Contacts of the helix formed by residues 435 - 446 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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434J LYS* 3.5 25.4 - - - +
436J LEU* 4.1 2.2 - - - +
280K ASP* 3.4 18.7 + - - +
433K THR* 3.0 7.7 + - - +
434K LYS* 1.3 78.5 - - - +
436K LEU* 1.3 65.3 + - - +
437K ASP* 3.2 13.8 + - - +
438K LYS* 2.9 43.0 + - + +
439K ALA* 3.0 25.5 + - - +
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Residues in contact with LEU 436 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493I VAL* 4.3 11.2 - - + -
494I LYS 5.2 0.4 - - - +
433J THR 4.3 3.1 - - - +
434J LYS* 2.8 21.1 + - - +
435J ASP 4.2 0.4 - - - -
436J LEU* 3.7 35.4 - - + +
439J ALA* 4.1 16.8 - - + -
440J ASN* 5.8 1.1 - - - +
453J VAL* 3.7 30.1 - - + -
454J ASN* 3.8 17.7 - - - +
435K ASP* 1.3 71.4 - - - +
437K ASP* 1.3 68.0 + - - +
439K ALA* 3.2 3.6 + - - +
440K ASN* 2.9 47.5 + - - +
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Residues in contact with ASP 437 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494I LYS* 4.1 20.6 + - - +
495I VAL* 4.8 0.3 - - - -
496I PRO* 4.0 30.5 - - + +
434J LYS* 4.6 5.2 + - - +
454J ASN* 4.9 8.0 + - - -
435K ASP* 3.2 9.4 + - - +
436K LEU* 1.3 86.2 - - - +
438K LYS* 1.3 58.1 + - + +
440K ASN* 3.4 2.7 + - - -
441K TYR* 2.8 33.2 + - - +
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Residues in contact with LYS 438 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278K MET* 4.3 22.1 - - + +
279K SER* 4.8 7.5 + - - -
280K ASP* 3.0 29.5 + - - +
311K GLN* 5.2 1.2 + - - -
413K ILE* 4.2 22.7 - - + -
433K THR* 3.8 13.7 - - + +
435K ASP* 2.9 37.2 + - + +
436K LEU 3.3 0.2 - - - -
437K ASP* 1.3 75.2 - - + +
439K ALA* 1.3 58.2 + - - +
441K TYR* 3.6 1.7 - - - +
442K LEU* 2.9 37.7 + - + +
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Residues in contact with ALA 439 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436J LEU* 4.2 15.7 - - + -
431K VAL* 4.8 6.8 - - - +
433K THR* 3.9 15.4 - - + +
435K ASP 3.0 18.8 + - - +
436K LEU 3.5 4.3 - - - +
438K LYS* 1.3 77.9 - - - +
440K ASN* 1.3 58.8 + - - +
442K LEU* 4.0 1.0 - - - +
443K SER* 3.0 32.7 + - - -
453K VAL* 4.0 25.5 - - + +
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Residues in contact with ASN 440 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151I PHE* 4.8 7.5 - - - -
493I VAL* 4.0 9.7 - - - +
494I LYS 4.9 1.4 + - - -
495I VAL* 3.9 32.4 - - + +
496I PRO* 4.7 3.8 - - + -
436J LEU* 5.6 1.9 - - - +
436K LEU* 2.9 43.5 + - - +
437K ASP* 4.0 3.7 + - - +
439K ALA* 1.3 74.6 - - - +
441K TYR* 1.3 66.0 + - - +
443K SER* 3.4 7.6 + - - -
444K GLN* 3.2 26.3 + - - +
153L TYR* 4.5 5.0 + - - -
3129L EDO 3.7 16.6 - - - -
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Residues in contact with TYR 441 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496I PRO* 4.3 25.7 - - + +
497I GLN* 5.7 3.1 - - + -
413K ILE* 3.6 33.4 - - + -
414K GLU* 3.9 22.5 - - + +
417K VAL* 3.7 27.4 - - + +
437K ASP 2.8 19.9 + - - +
438K LYS* 3.6 4.9 - - - +
440K ASN* 1.3 77.6 - - - +
442K LEU* 1.3 61.6 + - + +
444K GLN* 3.9 3.2 - - - +
445K ALA* 3.0 35.9 + - + +
72L LEU* 6.0 3.1 - - + +
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Residues in contact with LEU 442 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276K ILE* 4.4 21.3 - - + -
278K MET* 4.0 18.8 - - + -
413K ILE* 3.9 25.8 - - + -
416K VAL* 4.5 2.7 - - + -
417K VAL* 3.5 30.3 - - + -
431K VAL* 3.5 40.6 - - + -
438K LYS 2.9 17.7 + - - +
439K ALA 4.1 1.1 - - - +
441K TYR* 1.3 74.2 - - + +
443K SER* 1.3 60.3 + - - +
444K GLN 3.1 1.6 - - - -
445K ALA* 4.3 0.9 - - - +
446K LEU* 2.9 41.7 + - + +
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Residues in contact with SER 443 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431K VAL* 4.9 0.6 - - - +
439K ALA 3.0 21.0 + - - -
440K ASN* 3.4 3.3 + - - -
441K TYR 3.5 0.2 - - - -
442K LEU* 1.3 76.4 - - - +
444K GLN* 1.3 57.6 + - - +
446K LEU 4.1 0.3 - - - +
451K VAL* 3.8 29.0 - - - +
453K VAL* 4.6 5.6 - - - -
153L TYR* 3.9 1.7 + - - -
155L ARG* 4.5 0.2 + - - -
489L LYS* 2.9 28.1 + - - +
491L VAL* 3.9 17.2 - - - +
3129L EDO 2.6 34.9 + - - -
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Residues in contact with GLN 444 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495I VAL* 4.9 10.7 - - - +
497I GLN 4.1 12.5 + - - -
498I LYS* 3.7 7.5 - - - +
499I ASN* 2.7 50.2 + - + +
440K ASN 3.2 14.1 + - - +
441K TYR* 4.0 2.7 - - - +
442K LEU 3.1 0.6 - - - -
443K SER* 1.3 81.7 + - - +
445K ALA* 1.3 61.6 + - - +
72L LEU* 5.1 7.0 - - + +
155L ARG* 3.4 32.8 + - - +
157L GLU* 4.5 0.9 - - - +
489L LYS* 3.1 15.8 + - - -
3129L EDO 4.1 15.7 - - - -
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Residues in contact with ALA 445 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417K VAL* 4.0 31.2 - - + -
421K ASN* 3.1 17.8 + - - -
441K TYR* 3.0 26.8 + - + +
442K LEU 3.2 1.8 + - - +
444K GLN* 1.3 77.6 - - - +
446K LEU* 1.3 64.9 + - - +
447K GLN* 3.3 7.8 + - - +
72L LEU* 4.3 24.3 - - + +
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Residues in contact with LEU 446 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274K PRO* 5.0 0.4 - - + -
276K ILE* 3.9 14.1 - - + -
417K VAL* 4.9 4.9 - - + +
420K ALA* 3.8 29.4 - - + -
421K ASN* 3.6 7.6 - - - +
429K ALA* 4.0 27.1 - - + -
430K ALA 4.7 1.3 - - - +
431K VAL* 3.6 29.2 - - + -
442K LEU* 2.9 33.8 + - + +
445K ALA* 1.3 70.3 - - - +
447K GLN* 1.3 60.5 + - - +
448K ALA 3.2 5.0 + - - -
451K VAL* 4.1 19.2 - - + +
489L LYS* 3.0 26.3 + - - -
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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