Contacts of the helix formed by residues 462 - 478 (chain P) 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 P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445P GLU* 3.4 9.6 - - - -
460P THR 3.3 3.0 + - - -
461P LYS* 1.3 76.5 - - - +
463P ARG* 1.3 67.7 + - - +
464P ALA 3.3 2.7 - - - -
465P LEU* 3.3 17.3 + - - +
466P VAL* 4.4 1.4 + - - +
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Residues in contact with ARG 463 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418P THR 4.6 0.5 - - - +
421P HIS* 3.6 57.3 + - + +
445P GLU* 3.3 7.4 + - - +
462P GLY* 1.3 72.2 - - - +
464P ALA* 1.3 64.5 + - - +
466P VAL* 3.2 23.7 - - - +
188R ASP* 3.9 20.8 + - - -
191R GLN* 4.2 5.3 - - - +
192R LEU* 5.4 15.4 - - + +
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Residues in contact with ALA 464 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418P THR* 3.1 26.1 - - - +
419P ALA* 4.0 2.2 - - + -
421P HIS* 3.8 6.0 - - + -
445P GLU* 3.1 24.3 + - - +
446P ILE* 3.9 25.6 - - + -
459P TRP* 3.8 4.3 - - + -
463P ARG* 1.3 77.6 - - - +
465P LEU* 1.3 59.5 + - - +
467P GLY* 2.8 21.2 + - - -
468P GLY 3.0 10.0 + - - -
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Residues in contact with LEU 465 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318P SER* 3.5 26.9 - - - -
319P LEU* 4.0 19.3 - - + -
445P GLU* 4.2 1.4 + - - -
459P TRP* 4.1 14.3 - - + -
460P THR 3.5 17.5 + - - +
461P LYS* 3.9 22.0 - - + +
462P GLY 3.3 14.4 + - - +
463P ARG 3.3 1.6 - - - -
464P ALA* 1.3 75.2 - - - +
466P VAL* 1.3 66.2 + - - +
468P GLY 3.3 0.3 + - - -
469P HIS* 3.1 43.4 + - + +
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Residues in contact with VAL 466 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462P GLY 4.4 1.4 + - - +
463P ARG 3.2 19.2 + - - +
465P LEU* 1.3 77.3 - - - +
467P GLY* 1.3 66.6 + - - +
469P HIS* 3.3 12.2 + - + +
470P ARG* 3.3 37.1 + - + +
169R ARG* 6.1 0.9 - - - +
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Residues in contact with GLY 467 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417P HIS 3.7 15.4 - - - +
418P THR* 3.2 16.2 - - - +
463P ARG 4.5 0.2 + - - -
464P ALA 2.8 8.4 + - - -
466P VAL* 1.3 82.2 - - - +
468P GLY* 1.3 67.0 + - - +
470P ARG* 2.9 28.3 + - - +
471P LEU 2.9 10.2 + - - -
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Residues in contact with GLY 468 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319P LEU* 3.6 8.4 - - - +
418P THR* 3.2 13.9 - - - +
459P TRP* 3.6 28.5 - - - -
464P ALA 3.0 10.5 + - - -
465P LEU 3.3 4.6 + - - -
467P GLY* 1.3 73.9 - - - +
469P HIS* 1.3 61.1 + - - +
471P LEU* 3.0 5.1 + - - +
472P PHE* 2.9 23.6 + - - +
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Residues in contact with HIS 469 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318P SER 4.9 4.7 + - - -
319P LEU* 3.6 26.3 - - + +
465P LEU* 3.1 47.8 + - + +
466P VAL* 3.5 11.4 - - + +
467P GLY 3.1 0.6 - - - -
468P GLY* 1.3 76.2 - - - +
470P ARG* 1.3 62.0 + - + +
472P PHE* 3.6 6.4 + - - +
473P GLU* 3.1 22.7 + - - +
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Residues in contact with ARG 470 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417P HIS* 4.2 11.1 + - + +
418P THR* 5.6 0.6 - - - +
466P VAL* 3.3 33.8 + - + +
467P GLY* 2.9 23.1 + - - +
469P HIS* 1.3 78.1 - - - +
471P LEU* 1.3 51.7 + - - +
473P GLU* 3.1 9.5 + - - +
474P MET* 2.8 35.0 + - + +
169R ARG* 4.3 25.1 - - - +
192R LEU 5.9 0.8 + - - -
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Residues in contact with LEU 471 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321P VAL* 5.9 0.4 - - + -
413P MET* 4.1 33.2 - - + +
414P GLN* 4.9 1.3 - - + -
417P HIS* 4.0 11.3 + - + +
418P THR* 4.3 7.2 - - + -
457P LEU* 5.5 2.5 - - + -
459P TRP* 4.0 28.0 - - + -
467P GLY 2.9 11.0 + - - +
468P GLY 3.2 10.1 - - - +
470P ARG* 1.3 74.6 - - - +
472P PHE* 1.3 59.1 + - - +
474P MET* 2.7 42.0 + - + +
475P LEU* 2.8 23.7 + - + +
482P PRO* 3.9 28.7 - - + -
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Residues in contact with PHE 472 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72P TYR* 3.3 57.0 - + + -
74P ARG* 4.4 18.6 - - + -
319P LEU* 3.7 30.1 - - + -
320P CYS 4.3 11.2 - - - -
321P VAL* 3.7 24.9 - - + +
322P ALA 5.9 0.9 - - - -
468P GLY 2.9 14.5 + - - +
469P HIS* 3.7 9.9 - - - +
471P LEU* 1.3 76.0 - - - +
473P GLU* 1.3 57.1 - - - +
475P LEU* 3.1 14.2 + - + +
476P LYS* 2.8 26.6 + - + +
490P TYR* 4.9 10.8 - + + -
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Residues in contact with GLU 473 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72P TYR* 2.6 33.4 + - - -
469P HIS 3.1 14.6 + - - +
470P ARG* 3.2 12.6 - - - +
471P LEU 3.1 0.6 - - - -
472P PHE* 1.3 79.1 - - - +
474P MET* 1.3 56.3 + - - +
476P LYS* 3.2 19.3 + - - +
477P GLU* 2.9 54.7 + - - +
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Residues in contact with MET 474 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417P HIS* 3.1 39.3 - - + +
470P ARG* 2.8 11.8 + - + +
471P LEU* 2.7 27.4 + - + +
473P GLU* 1.3 72.5 - - - +
475P LEU* 1.3 54.0 + - - +
477P GLU* 3.5 8.4 + - - +
478P GLY* 2.9 24.9 + - - -
479P LYS 4.2 2.6 + - - -
480P VAL* 3.6 41.8 - - + +
482P PRO* 3.9 21.1 - - + -
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Residues in contact with LEU 475 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321P VAL* 3.5 31.4 - - + -
323P THR* 5.2 5.6 - - + -
413P MET* 5.1 2.5 - - - -
471P LEU* 2.8 31.5 + - + +
472P PHE* 3.3 12.1 - - + +
474P MET* 1.3 73.6 - - - +
476P LYS* 1.3 65.9 + - - +
478P GLY* 3.0 14.2 + - - -
480P VAL 5.8 0.7 - - - -
482P PRO* 3.8 29.2 - - + -
488P ILE* 4.5 4.3 - - + +
489P SER* 3.8 31.4 - - - +
490P TYR* 3.4 31.1 + - + +
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Residues in contact with LYS 476 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71P GLU* 3.5 30.9 + - + +
72P TYR* 3.2 49.4 - - + -
472P PHE* 2.8 17.9 + - + +
473P GLU* 3.5 19.1 - - - +
475P LEU* 1.3 75.3 - - - +
477P GLU* 1.3 69.6 + - - +
478P GLY* 3.0 2.1 + - - -
490P TYR* 4.0 19.7 + - + +
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Residues in contact with GLU 477 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473P GLU* 2.9 45.2 + - - +
474P MET* 4.0 6.5 + - - +
476P LYS* 1.3 81.5 - - + +
478P GLY* 1.3 65.8 + - - +
479P LYS* 3.1 25.1 + - + +
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Residues in contact with GLY 478 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474P MET 2.9 13.3 + - - -
475P LEU* 3.0 13.9 + - - -
476P LYS 2.9 5.7 - - - -
477P GLU* 1.3 76.9 - - - +
479P LYS* 1.3 58.7 + - - +
480P VAL 3.5 4.5 - - - -
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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
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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