Contacts of the helix formed by residues 472 - 490 (chain G) in PDB entry 1H1V
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 THR 472 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470G GLN 3.9 4.0 + - - +
471G SER* 1.3 73.7 - - - +
473G GLN* 1.3 61.2 + - - +
474G ASP* 2.5 23.0 + - - -
475G GLU* 2.8 36.0 + - - +
476G VAL* 2.9 13.8 + - - +
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Residues in contact with GLN 473 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A ALA* 2.6 40.0 + - - +
145A SER* 4.9 0.8 - - - +
334A GLU* 3.5 37.9 + - - +
341A ILE* 4.1 20.2 - - + +
345A ILE* 4.5 5.4 - - + -
471G SER 4.1 0.2 + - - -
472G THR* 1.3 73.1 - - - +
474G ASP* 1.3 55.8 + - - +
476G VAL* 4.0 8.5 - - + -
477G ALA* 2.5 42.1 + - + +
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Residues in contact with ASP 474 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ASP* 6.0 2.0 - - - +
345A ILE* 4.1 23.4 - - + +
426G GLU 5.7 0.5 - - - +
427G GLY 5.2 6.6 - - - +
472G THR* 2.5 34.5 + - - -
473G GLN* 1.3 75.2 - - - +
475G GLU* 1.3 66.5 + - - +
478G ALA* 3.0 26.0 + - - +
526G ARG* 6.0 1.9 - - - +
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Residues in contact with GLU 475 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425G ILE* 3.9 14.5 - - + +
426G GLU 4.1 14.4 - - - +
444G GLY 3.2 5.2 - - - +
445G ASP* 2.6 14.8 - - - +
446G SER* 4.0 7.4 - - - +
471G SER* 2.6 28.6 + - - +
472G THR* 2.8 24.2 + - - +
474G ASP* 1.3 89.0 - - - +
476G VAL* 1.3 55.9 + - - +
478G ALA* 2.9 6.1 + - - +
479G SER* 2.6 37.5 + - - -
524G THR 3.3 9.4 - - - +
525G SER* 4.7 0.9 - - - -
526G ARG 5.2 0.3 + - - -
1744G CA 2.3 30.9 - - - -
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Residues in contact with VAL 476 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A ALA 5.9 0.4 - - - +
145A SER 4.7 3.6 - - - +
146A GLY* 4.2 10.8 - - - +
446G SER* 3.9 5.4 - - - +
467G GLN* 3.0 43.5 - - + +
468G GLY 5.6 0.7 - - - +
471G SER* 3.6 21.3 - - - +
472G THR 2.9 22.9 - - - +
473G GLN* 3.8 6.3 - - - +
475G GLU* 1.3 77.0 - - - +
477G ALA* 1.3 63.5 + - - +
479G SER* 2.9 21.9 + - - -
480G ALA* 3.0 11.1 + - - +
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Residues in contact with ALA 477 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A TYR 3.6 23.4 - - - +
144A ALA* 4.0 11.6 + - - +
146A GLY* 4.5 0.6 - - - +
342A GLY* 5.8 0.7 - - - -
345A ILE* 3.6 33.0 - - + -
473G GLN 2.5 22.3 + - - +
476G VAL* 1.3 73.8 - - - +
478G ALA* 1.3 63.4 + - - +
480G ALA* 3.2 3.8 + - - +
481G ILE* 3.2 27.3 + - + +
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Residues in contact with ALA 478 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A ILE* 4.0 8.4 - - + +
349A LEU* 3.8 26.9 - - + -
425G ILE* 3.7 18.4 - - + -
427G GLY 5.6 3.1 - - - +
474G ASP 3.0 19.3 + - - +
475G GLU 2.9 4.6 + - - +
477G ALA* 1.3 80.3 - - - +
479G SER* 1.3 61.2 + - - +
481G ILE* 3.1 4.7 + - - +
482G LEU* 3.0 29.4 + - - +
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Residues in contact with SER 479 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425G ILE* 3.6 23.1 - - - +
446G SER* 3.6 19.1 - - - -
448G ILE* 3.7 3.8 - - - +
465G ASN* 2.9 26.8 + - - -
467G GLN* 3.7 4.0 + - - -
475G GLU 2.6 18.1 + - - -
476G VAL* 2.9 14.6 + - - -
478G ALA* 1.3 74.0 - - - +
480G ALA* 1.3 53.0 + - - +
482G LEU 4.0 0.2 - - - -
483G THR* 2.5 35.2 + - - -
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Residues in contact with ALA 480 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A TYR* 4.5 4.5 - - - +
146A GLY* 3.3 43.5 - - - +
147A ARG 4.1 2.9 - - - +
148A THR* 3.3 26.6 - - + +
465G ASN* 3.7 7.2 - - - +
476G VAL 3.0 4.7 + - - +
477G ALA 3.7 3.6 - - - +
478G ALA 3.1 0.2 - - - -
479G SER* 1.3 78.8 + - - +
481G ILE* 1.3 65.9 + - - +
483G THR* 3.3 3.4 + - - -
484G ALA* 3.2 16.5 + - - +
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Residues in contact with ILE 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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143A TYR* 3.5 44.0 - - + +
342A GLY* 4.3 3.1 - - - +
345A ILE* 4.4 6.5 - - + -
346A LEU* 3.6 44.4 - - + +
349A LEU* 3.7 15.9 - - + -
477G ALA* 3.2 14.8 + - + +
478G ALA 3.1 6.2 + - - +
480G ALA* 1.3 77.8 - - - +
482G LEU* 1.3 56.9 + - - +
484G ALA* 3.2 5.0 + - - +
485G GLN* 2.9 51.7 + - + +
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Residues in contact with LEU 482 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A LEU* 3.7 22.4 - - + -
351A THR* 3.4 35.4 - - + +
425G ILE* 3.6 27.6 - - + -
428G SER 5.6 0.2 - - - -
429G ASN* 4.6 4.0 - - - -
430G LYS* 4.1 36.1 + - + +
448G ILE* 3.6 18.7 - - + +
478G ALA* 3.0 16.8 + - + +
481G ILE* 1.3 72.8 - - - +
483G THR* 1.3 60.4 + - - +
485G GLN* 3.6 14.0 - - + +
486G LEU* 2.8 31.4 + - - +
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Residues in contact with THR 483 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A THR* 5.1 1.1 - - + -
448G ILE* 3.7 12.5 - - - +
463G ILE* 3.6 28.2 - - + +
465G ASN* 3.4 27.7 - - + +
479G SER 2.5 24.5 + - - -
480G ALA* 3.4 7.9 - - - -
482G LEU* 1.3 76.8 - - - +
484G ALA* 1.3 59.8 + - - +
486G LEU* 3.7 4.7 - - - +
487G ASP* 3.1 26.5 + - - +
496G GLN* 3.7 26.6 - - + +
497G SER 5.5 0.4 - - - +
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Residues in contact with ALA 484 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A TYR* 4.2 18.2 - - - +
148A THR* 4.4 9.6 - - + -
167A GLU 4.4 9.5 - - - +
168A GLY* 4.5 2.2 - - - -
169A TYR* 5.9 1.4 - - - -
480G ALA 3.2 8.4 + - - +
481G ILE* 3.2 9.1 + - - +
482G LEU 3.2 0.2 - - - -
483G THR* 1.3 79.2 - - - +
485G GLN* 1.3 60.4 + - + +
487G ASP* 3.2 3.5 + - - +
488G GLU* 2.9 28.8 + - - +
496G GLN* 3.6 17.9 - - - +
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Residues in contact with GLN 485 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A TYR* 6.1 0.4 - - - +
346A LEU* 3.8 12.3 - - - +
349A LEU* 4.9 0.4 - - - +
351A THR* 2.6 35.1 + - + -
352A PHE* 5.4 0.2 - - - -
355A MET* 3.5 29.5 - - - +
430G LYS* 5.6 1.3 - - - +
481G ILE* 2.9 41.6 + - + +
482G LEU* 3.6 13.6 - - + +
484G ALA* 1.3 76.3 - - + +
486G LEU* 1.3 63.6 + - - +
488G GLU* 3.3 17.5 + - - +
489G GLU* 3.0 26.1 + - - +
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Residues in contact with LEU 486 (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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423G TRP* 3.8 33.4 - - + -
430G LYS* 4.0 17.2 - - - +
448G ILE* 4.3 12.6 - - + -
450G LEU* 3.8 13.5 - - + -
463G ILE* 4.2 20.0 - - + -
482G LEU 2.8 18.7 + - - +
483G THR* 3.7 4.5 - - - +
485G GLN* 1.3 74.8 - - - +
487G ASP* 1.3 66.5 + - - +
488G GLU 3.3 0.2 + - - -
489G GLU* 3.3 15.2 + - - +
490G LEU* 3.1 47.6 + - + +
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Residues in contact with ASP 487 (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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167A GLU* 3.2 8.9 - - - +
463G ILE* 4.1 5.6 - - + +
483G THR 3.1 9.2 + - - +
484G ALA 3.4 5.4 - - - +
486G LEU* 1.3 76.7 - - - +
488G GLU* 1.3 54.2 + - - +
490G LEU* 3.4 4.9 + - - +
492G GLY* 2.6 52.4 + - - -
494G PRO* 3.3 22.8 - - - +
496G GLN* 2.8 39.7 + - - +
1743G CA 2.5 30.8 - - - -
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Residues in contact with GLU 488 (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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169A TYR* 2.6 35.1 + - + +
355A MET* 5.2 7.1 - - - +
375A PHE* 3.0 28.3 - - + -
484G ALA 2.9 13.6 + - - +
485G GLN* 3.4 22.8 - - - +
487G ASP* 1.3 75.5 - - - +
489G GLU* 1.3 53.4 + - - +
491G GLY* 2.7 28.8 + - - -
492G GLY* 4.3 4.0 - - - +
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Residues in contact with GLU 489 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430G LYS* 4.8 7.5 + - - -
485G GLN 3.0 18.3 + - - +
486G LEU* 3.4 15.8 - - - +
488G GLU* 1.3 76.8 + - - +
490G LEU* 1.3 73.1 + - + +
491G GLY 3.2 3.2 + - - -
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Residues in contact with LEU 490 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450G LEU* 3.4 31.9 - - + -
461G GLN* 3.5 29.4 + - - +
463G ILE* 5.4 0.7 - - + -
486G LEU* 3.1 35.8 + - + +
487G ASP 4.1 2.7 - - - +
488G GLU 3.1 0.8 + - - -
489G GLU* 1.3 92.0 - - + +
491G GLY* 1.3 57.6 + - - +
492G GLY 3.1 5.4 + - - -
493G THR* 3.6 16.1 + - - +
494G PRO* 4.4 8.7 - - + -
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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