Contacts of the helix formed by residues 474 - 485 (chain G) in PDB entry 2VKZ
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 SER 474 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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449G SER* 6.1 0.9 - - - -
450G PHE 5.7 0.5 + - - -
471G LEU* 4.1 3.1 - - - +
473G GLY* 1.3 71.3 - - - -
475G ILE* 1.3 64.6 + - - +
476G SER* 3.4 10.0 + - - -
477G GLU* 3.3 43.9 + - - +
478G ARG* 3.1 19.8 + - - +
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Residues in contact with ILE 475 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281G VAL* 4.4 10.8 - - + -
450G PHE* 3.4 31.9 + - + +
451G ASN 4.3 0.4 - - - -
452G ALA* 3.7 31.0 - - + +
455G ILE* 4.7 9.4 - - + -
468G LEU* 3.5 49.4 - - + +
469G ARG* 4.3 1.1 - - + +
471G LEU* 4.1 11.2 - - + +
473G GLY 3.7 4.9 + - - +
474G SER* 1.3 70.9 + - - +
476G SER* 1.3 69.7 + - - +
478G ARG* 3.2 1.9 + - - +
479G ILE* 3.2 28.8 + - + +
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Residues in contact with SER 476 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302G VAL* 6.3 0.2 - - - -
440G ASN* 3.5 5.6 + - - -
443G LEU* 3.5 26.5 - - - +
448G VAL* 5.2 2.4 + - - +
449G SER* 4.6 8.5 - - - -
450G PHE* 4.2 35.1 + - - +
474G SER* 3.4 8.8 + - - -
475G ILE* 1.3 77.4 - - - +
477G GLU* 1.3 65.7 + - - +
478G ARG 3.0 1.7 + - - -
479G ILE* 3.1 9.9 + - - +
480G VAL* 3.0 22.8 + - - +
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Residues in contact with GLU 477 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440G ASN* 3.2 41.7 - - - +
474G SER* 3.3 30.3 + - - +
476G SER* 1.3 81.2 + - - +
478G ARG* 1.3 60.8 + - - +
480G VAL* 3.6 2.5 + - - +
481G ASP* 3.2 23.2 + - - +
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Residues in contact with ARG 478 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461G ASP* 2.5 53.0 + - - +
463G PHE* 4.3 6.5 - - - +
464G ASP* 3.8 18.7 + - - -
468G LEU* 4.1 5.6 - - + -
471G LEU* 3.7 26.9 - - + -
474G SER 3.1 13.8 + - - +
475G ILE 3.4 9.6 - - - +
476G SER 3.1 0.8 - - - -
477G GLU* 1.3 76.1 - - - +
479G ILE* 1.3 60.3 + - - +
481G ASP* 2.9 11.4 + - - +
482G CYS* 2.8 35.9 + - - +
486G LEU* 3.5 27.7 - - - +
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Residues in contact with ILE 479 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277G LEU* 3.4 33.4 - - + -
278G VAL* 4.3 23.3 - - + -
281G VAL* 4.0 27.6 - - + -
302G VAL* 5.6 3.6 - - + -
450G PHE* 4.4 15.5 - - + -
468G LEU* 3.7 20.9 - - + -
475G ILE* 3.2 16.8 - - + +
476G SER* 3.1 10.3 + - - +
478G ARG* 1.3 74.2 - - - +
480G VAL* 1.3 64.9 + - + +
482G CYS* 3.7 8.4 - - - +
483G ILE* 3.4 30.9 + - - +
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Residues in contact with VAL 480 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302G VAL* 5.3 3.8 - - + -
306G ILE* 5.2 12.1 - - + -
436G SER* 4.3 13.0 - - - +
439G ILE* 3.9 16.2 - - + -
440G ASN* 3.8 20.0 - - - +
443G LEU* 3.7 28.0 - - + -
476G SER 3.0 16.3 + - - +
477G GLU 3.6 8.3 - - - +
479G ILE* 1.3 79.6 - - + +
481G ASP* 1.3 56.1 + - - +
482G CYS 3.1 0.9 - - - -
483G ILE* 3.4 2.7 + - - +
484G ILE* 3.0 54.5 + - + +
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Residues in contact with ASP 481 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436G SER* 3.8 18.2 + - - +
477G GLU 3.2 12.9 + - - +
478G ARG* 2.9 10.2 + - - +
480G VAL* 1.3 79.9 - - - +
482G CYS* 1.3 56.8 + - - +
483G ILE 3.3 0.7 - - - -
484G ILE* 4.0 3.1 - - - +
485G ARG* 2.5 51.0 + - - +
486G LEU* 3.1 33.8 + - + +
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Residues in contact with CYS 482 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274G SER* 5.6 0.2 - - - -
277G LEU* 4.0 9.2 - - + -
428G HIS* 3.7 6.8 + - - -
461G ASP* 3.8 20.6 - - - -
462G THR* 3.4 45.0 + - - +
463G PHE* 4.1 5.8 - - - -
478G ARG* 2.8 27.0 + - - +
479G ILE* 3.7 13.5 - - - +
480G VAL 3.1 0.4 - - - -
481G ASP* 1.3 78.1 - - - +
483G ILE* 1.3 59.7 + - - +
486G LEU* 3.5 22.9 - - - +
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Residues in contact with ILE 483 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274G SER* 3.1 31.4 - - - +
275G GLN* 3.6 18.2 - - - +
277G LEU* 4.4 9.2 - - + -
278G VAL* 3.7 24.7 - - + -
306G ILE* 4.0 18.2 - - + -
427G PHE* 4.0 24.8 - - + -
428G HIS* 3.3 33.3 + - - -
462G THR* 6.1 0.2 - - - +
479G ILE 3.4 18.8 + - - +
480G VAL 3.4 2.4 + - - +
482G CYS* 1.3 83.2 - - - +
484G ILE* 1.3 68.4 + - + +
485G ARG 3.7 0.2 - - - -
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Residues in contact with ILE 484 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306G ILE* 4.6 5.2 - - + -
310G CYS* 3.4 21.5 - - - -
427G PHE* 5.8 0.4 - - + -
428G HIS* 3.5 4.6 + - - +
429G SER 3.4 23.2 + - - +
432G LEU* 3.7 36.2 - - + +
433G VAL* 4.3 4.3 - - - +
435G ALA 4.8 0.4 - - - +
436G SER* 4.5 15.0 - - - +
439G ILE* 3.3 34.3 - - + -
480G VAL* 3.0 31.0 + - + +
481G ASP* 4.7 0.4 - - - -
483G ILE* 1.3 92.0 - - + +
485G ARG* 1.3 62.6 + - + +
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Residues in contact with ARG 485 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367G GLU* 4.5 6.1 - - - +
428G HIS* 3.8 15.1 - - - +
429G SER* 4.2 5.5 + - - +
433G VAL* 3.9 34.8 - - + -
436G SER* 6.5 0.2 - - - -
481G ASP* 2.5 51.0 + - - +
483G ILE 3.7 0.2 - - - -
484G ILE* 1.3 82.6 - - + +
486G LEU* 1.3 100.6 + - + +
487G PRO* 3.8 3.6 - - - +
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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