A LEU* 3.6 12.7 + - + +
498A SER* 3.2 21.7 + - - -
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Residues in contact with GLU 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A PHE* 3.9 21.9 - - + -
460A TYR* 3.6 26.5 + - + -
491A GLU* 3.2 14.6 + - - +
492A VAL 3.1 9.3 + - - +
494A LYS* 1.3 77.3 - - - +
496A LEU* 1.3 56.0 + - - +
498A SER* 3.3 11.2 + - - -
499A SER* 3.0 24.6 + - - -
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Residues in contact with LEU 496 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460A TYR* 3.6 29.6 - - + -
463A ALA* 3.8 28.7 - - + +
464A TYR* 4.4 8.1 - - + +
467A ILE* 3.8 15.7 - - + -
492A VAL* 3.1 24.6 + - + +
493A VAL* 3.9 13.7 - - + -
495A GLU* 1.3 75.7 - - - +
497A LEU* 1.3 59.4 + - - +
499A SER* 3.8 8.5 - - - -
500A SER* 3.2 16.6 + - - -
505A ILE* 3.6 13.3 - - + +
508A PHE* 3.2 46.0 - - + -
562A VAL* 5.1 2.5 - - + -
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Residues in contact with LEU 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493A VAL* 3.0 28.0 + - + +
494A LYS* 3.8 14.6 - - + +
495A GLU 3.4 0.2 - - - -
496A LEU* 1.3 77.9 - - - +
498A SER* 1.3 56.7 + - - +
499A SER 3.2 0.4 - - - -
500A SER* 3.2 3.3 + - - -
501A ALA* 2.8 30.7 + - - +
508A PHE* 3.6 34.1 - - + +
510A TYR* 5.6 10.1 - - + -
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Residues in contact with SER 498 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494A LYS 3.2 11.3 + - - -
495A GLU* 3.3 14.3 + - - -
497A LEU* 1.3 79.1 - - - +
499A SER* 1.3 59.4 + - - +
501A ALA* 4.1 7.3 - - - +
502A GLN* 3.5 22.9 + - - +
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Residues in contact with SER 499 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460A TYR* 4.1 11.9 + - - -
464A TYR* 3.6 15.3 - - - -
495A GLU* 3.0 18.6 + - - -
496A LEU* 3.9 11.0 - - - -
497A LEU 3.2 0.2 - - - -
498A SER* 1.3 77.7 - - - +
500A SER* 1.3 61.4 + - - +
502A GLN* 3.5 4.1 + - - -
504A GLU* 3.1 58.0 + - - +
505A ILE* 4.1 5.9 - - - +
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Residues in contact with SER 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496A LEU 3.2 20.4 + - - -
497A LEU* 3.2 5.1 + - - -
499A SER* 1.3 76.5 - - - +
501A ALA* 1.3 59.1 + - - +
502A GLN 3.2 0.4 - - - -
503A ARG* 3.1 20.3 + - - +
505A ILE* 3.6 21.9 - - - +
506A PRO 2.9 22.0 + - - -
507A ASP* 3.3 25.4 + - - +
508A PHE* 4.1 10.4 - - - -
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Residues in contact with ALA 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497A LEU 2.8 17.4 + - - +
498A SER* 3.7 8.3 + - - +
499A SER 3.4 0.4 - - - -
500A SER* 1.3 75.6 - - - +
502A GLN* 1.3 51.1 + - - +
503A ARG* 2.6 34.6 + - - +
507A ASP* 5.3 1.8 - - - -
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Residues in contact with GLN 502 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498A SER 3.5 16.7 + - - +
499A SER* 3.9 0.7 - - - +
500A SER 3.2 0.8 - - - -
501A ALA* 1.3 76.0 - - - +
503A ARG* 1.3 78.3 + - - +
504A GLU* 3.3 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