Contacts of the helix formed by residues 437 - 457 (chain G) in PDB entry 1Q57
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 ASP 437 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436G SER* 1.3 82.0 - - - +
438G GLU* 1.3 58.8 + - - +
439G ARG* 2.9 64.0 + - + +
440G LYS* 2.9 26.7 + - + +
441G MET* 3.0 10.4 + - - +
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Residues in contact with GLU 438 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494B GLN* 5.2 2.1 + - - -
427G SER* 3.2 20.0 - - - +
428G ILE* 5.1 0.2 - - - -
429G VAL* 2.8 49.8 - - + +
436G SER 3.6 1.6 + - - -
437G ASP* 1.3 71.1 + - - +
439G ARG* 1.3 53.5 + - - +
441G MET* 4.4 6.7 - - + +
442G ILE* 2.8 47.4 + - + +
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Residues in contact with ARG 439 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437G ASP* 3.0 43.7 + - + +
438G GLU* 1.3 75.7 - - - +
440G LYS* 1.3 57.1 + - - +
442G ILE* 2.6 25.9 - - - +
443G ASP* 3.4 9.4 - - - +
488G GLY* 4.7 5.6 - - - +
489G SER* 3.0 34.4 - - - +
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Residues in contact with LYS 440 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436G SER 5.4 2.5 - - - +
437G ASP* 2.9 15.9 + - + +
439G ARG* 1.3 77.5 - - + +
441G MET* 1.3 100.0 + - + +
443G ASP* 3.0 23.7 + - - +
444G ASN* 3.0 34.2 + - - +
489G SER* 5.7 0.4 - - - -
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Residues in contact with MET 441 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402G THR* 3.6 41.3 - - + +
429G VAL* 3.8 27.8 - - + -
435G GLU* 4.0 22.7 - - + +
436G SER 4.9 2.5 - - - +
437G ASP 3.0 11.7 + - - +
438G GLU* 4.4 7.0 - - + +
440G LYS* 1.3 96.5 - - + +
442G ILE* 1.3 66.5 + - - +
443G ASP 3.0 1.0 + - - -
444G ASN* 3.0 21.2 + - + +
445G LEU* 3.1 25.8 + - + +
448G LYS* 5.0 0.2 - - - +
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Residues in contact with ILE 442 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426G ILE* 3.7 27.5 - - + +
427G SER* 6.4 0.4 - - - -
429G VAL* 4.7 6.1 - - - +
438G GLU* 2.8 30.1 + - + +
439G ARG* 2.6 32.3 - - - +
441G MET* 1.3 72.5 - - - +
443G ASP* 1.3 63.1 + - - +
445G LEU* 3.7 4.0 + - - +
446G MET* 3.0 26.3 + - - +
487G ARG* 5.8 1.1 - - + -
488G GLY* 3.2 18.4 - - - +
492G LEU* 3.0 48.7 - - + -
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Residues in contact with ASP 443 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439G ARG 3.4 9.6 - - - +
440G LYS* 3.0 12.2 + - - +
441G MET 3.0 0.6 - - - -
442G ILE* 1.3 88.9 - - - +
444G ASN* 1.3 66.0 + - - +
446G MET* 2.9 18.9 + - - +
447G THR* 3.0 14.0 + - + +
489G SER* 3.4 25.2 + - - +
490G GLY 4.0 0.4 - - - -
491G ALA* 3.1 38.1 + - + +
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Residues in contact with ASN 444 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440G LYS* 3.0 38.4 + - - +
441G MET* 3.0 8.7 + - + +
443G ASP* 1.3 75.9 - - - +
445G LEU* 1.3 62.4 + - - +
447G THR* 2.8 25.7 + - - -
448G LYS* 3.0 36.5 + - - +
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Residues in contact with LEU 445 (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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402G THR* 4.1 17.9 - - - +
405G LEU* 5.7 7.2 - - + -
406G LEU* 3.2 32.1 - - + -
423G LEU* 5.3 5.8 - - + -
426G ILE* 4.0 33.0 - - + +
428G ILE 5.2 2.0 - - - +
429G VAL* 5.2 14.4 - - + +
441G MET* 3.1 19.0 + - + +
442G ILE* 3.9 6.3 - - - +
444G ASN* 1.3 76.2 + - - +
446G MET* 1.3 68.5 + - - +
448G LYS* 2.8 18.8 + - - +
449G LEU* 2.9 29.6 + - + +
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Residues in contact with MET 446 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307G VAL* 4.5 9.4 - - + -
309G MET* 3.6 16.6 - - + -
426G ILE* 5.2 8.5 - - - -
442G ILE 3.0 14.3 + - - +
443G ASP 2.9 15.4 + - - +
445G LEU* 1.3 77.9 - - - +
447G THR* 1.3 54.8 + - - +
449G LEU* 3.3 18.1 - - - +
450G LYS* 3.0 23.3 + - + +
462G VAL* 5.5 0.7 - - + -
491G ALA* 3.4 13.0 - - + +
492G LEU* 3.3 46.4 - - + +
495G LEU* 3.4 10.0 - - + +
496G SER* 3.1 34.3 - - - +
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Residues in contact with THR 447 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443G ASP* 3.0 13.9 + - + +
444G ASN* 2.8 19.8 + - - -
445G LEU 2.9 1.8 + - - -
446G MET* 1.3 72.2 - - - +
448G LYS* 1.3 71.3 + - - +
449G LEU 2.8 3.1 + - - -
450G LYS* 2.8 3.3 + - - +
451G GLY* 2.8 21.0 + - - -
491G ALA* 4.9 2.7 - - + -
495G LEU* 3.1 27.1 - - + -
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Residues in contact with LYS 448 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402G THR* 3.7 25.2 + - - +
403G ASP* 3.0 28.8 + - - +
406G LEU* 3.9 24.4 - - + +
444G ASN* 3.0 36.7 + - - +
445G LEU* 2.8 12.2 + - - +
447G THR* 1.3 74.7 + - - +
449G LEU* 1.3 58.0 + - - +
451G GLY* 3.4 1.8 + - - +
452G PHE* 2.8 29.8 + - - +
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Residues in contact with LEU 449 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307G VAL* 5.3 2.2 - - + -
406G LEU* 3.2 38.4 - - + -
409G LEU* 5.4 5.4 - - + -
423G LEU* 4.1 17.9 - - + -
426G ILE* 5.1 1.6 - - + -
445G LEU* 2.9 29.6 + - + +
446G MET* 3.3 21.1 - - - +
447G THR 2.8 1.0 + - - -
448G LYS* 1.3 77.4 - - - +
450G LYS* 1.3 53.6 + - - +
451G GLY 3.0 0.5 + - - -
452G PHE* 3.0 11.1 + - + +
453G ALA* 2.8 34.0 + - - +
460G LEU* 3.8 29.1 - - + +
462G VAL* 3.9 17.9 - - + -
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Residues in contact with LYS 450 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305G GLY 3.5 7.6 - - - -
307G VAL* 3.7 19.7 - - + +
446G MET* 3.0 9.8 + - + +
447G THR* 2.8 10.6 + - - +
449G LEU* 1.3 75.9 - - - +
451G GLY* 1.3 56.2 + - - +
453G ALA* 3.7 3.1 - - + -
454G LYS* 2.8 61.1 + - + +
495G LEU* 3.5 38.9 + - + +
497G ASP* 3.0 27.5 + - - -
522G ARG* 3.0 16.8 - - - +
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Residues in contact with GLY 451 (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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447G THR 2.8 12.4 + - - -
448G LYS* 3.6 4.9 - - - -
450G LYS* 1.3 73.4 - - - +
452G PHE* 1.3 67.6 + - - +
453G ALA 2.8 1.0 + - - -
454G LYS* 5.2 1.3 - - - -
455G SER* 2.7 33.8 + - - -
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Residues in contact with PHE 452 (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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406G LEU* 4.1 21.5 - - + -
409G LEU* 3.3 37.0 - - + -
410G ALA* 3.4 26.0 - - + -
413G ARG* 3.5 22.9 - - + -
414G SER* 5.8 0.4 - - - -
421G ILE* 4.4 3.6 - - + -
448G LYS 2.8 16.2 + - - +
449G LEU* 3.1 11.9 - - + +
451G GLY* 1.3 68.3 - - - +
453G ALA* 1.3 58.8 + - - +
455G SER* 4.2 4.9 + - - -
456G THR* 2.8 46.4 + - + +
458G VAL* 4.0 9.2 - - + -
460G LEU* 3.9 32.1 - - + -
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Residues in contact with ALA 453 (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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305G GLY* 3.4 15.7 - - - +
306G GLU 3.6 4.9 - - - +
307G VAL* 3.5 31.2 - - + -
449G LEU 2.8 11.3 + - - +
450G LYS* 3.3 10.1 - - + +
451G GLY 2.8 2.0 + - - -
452G PHE* 1.3 72.9 - - - +
454G LYS* 1.3 53.8 + - - +
456G THR 3.6 0.2 - - - -
457G GLY* 2.7 35.9 + - - -
458G VAL* 3.7 14.2 + - - +
460G LEU* 4.5 5.2 - - + -
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Residues in contact with LYS 454 (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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348F GLU* 4.8 6.3 + - - -
305G GLY* 2.9 23.5 + - - +
306G GLU* 4.9 1.3 - - - +
450G LYS* 2.8 38.5 + - + +
451G GLY* 5.2 1.3 - - - -
453G ALA* 1.3 75.8 - - - +
455G SER* 1.3 65.5 + - - +
456G THR 3.2 1.0 + - - -
457G GLY* 3.8 5.4 + - - -
497G ASP* 3.8 4.5 - - - -
522G ARG* 3.3 37.0 - - - +
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Residues in contact with SER 455 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451G GLY* 2.7 27.2 + - - -
452G PHE* 3.7 1.7 + - - -
454G LYS* 1.3 73.3 - - - +
456G THR* 1.3 73.3 + - - +
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Residues in contact with THR 456 (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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413G ARG* 3.0 39.0 + - + +
414G SER* 5.6 4.9 - - - +
452G PHE* 2.8 34.9 + - + +
455G SER* 1.3 95.5 - - - +
457G GLY* 1.3 58.5 + - - +
458G VAL* 3.1 17.4 - - - +
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Residues in contact with GLY 457 (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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304G GLY* 3.3 11.2 - - - -
305G GLY* 3.1 19.6 + - - -
413G ARG* 3.0 12.3 + - - -
419G ASP* 4.9 0.7 - - - +
453G ALA 2.7 17.1 + - - -
454G LYS 3.8 5.0 + - - -
456G THR* 1.3 68.7 - - - +
458G VAL* 1.3 62.8 + - - -
459G VAL* 3.7 0.7 + - - +
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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