Contacts of the helix formed by residues 462 - 478 (chain R) in PDB entry 1HI0
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 462 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445R GLU* 3.4 9.0 - - - -
460R THR 3.3 2.8 + - - -
461R LYS* 1.3 75.9 - - - +
463R ARG* 1.3 67.9 + - - +
464R ALA 3.3 2.7 - - - -
465R LEU* 3.3 17.5 + - - +
466R VAL* 4.4 1.0 + - - +
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Residues in contact with ARG 463 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418R THR 4.6 0.7 - - - +
421R HIS* 3.6 57.4 + - + +
445R GLU* 3.3 7.7 + - - +
462R GLY* 1.3 71.6 - - - +
464R ALA* 1.3 63.9 + - - +
466R VAL* 3.2 24.6 - - - +
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Residues in contact with ALA 464 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418R THR* 3.1 26.0 - - - +
419R ALA* 4.0 2.2 - - + -
421R HIS* 3.8 5.8 - - + -
445R GLU* 3.1 23.2 + - - +
446R ILE* 3.9 25.4 - - + -
459R TRP* 3.8 4.4 - - + -
463R ARG* 1.3 78.0 - - - +
465R LEU* 1.3 59.5 + - - +
467R GLY* 2.8 20.7 + - - -
468R GLY 3.0 9.9 + - - -
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Residues in contact with LEU 465 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318R SER* 3.5 27.1 - - - -
319R LEU* 4.0 20.0 - - + -
445R GLU* 4.2 0.8 + - - -
459R TRP* 4.1 14.3 - - + -
460R THR 3.5 17.9 + - - +
461R LYS* 3.9 22.2 - - + +
462R GLY 3.3 13.7 + - - +
463R ARG 3.3 1.2 - - - -
464R ALA* 1.3 74.4 - - - +
466R VAL* 1.3 65.9 + - - +
468R GLY 3.3 0.3 + - - -
469R HIS* 3.1 42.2 + - + +
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Residues in contact with VAL 466 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462R GLY 4.4 1.4 + - - +
463R ARG 3.2 18.6 + - - +
465R LEU* 1.3 77.9 - - - +
467R GLY* 1.3 66.3 + - - +
469R HIS* 3.3 12.7 + - + +
470R ARG* 3.3 38.6 + - + +
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Residues in contact with GLY 467 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417R HIS 3.7 15.8 - - - +
418R THR* 3.2 16.4 - - - +
463R ARG 4.5 0.2 + - - -
464R ALA 2.8 8.7 + - - -
466R VAL* 1.3 82.3 - - - +
468R GLY* 1.3 64.9 + - - +
470R ARG* 2.9 29.3 + - - +
471R LEU 2.9 10.4 + - - -
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Residues in contact with GLY 468 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319R LEU* 3.6 8.4 - - - +
418R THR* 3.2 13.9 - - - +
459R TRP* 3.6 28.7 - - - -
464R ALA 3.0 10.5 + - - -
465R LEU 3.3 4.6 + - - -
467R GLY* 1.3 73.7 - - - +
469R HIS* 1.3 62.0 + - - +
471R LEU* 3.0 4.7 + - - +
472R PHE* 2.9 23.6 + - - +
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Residues in contact with HIS 469 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318R SER 4.9 4.9 + - - -
319R LEU* 3.6 25.4 - - + +
465R LEU* 3.1 47.0 + - + +
466R VAL* 3.5 11.0 - - + +
467R GLY 3.1 0.6 - - - -
468R GLY* 1.3 76.2 - - - +
470R ARG* 1.3 61.6 + - + +
472R PHE* 3.6 6.5 + - - +
473R GLU* 3.1 22.9 + - - +
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Residues in contact with ARG 470 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417R HIS 4.2 10.7 + - - +
418R THR* 5.6 0.8 - - - +
466R VAL* 3.3 34.6 + - + +
467R GLY* 2.9 24.2 + - - +
469R HIS* 1.3 78.3 - - + +
471R LEU* 1.3 53.2 + - - +
473R GLU* 3.1 8.8 + - - +
474R MET* 2.8 34.1 + - + +
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Residues in contact with LEU 471 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321R VAL* 5.9 0.7 - - + -
413R MET* 4.1 33.0 - - + +
414R GLN* 4.9 1.3 - - + -
417R HIS* 4.0 11.3 + - + +
418R THR* 4.3 8.1 - - + -
457R LEU* 5.5 2.0 - - + -
459R TRP* 4.0 28.7 - - + -
467R GLY 2.9 10.4 + - - +
468R GLY 3.2 9.4 - - - +
470R ARG* 1.3 73.7 - - - +
472R PHE* 1.3 58.6 + - - +
474R MET* 2.7 41.2 + - + +
475R LEU* 2.8 24.0 + - + +
482R PRO* 3.9 28.3 - - + -
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Residues in contact with PHE 472 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72R TYR* 3.3 55.9 - + + -
74R ARG* 4.4 19.1 - - + -
319R LEU* 3.7 30.3 - - + -
320R CYS 4.3 11.2 - - - -
321R VAL* 3.7 25.5 - - + +
322R ALA 5.9 0.9 - - - -
468R GLY 2.9 14.9 + - - +
469R HIS* 3.7 10.3 - - - +
471R LEU* 1.3 75.0 - - - +
473R GLU* 1.3 57.9 + - - +
475R LEU* 3.1 14.6 + - + +
476R LYS* 2.8 26.5 + - + +
490R TYR* 4.9 11.2 - + + -
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Residues in contact with GLU 473 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72R TYR* 2.6 35.7 + - - -
469R HIS 3.1 15.2 + - - +
470R ARG* 3.2 12.6 - - - +
471R LEU 3.1 0.6 - - - -
472R PHE* 1.3 78.5 - - - +
474R MET* 1.3 57.2 + - - +
476R LYS* 3.2 19.2 + - - +
477R GLU* 2.9 54.9 + - - +
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Residues in contact with MET 474 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417R HIS* 3.1 39.9 - - + +
470R ARG* 2.8 10.7 + - + +
471R LEU* 2.7 28.9 + - + +
473R GLU* 1.3 72.7 - - - +
475R LEU* 1.3 54.1 + - + +
477R GLU* 3.5 8.4 + - - +
478R GLY* 2.9 25.5 + - - -
479R LYS 4.2 2.3 + - - -
480R VAL* 3.6 41.6 - - + +
482R PRO* 3.9 20.6 - - + -
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Residues in contact with LEU 475 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321R VAL* 3.5 32.1 - - + -
323R THR* 5.2 5.2 - - + -
413R MET* 5.1 2.5 - - - -
457R LEU* 6.4 0.2 - - + -
471R LEU* 2.8 29.9 + - + +
472R PHE* 3.3 11.4 - - + +
474R MET* 1.3 75.5 - - + +
476R LYS* 1.3 66.0 + - - +
478R GLY* 3.0 14.4 + - - -
480R VAL 5.8 0.7 - - - -
482R PRO* 3.8 29.4 - - + -
488R ILE* 4.5 4.3 - - + -
489R SER* 3.8 31.9 - - - +
490R TYR* 3.4 31.2 + - + +
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Residues in contact with LYS 476 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71R GLU* 3.5 32.2 + - + +
72R TYR* 3.2 50.0 - - + -
472R PHE* 2.8 17.6 + - + +
473R GLU* 3.2 19.9 + - - +
475R LEU* 1.3 75.4 - - - +
477R GLU* 1.3 69.1 + - - +
478R GLY* 3.0 1.6 + - - -
490R TYR* 4.0 19.2 + - + +
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Residues in contact with GLU 477 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473R GLU* 2.9 45.0 + - - +
474R MET* 4.0 6.4 + - - +
476R LYS* 1.3 80.7 - - - +
478R GLY* 1.3 66.0 + - - +
479R LYS* 3.1 25.6 + - + +
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Residues in contact with GLY 478 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474R MET 2.9 13.9 + - - -
475R LEU* 3.3 13.9 - - - -
476R LYS 2.9 4.5 - - - -
477R GLU* 1.3 76.7 - - - +
479R LYS* 1.3 60.0 + - - +
480R VAL 3.5 4.3 - - - -
489R SER* 6.5 0.9 - - - -
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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
------------------------------------------------------------
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