Contacts of the helix formed by residues 482 - 493 (chain A) in PDB entry 3GZN
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 LYS 482 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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426A PRO* 4.4 22.8 + - + +
427A ASP* 2.8 43.1 + - - -
480A MET* 4.0 19.5 + - + -
481A VAL* 1.3 75.6 - - - +
483A ASP* 1.3 60.8 + - - +
484A ASP* 4.3 17.4 + - + +
485A TYR* 2.9 40.6 + - + +
486A VAL* 4.1 1.2 + - - +
51B PHE* 5.1 8.9 - - - -
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Residues in contact with ASP 483 (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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465A LYS* 5.6 4.5 - - - +
481A VAL 3.4 8.4 + - - +
482A LYS* 1.3 68.0 - - - +
484A ASP* 1.3 67.8 + - - +
486A VAL* 3.0 26.5 + - - +
487A HIS* 3.1 25.6 + - + -
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Residues in contact with ASP 484 (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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482A LYS* 4.7 17.4 + - + +
483A ASP* 1.3 79.2 - - - +
485A TYR* 1.3 55.4 + - - +
487A HIS* 4.3 6.7 - - - -
488A GLU* 3.0 29.6 + - - +
50B PRO* 3.3 34.6 - - + +
51B PHE* 3.4 20.3 - - + -
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Residues in contact with TYR 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A PRO 3.9 6.5 - - - -
427A ASP* 2.8 41.5 + - - +
431A VAL* 3.7 29.7 - - + +
432A LEU* 3.9 28.0 - - + +
435A MET* 4.0 18.6 - - + -
481A VAL* 4.0 5.8 - - + -
482A LYS* 2.9 29.2 + - + +
484A ASP* 1.3 75.8 - - - +
486A VAL* 1.3 60.0 + - - +
488A GLU* 3.1 2.9 + - + -
489A PHE* 2.8 41.4 + + - +
532A MET* 4.8 11.1 - - + +
51B PHE* 3.8 30.6 - + - -
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Residues in contact with VAL 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A MET* 3.7 20.4 - - + +
461A ILE* 3.4 40.6 - - + +
464A LEU* 3.8 11.2 - - + +
465A LYS* 3.9 23.1 - - + +
468A LEU* 4.0 21.1 - - + -
481A VAL* 5.3 0.2 - - + -
482A LYS 5.0 2.0 - - - +
483A ASP* 3.0 21.1 + - + +
485A TYR* 1.3 75.3 - - - +
487A HIS* 1.3 62.8 + - - +
489A PHE 3.5 0.2 + - - -
490A CYS* 3.2 24.4 + - - -
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Residues in contact with HIS 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A VAL* 5.9 0.3 - - - +
461A ILE* 3.5 46.3 - - + +
483A ASP* 3.1 30.9 + - + +
484A ASP* 3.7 13.0 - - - +
486A VAL* 1.3 76.9 - - - +
488A GLU* 1.3 57.5 + - - +
490A CYS* 3.5 3.1 + - - +
491A ARG* 3.0 25.6 + - - +
49B GLY* 5.8 0.2 - - - -
50B PRO* 3.9 19.8 - - + +
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Residues in contact with GLU 488 (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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484A ASP 3.0 19.8 + - - +
485A TYR* 3.1 5.6 + - + +
487A HIS* 1.3 74.4 - - - +
489A PHE* 1.3 63.9 + - + +
491A ARG* 3.1 25.6 + - - +
492A TYR* 3.1 51.1 + - + +
532A MET* 3.9 3.3 - - - +
50B PRO* 3.9 9.2 - - + +
51B PHE* 3.4 34.2 + - + -
336B TYR* 2.6 38.8 + - - -
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Residues in contact with PHE 489 (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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163A TYR* 3.9 41.7 + + - -
166A VAL* 3.6 23.6 - - + -
432A LEU* 3.8 26.0 - - + -
435A MET* 3.4 47.6 - - + -
436A LEU* 4.1 14.1 - - + -
439A VAL* 3.9 10.3 - - + -
450A PRO* 4.6 2.0 - - - +
464A LEU* 4.1 8.3 - - + -
485A TYR* 2.8 26.0 + + - +
486A VAL 4.1 1.8 - - - +
488A GLU* 1.3 79.1 - - + +
490A CYS* 1.3 62.4 + - - +
492A TYR* 3.4 33.3 - + - +
493A GLY 3.7 3.6 + - - -
532A MET* 6.3 0.7 - - - -
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Residues in contact with CYS 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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450A PRO* 4.1 15.7 - - - -
451A GLY* 3.6 9.6 - - - +
457A VAL* 4.5 14.1 - - + +
460A ASP* 3.9 7.9 - - - -
461A ILE* 3.7 38.6 - - + -
464A LEU* 3.7 18.4 - - - -
486A VAL 3.2 21.8 + - - +
487A HIS 3.8 4.3 - - - +
489A PHE* 1.3 73.2 - - - +
491A ARG* 1.3 69.6 + - - +
493A GLY* 3.0 12.1 + - - -
47B ARG* 3.2 9.1 + - - -
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Residues in contact with ARG 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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457A VAL* 5.1 4.2 - - - +
487A HIS 3.0 14.9 + - - +
488A GLU* 3.1 21.1 + - - +
490A CYS* 1.3 73.9 - - - +
492A TYR* 1.3 62.3 + - + +
43B LYS* 3.9 10.8 + - - +
44B PHE* 3.2 37.9 + - + +
47B ARG* 2.6 54.4 + - + +
48B SER 3.0 28.8 + - - +
49B GLY* 3.6 9.6 - - - -
52B THR* 3.5 25.7 - - - +
56B PHE* 4.0 1.4 - - - -
335B ALA 3.9 5.9 + - - -
336B TYR* 2.7 40.8 + - - -
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Residues in contact with TYR 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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163A TYR* 4.1 11.7 - + + -
164A GLY* 3.4 26.2 - - - +
165A LEU* 3.5 24.1 - - + +
166A VAL* 4.2 9.3 - - + +
488A GLU* 3.1 26.3 + - + +
489A PHE* 3.4 46.4 - + - +
490A CYS 3.2 0.2 - - - -
491A ARG* 1.3 81.2 - - + +
493A GLY* 1.3 63.2 + - - +
494A ALA 3.3 0.4 - - - +
495A ALA* 3.0 22.2 + - - +
532A MET* 3.2 35.9 - - - +
43B LYS* 3.9 8.4 - - - +
44B PHE* 3.7 16.4 - + - -
336B TYR* 3.4 20.6 - - - -
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Residues in contact with GLY 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450A PRO 3.4 13.0 - - - -
451A GLY 3.3 26.0 - - - -
452A VAL* 4.0 11.9 - - - +
489A PHE 3.7 2.4 + - - -
490A CYS 3.0 7.9 + - - -
492A TYR* 1.3 76.9 - - - +
494A ALA* 1.3 67.2 + - - +
495A ALA 3.1 1.2 + - - -
43B LYS* 3.3 16.5 + - - -
47B ARG* 3.9 2.9 - - - -
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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