Contacts of the helix formed by residues 435 - 446 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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434I LYS* 2.8 33.4 - - - +
436I LEU* 3.8 2.2 - - - -
280L ASP* 3.4 18.1 + - - +
433L THR* 2.9 7.9 + - - +
434L LYS* 1.3 78.9 - - - +
436L LEU* 1.3 59.4 - - - +
437L ASP* 3.5 10.2 + - - +
438L LYS* 3.0 43.2 + - + +
439L ALA* 2.9 31.0 + - - +
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Residues in contact with LEU 436 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433I THR 4.0 4.5 - - - +
434I LYS 2.8 19.7 + - - +
435I ASP 3.8 1.6 - - - -
436I LEU* 3.1 36.5 - - + +
439I ALA* 3.8 19.3 - - + -
440I ASN* 5.4 3.6 - - - +
453I VAL* 3.7 20.0 - - + -
454I ASN* 3.6 27.8 - - - +
493J VAL* 4.3 11.4 - - + -
435L ASP* 1.3 69.6 - - - +
437L ASP* 1.3 68.4 + - - +
439L ALA* 3.3 4.2 + - - +
440L ASN* 3.0 49.7 + - - +
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Residues in contact with ASP 437 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434I LYS* 4.3 8.5 + - - +
454I ASN* 4.3 8.1 + - - -
494J LYS* 4.2 14.2 - - - +
496J PRO* 3.9 20.4 - - + +
435L ASP* 3.5 10.0 + - - +
436L LEU* 1.3 94.1 - - - +
438L LYS* 1.3 57.2 + - + +
440L ASN* 4.6 5.0 + - - +
441L TYR* 2.8 33.1 + - - +
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Residues in contact with LYS 438 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278L MET* 4.1 23.9 - - + +
279L SER* 4.8 8.3 + - - -
280L ASP* 3.9 20.1 + - - +
311L GLN* 5.0 2.0 + - - +
413L ILE* 4.0 21.8 - - + -
433L THR* 4.1 15.3 - - + +
435L ASP* 3.0 40.2 + - + +
436L LEU 3.3 0.2 - - - -
437L ASP* 1.3 72.5 - - + +
439L ALA* 1.3 64.7 + - - +
441L TYR* 3.6 2.4 - - - +
442L LEU* 3.0 30.4 + - - +
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Residues in contact with ALA 439 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436I LEU* 3.8 30.5 - - + -
493K VAL* 6.4 0.2 - - + -
431L VAL* 4.7 6.4 - - - +
433L THR* 4.0 10.7 - - + +
435L ASP 2.9 17.0 + - - +
436L LEU 3.5 4.9 - - - +
438L LYS* 1.3 76.8 - - - +
440L ASN* 1.3 58.1 + - - +
442L LEU* 4.0 0.9 - - - +
443L SER* 2.9 32.8 + - - -
453L VAL* 4.0 17.3 - - + +
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Residues in contact with ASN 440 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436I LEU* 5.6 2.2 - - - +
151J PHE* 4.9 10.8 - - - -
493J VAL* 4.2 14.6 - - - +
494J LYS 5.1 1.0 + - - -
495J VAL* 4.3 22.0 - - + +
496J PRO* 4.6 5.4 - - + -
153K TYR* 4.6 8.0 + - - -
436L LEU* 3.0 45.2 + - - +
437L ASP* 4.0 4.8 + - - +
439L ALA* 1.3 76.2 - - - +
441L TYR* 1.3 68.2 + - - +
443L SER* 3.1 18.4 + - - -
444L GLN* 3.3 15.5 + - - +
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Residues in contact with TYR 441 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496J PRO* 3.9 30.2 - - + +
497J GLN* 5.6 3.1 - - + -
413L ILE* 3.6 37.7 - - + -
414L GLU* 4.1 22.1 - - + +
417L VAL* 3.8 26.5 - - + +
437L ASP 2.8 23.6 + - - +
438L LYS* 3.3 5.4 + - - +
440L ASN* 1.3 75.0 - - - +
442L LEU* 1.3 58.9 + - + +
444L GLN* 4.0 5.9 + - - +
445L ALA* 3.1 35.3 + - + +
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Residues in contact with LEU 442 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276L ILE* 4.4 15.0 - - + -
278L MET* 4.2 16.2 - - + -
413L ILE* 3.7 30.7 - - + -
416L VAL* 4.4 8.7 - - + -
417L VAL* 3.5 31.4 - - + -
431L VAL* 3.6 39.7 - - + -
438L LYS 3.0 15.3 + - - +
439L ALA 4.1 1.1 - - - +
441L TYR* 1.3 74.4 - - + +
443L SER* 1.3 59.2 + - - +
444L GLN 3.1 2.0 - - - -
445L ALA* 4.4 1.1 - - - +
446L LEU* 2.9 42.9 + - + +
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Residues in contact with SER 443 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153K TYR* 4.0 11.1 + - - -
155K ARG* 5.9 0.4 - - - -
489K LYS* 3.2 25.6 + - - +
491K VAL* 3.9 28.8 - - - +
431L VAL* 5.1 0.4 - - - +
439L ALA 2.9 18.1 + - - -
440L ASN* 3.1 20.4 + - - -
442L LEU* 1.3 76.2 - - - +
444L GLN* 1.3 57.3 + - - +
446L LEU 4.1 0.5 - - - +
451L VAL* 3.8 24.7 - - - +
453L VAL* 4.6 5.8 - - - -
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Residues in contact with GLN 444 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495J VAL* 5.3 8.5 - - - +
496J PRO* 5.9 2.2 - - - +
497J GLN 3.1 24.9 + - - +
498J LYS* 3.6 4.5 - - - +
499J ASN* 2.7 48.4 + - + +
72K LEU* 5.6 5.1 - - + +
155K ARG* 3.8 26.2 + - - +
157K GLU* 4.2 1.0 - - - +
489K LYS* 2.9 19.2 + - - +
440L ASN 3.3 14.6 + - - +
441L TYR* 4.0 5.4 + - - +
442L LEU 3.1 0.2 - - - -
443L SER* 1.3 80.9 + - - +
445L ALA* 1.3 61.0 + - - +
446L LEU 3.5 0.2 - - - -
447L GLN* 5.9 0.3 - - - +
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Residues in contact with ALA 445 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72K LEU* 4.6 23.1 - - + +
417L VAL* 3.9 36.4 - - + +
421L ASN* 4.8 2.8 - - - +
441L TYR* 3.1 28.7 + - + +
442L LEU* 3.3 2.2 + - - +
444L GLN* 1.3 77.4 - - - +
446L LEU* 1.3 64.2 + - - +
447L GLN* 3.3 14.7 + - - +
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Residues in contact with LEU 446 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489K LYS* 2.8 29.3 + - - -
274L PRO* 5.0 0.2 - - + -
276L ILE* 3.9 13.5 - - + -
417L VAL* 4.9 10.5 - - - +
420L ALA* 3.9 28.0 - - + -
421L ASN* 5.2 3.8 - - - +
429L ALA* 3.9 26.9 - - + -
430L ALA 4.5 0.9 - - - +
431L VAL* 3.6 29.6 - - + -
442L LEU* 2.9 30.2 + - + +
443L SER 4.1 0.3 - - - +
445L ALA* 1.3 73.6 - - - +
447L GLN* 1.3 60.2 + - - +
448L ALA 3.3 4.0 + - - -
451L VAL* 4.1 20.5 - - + +
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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