Contacts of the helix formed by residues 435 - 446 (chain G) in PDB entry 1ZUM
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 435 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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434F LYS* 3.5 25.1 - - - +
436F LEU* 4.3 2.0 - - - -
280G ASP* 3.3 17.4 + - - +
433G THR* 3.2 2.8 + - - +
434G LYS* 1.3 77.8 - - - +
436G LEU* 1.3 65.7 + - - +
437G ASP* 3.3 13.1 + - - +
438G LYS* 2.9 48.8 + - + +
439G ALA* 3.0 22.3 + - - +
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Residues in contact with LEU 436 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493E VAL* 4.3 12.1 - - + -
494E LYS 5.1 0.4 - - - +
433F THR 4.2 3.4 - - - +
434F LYS* 3.0 20.0 + - - +
435F ASP 4.3 0.2 - - - -
436F LEU* 3.7 35.5 - - + +
439F ALA* 4.2 17.5 - - + -
440F ASN* 5.7 2.2 - - - +
453F VAL* 3.8 20.0 - - + -
454F ASN* 3.7 27.1 - - - +
434G LYS 3.6 2.4 + - - -
435G ASP* 1.3 69.4 - - - +
437G ASP* 1.3 70.7 + - - +
439G ALA* 3.2 5.4 + - - +
440G ASN* 3.0 46.3 + - - +
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Residues in contact with ASP 437 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494E LYS* 4.0 17.0 - - - +
495E VAL* 4.8 0.6 - - - -
496E PRO* 3.8 29.1 - - + +
434F LYS* 4.9 1.9 + - - +
454F ASN* 4.9 7.0 + - - -
435G ASP* 3.3 9.9 + - - +
436G LEU* 1.3 85.3 - - - +
438G LYS* 1.3 57.6 + - + +
440G ASN* 3.7 2.2 + - - +
441G TYR* 2.8 33.2 + - - +
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Residues in contact with LYS 438 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278G MET* 4.4 21.0 - - + +
279G SER* 5.2 4.9 + - - -
280G ASP* 3.4 27.6 + - - +
311G GLN* 5.5 1.0 + - - -
413G ILE* 4.0 22.4 - - + -
433G THR* 3.8 19.3 - - + +
435G ASP* 2.9 36.4 + - + +
437G ASP* 1.3 71.5 - - - +
439G ALA* 1.3 64.8 + - - +
441G TYR* 3.7 2.3 - - - +
442G LEU* 3.0 30.0 + - + +
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Residues in contact with ALA 439 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436F LEU* 4.4 15.9 - - + -
431G VAL* 4.8 6.3 - - - +
433G THR* 3.9 12.0 - - + +
435G ASP 3.0 12.4 + - - +
436G LEU 3.2 8.3 + - - +
438G LYS* 1.3 77.4 - - - +
440G ASN* 1.3 61.0 + - - +
442G LEU* 3.8 1.0 - - - +
443G SER* 2.9 32.2 + - - -
453G VAL* 3.8 30.6 - - + +
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Residues in contact with ASN 440 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151E PHE* 4.8 10.4 - - - -
493E VAL* 4.1 9.3 - - - +
494E LYS 4.8 1.4 + - - -
495E VAL* 3.9 33.7 - - + +
496E PRO* 4.6 3.6 - - + -
436F LEU* 5.9 1.2 - - - +
436G LEU* 3.0 43.9 + - - +
437G ASP* 4.0 3.9 + - - +
439G ALA* 1.3 74.1 - - - +
441G TYR* 1.3 67.0 + - - +
443G SER* 3.5 9.1 + - - -
444G GLN* 3.2 24.9 + - - +
153H TYR* 4.4 9.7 + - - -
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Residues in contact with TYR 441 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496E PRO* 4.4 24.8 - - + +
497E GLN* 6.0 2.5 - - + -
413G ILE* 3.7 34.8 - - + -
414G GLU* 3.6 28.2 - - + +
417G VAL* 3.7 27.3 - - + +
437G ASP 2.8 23.7 + - - +
438G LYS* 3.7 4.5 - - - +
440G ASN* 1.3 75.0 - - - +
442G LEU* 1.3 62.0 + - + +
444G GLN* 3.9 6.4 + - - +
445G ALA* 3.0 35.4 + - + +
72H LEU* 6.0 4.5 - - + +
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Residues in contact with LEU 442 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276G ILE* 4.5 13.9 - - + -
278G MET* 4.1 14.1 - - + -
413G ILE* 3.6 33.0 - - + -
416G VAL* 4.5 9.4 - - + -
417G VAL* 3.5 29.6 - - + -
431G VAL* 3.4 42.0 - - + -
438G LYS 3.0 16.2 + - - +
439G ALA 4.1 0.9 - - - +
441G TYR* 1.3 75.6 - - + +
443G SER* 1.3 66.2 + - - +
444G GLN 3.1 1.6 - - - -
445G ALA* 4.3 1.1 - - - +
446G LEU* 2.9 35.0 + - + +
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Residues in contact with SER 443 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431G VAL* 5.0 0.6 - - - +
439G ALA 2.9 20.5 + - - -
440G ASN* 3.5 11.3 + - - -
442G LEU* 1.3 78.5 - - - +
444G GLN* 1.3 59.7 + - - +
451G VAL* 3.9 22.9 - - - +
453G VAL* 4.6 5.6 - - - -
153H TYR* 3.9 13.3 + - - -
155H ARG* 5.7 1.5 - - - -
489H LYS* 2.8 30.1 + - - +
491H VAL* 4.0 25.9 - - - +
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Residues in contact with GLN 444 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495E VAL* 5.7 3.4 - - - +
497E GLN 2.7 28.3 + - - +
498E LYS* 3.7 6.1 - - - +
499E ASN* 2.9 44.2 + - + +
440G ASN 3.2 14.1 + - - +
441G TYR* 3.9 5.1 + - - +
442G LEU 3.1 0.6 - - - -
443G SER* 1.3 81.9 + - - +
445G ALA* 1.3 60.7 + - - +
446G LEU 3.9 0.2 - - - +
72H LEU* 5.1 8.5 - - + +
77H ARG* 5.9 1.4 + - - +
155H ARG* 3.3 35.8 + - - +
157H GLU* 4.1 2.9 - - - +
489H LYS* 3.0 19.0 + - - +
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Residues in contact with ALA 445 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417G VAL* 3.9 30.6 - - + +
421G ASN* 2.9 20.9 + - - -
441G TYR* 3.0 26.6 + - + +
442G LEU 4.2 1.3 - - - +
444G GLN* 1.3 75.4 - - - +
446G LEU* 1.3 61.2 + - - +
447G GLN* 3.4 7.1 + - - +
72H LEU* 4.0 26.5 - - + +
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Residues in contact with LEU 446 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274G PRO* 4.9 0.9 - - + -
276G ILE* 3.8 14.6 - - + -
417G VAL* 4.9 5.2 - - - +
420G ALA* 3.7 30.5 - - + -
421G ASN* 3.5 8.5 - - - +
429G ALA* 4.1 25.6 - - + -
430G ALA 4.7 0.2 - - - +
431G VAL* 3.5 30.3 - - + -
442G LEU* 2.9 36.3 + - + +
444G GLN 3.4 0.4 - - - -
445G ALA* 1.3 72.0 - - - +
447G GLN* 1.3 59.4 + - - +
448G ALA 3.2 4.4 + - - -
451G VAL* 4.2 17.4 - - + +
489H LYS* 2.8 29.5 + - - -
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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