Contacts of the helix formed by residues 462 - 478 (chain Q) 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 Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445Q GLU* 3.4 10.1 - - - -
460Q THR 3.3 2.4 + - - -
461Q LYS* 1.3 77.3 - - - +
463Q ARG* 1.3 67.8 + - - +
464Q ALA 3.3 2.7 - - - -
465Q LEU* 3.3 17.3 + - - +
466Q VAL* 4.4 1.2 + - - +
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Residues in contact with ARG 463 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418Q THR 4.6 0.7 - - - +
421Q HIS* 3.6 57.3 + - + +
445Q GLU* 3.3 7.4 + - - +
462Q GLY* 1.3 71.4 - - - +
464Q ALA* 1.3 63.6 + - - +
466Q VAL* 3.2 24.4 - - - +
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Residues in contact with ALA 464 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418Q THR* 3.1 27.0 - - - +
419Q ALA* 4.0 2.5 - - + -
421Q HIS* 3.8 5.8 - - + -
445Q GLU* 3.1 24.8 + - - +
446Q ILE* 3.9 24.9 - - + -
459Q TRP* 3.8 4.4 - - + -
463Q ARG* 1.3 77.0 - - - +
465Q LEU* 1.3 59.6 + - - +
467Q GLY* 2.8 21.0 + - - -
468Q GLY 3.0 10.0 + - - -
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Residues in contact with LEU 465 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318Q SER* 3.5 27.8 - - - +
319Q LEU* 4.0 20.6 - - + -
445Q GLU* 4.2 1.0 + - - -
459Q TRP* 4.1 15.1 - - + -
460Q THR 3.5 18.4 + - - +
461Q LYS* 3.9 21.5 - - + +
462Q GLY 3.3 13.9 + - - +
463Q ARG 3.3 1.4 - - - -
464Q ALA* 1.3 74.6 - - - +
466Q VAL* 1.3 66.3 + - - +
468Q GLY 3.3 0.5 + - - -
469Q HIS* 3.1 41.7 + - + +
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Residues in contact with VAL 466 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462Q GLY 4.4 1.2 + - - +
463Q ARG 3.2 18.5 + - - +
465Q LEU* 1.3 78.1 - - - +
467Q GLY* 1.3 66.5 + - - +
469Q HIS* 3.3 12.0 + - + +
470Q ARG* 3.3 37.0 + - + +
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Residues in contact with GLY 467 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417Q HIS 3.7 15.0 - - - +
418Q THR* 3.2 17.9 + - - +
464Q ALA 2.8 8.6 + - - -
466Q VAL* 1.3 81.4 - - - +
468Q GLY* 1.3 65.9 + - - +
470Q ARG* 2.9 30.4 + - - +
471Q LEU 2.9 10.2 + - - -
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Residues in contact with GLY 468 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319Q LEU* 3.6 8.2 - - - +
418Q THR* 3.2 13.5 - - - +
459Q TRP* 3.6 28.5 - - - -
464Q ALA 3.0 10.5 + - - -
465Q LEU 3.3 4.8 + - - -
467Q GLY* 1.3 75.0 - - - +
469Q HIS* 1.3 61.7 + - - +
471Q LEU* 3.0 4.7 + - - +
472Q PHE* 2.9 23.6 + - - +
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Residues in contact with HIS 469 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318Q SER 4.9 4.9 + - - -
319Q LEU* 3.6 27.8 - - + +
465Q LEU* 3.1 46.5 + - + +
466Q VAL* 3.5 10.5 - - + +
467Q GLY 3.1 0.4 - - - -
468Q GLY* 1.3 76.0 - - - +
470Q ARG* 1.3 62.2 + - + +
472Q PHE* 3.6 6.9 + - - +
473Q GLU* 3.1 23.2 + - - +
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Residues in contact with ARG 470 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417Q HIS* 4.2 11.5 + - + +
418Q THR* 5.6 0.6 - - - +
466Q VAL* 3.3 34.6 + - + +
467Q GLY* 2.9 22.3 + - - +
469Q HIS* 1.3 79.1 - - - +
471Q LEU* 1.3 53.8 + - - +
473Q GLU* 3.1 9.2 + - - +
474Q MET* 2.8 35.1 + - + +
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Residues in contact with LEU 471 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321Q VAL* 5.9 1.1 - - + -
413Q MET* 4.1 33.4 - - + +
414Q GLN* 4.9 1.1 - - + -
417Q HIS* 4.0 11.4 + - + +
418Q THR* 4.3 7.2 - - + -
457Q LEU* 5.5 2.2 - - + -
459Q TRP* 4.0 28.0 - - + -
467Q GLY 2.9 10.8 + - - +
468Q GLY 3.2 9.0 - - - +
470Q ARG* 1.3 73.9 - - - +
472Q PHE* 1.3 58.6 + - - +
474Q MET* 2.7 41.6 + - + +
475Q LEU* 2.8 24.8 + - + +
482Q PRO* 3.9 28.7 - - + -
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Residues in contact with PHE 472 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72Q TYR* 3.3 57.0 - + + -
74Q ARG* 4.4 18.8 - - + -
319Q LEU* 3.7 30.1 - - + -
320Q CYS 4.3 11.0 - - - -
321Q VAL* 3.7 24.2 - - + +
322Q ALA 5.9 0.7 - - - -
468Q GLY 2.9 14.9 + - - +
469Q HIS* 3.7 9.9 - - - +
471Q LEU* 1.3 75.9 - - - +
473Q GLU* 1.3 58.2 + - - +
475Q LEU* 3.1 14.8 + - + +
476Q LYS* 2.8 26.6 + - + +
490Q TYR* 4.9 11.0 - + + -
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Residues in contact with GLU 473 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72Q TYR* 2.6 33.8 + - - -
469Q HIS 3.1 14.8 + - - +
470Q ARG* 3.2 12.1 - - - +
471Q LEU 3.1 0.4 - - - -
472Q PHE* 1.3 78.6 - - - +
474Q MET* 1.3 55.4 + - - +
476Q LYS* 3.2 19.9 + - - +
477Q GLU* 2.9 55.1 + - - +
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Residues in contact with MET 474 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417Q HIS* 3.1 39.3 - - + +
470Q ARG* 2.8 10.5 + - + +
471Q LEU* 2.7 28.7 + - + +
473Q GLU* 1.3 72.4 - - - +
475Q LEU* 1.3 53.3 + - - +
477Q GLU* 3.5 7.7 + - - +
478Q GLY* 2.9 26.0 + - - -
479Q LYS 4.2 1.9 + - - -
480Q VAL* 3.6 40.4 - - + +
482Q PRO* 3.9 20.6 - - + -
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Residues in contact with LEU 475 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321Q VAL* 3.5 31.6 - - + -
323Q THR* 5.2 5.8 - - + -
413Q MET* 5.1 2.7 - - - -
457Q LEU* 6.4 0.2 - - + -
471Q LEU* 2.8 30.6 + - + +
472Q PHE* 3.1 11.9 + - + +
474Q MET* 1.3 74.7 - - - +
476Q LYS* 1.3 66.8 + - - +
478Q GLY* 3.0 14.2 + - - +
480Q VAL 5.8 0.7 - - - -
482Q PRO* 3.8 29.6 - - + -
488Q ILE* 4.6 4.0 - - + -
489Q SER* 3.8 31.9 - - - +
490Q TYR* 3.4 32.4 + - + +
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Residues in contact with LYS 476 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71Q GLU* 3.5 30.9 + - + +
72Q TYR* 3.2 49.4 - - + -
472Q PHE* 2.8 18.3 + - + +
473Q GLU* 3.2 20.8 + - - +
475Q LEU* 1.3 76.0 - - - +
477Q GLU* 1.3 68.6 + - - +
478Q GLY* 3.0 2.1 + - - -
490Q TYR* 4.0 19.6 + - + +
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Residues in contact with GLU 477 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473Q GLU* 2.9 45.4 + - - +
474Q MET* 4.0 6.4 + - - +
476Q LYS* 1.3 81.3 - - + +
478Q GLY* 1.3 66.2 + - - +
479Q LYS* 3.1 25.1 + - + +
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Residues in contact with GLY 478 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474Q MET 2.9 13.0 + - - -
475Q LEU* 3.0 13.9 + - - -
476Q LYS 2.9 4.9 - - - -
477Q GLU* 1.3 77.9 - - - +
479Q LYS* 1.3 59.8 + - - +
480Q VAL 3.5 4.7 - - - -
489Q SER* 6.5 1.1 - - - -
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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