Contacts of the helix formed by residues 435 - 446 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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280J ASP* 3.3 18.9 + - - +
433J THR* 3.1 8.2 + - - +
434J LYS* 1.3 78.7 - - - +
436J LEU* 1.3 67.6 + - - +
437J ASP* 3.2 14.3 + - - +
438J LYS* 2.9 44.6 + - + +
439J ALA* 3.0 24.4 + - - +
434K LYS* 3.5 25.2 - - - +
436K LEU* 4.2 1.3 - - - -
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Residues in contact with LEU 436 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434J LYS 3.6 3.0 + - - -
435J ASP* 1.3 69.6 - - - +
437J ASP* 1.3 69.3 + - - +
439J ALA* 3.2 5.0 + - - +
440J ASN* 3.0 47.3 + - - +
433K THR 4.0 5.4 - - - +
434K LYS* 2.9 19.8 + - - +
436K LEU* 3.7 34.1 - - + +
439K ALA* 4.2 15.5 - - + -
440K ASN* 5.6 2.2 - - - +
453K VAL* 3.7 20.0 - - + -
454K ASN* 3.5 27.8 - - - +
493L VAL* 4.5 11.9 - - + -
494L LYS 5.3 0.2 - - - +
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Residues in contact with ASP 437 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435J ASP* 3.2 9.9 + - - +
436J LEU* 1.3 91.6 - - - +
438J LYS* 1.3 58.4 + - + +
440J ASN* 3.3 5.5 + - - +
441J TYR* 2.8 31.9 + - - +
434K LYS* 4.7 2.9 + - - +
454K ASN* 4.8 6.0 + - - -
494L LYS* 4.2 24.4 + - - +
495L VAL 5.9 0.2 - - - -
496L PRO* 3.9 22.2 - - + +
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Residues in contact with LYS 438 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278J MET* 4.1 21.9 - - + +
279J SER* 5.1 6.5 + - - -
280J ASP* 3.9 20.7 + - - +
311J GLN* 5.2 3.8 + - - +
413J ILE* 3.9 23.6 - - + -
433J THR* 4.0 16.4 - - + +
435J ASP* 2.9 38.2 + - + +
436J LEU 3.3 0.2 - - - -
437J ASP* 1.3 73.0 - - + +
439J ALA* 1.3 62.0 + - - +
441J TYR* 3.7 1.5 - - - +
442J LEU* 2.9 32.3 + - + +
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Residues in contact with ALA 439 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431J VAL* 5.0 4.9 - - - +
433J THR* 4.0 15.7 - - + +
435J ASP 3.0 18.3 + - - +
436J LEU 3.2 4.9 + - - +
438J LYS* 1.3 77.3 - - - +
440J ASN* 1.3 58.7 + - - +
442J LEU* 4.0 1.0 - - - +
443J SER* 3.0 31.9 + - - -
453J VAL* 4.1 26.4 - - + +
436K LEU* 4.1 17.0 - - + -
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Residues in contact with ASN 440 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153I TYR* 4.5 5.9 + - - -
436J LEU* 3.0 40.9 + - - +
437J ASP* 3.9 4.2 + - - +
439J ALA* 1.3 75.5 - - - +
441J TYR* 1.3 62.7 + - - +
443J SER* 3.1 8.2 + - - -
444J GLN* 2.9 45.3 + - - +
436K LEU* 6.1 1.1 - - - -
151L PHE* 4.5 14.4 - - - -
493L VAL* 4.0 10.1 - - - +
494L LYS 4.7 1.8 + - - -
495L VAL* 3.8 24.2 - - + +
496L PRO* 4.5 4.7 - - + -
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Residues in contact with TYR 441 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413J ILE* 3.6 36.3 - - + -
414J GLU* 4.0 21.6 - - + +
417J VAL* 3.5 32.5 - - + +
437J ASP 2.8 18.3 + - - +
438J LYS* 3.7 5.4 - - - +
440J ASN* 1.3 76.3 - - - +
442J LEU* 1.3 61.4 + - + +
444J GLN* 3.6 11.5 - - - +
445J ALA* 3.0 38.8 + - + +
496L PRO* 4.2 23.7 - - + +
497L GLN* 5.9 0.7 - - + -
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Residues in contact with LEU 442 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276J ILE* 4.5 8.7 - - + -
278J MET* 4.0 15.9 - - + -
413J ILE* 3.9 31.2 - - + -
416J VAL* 4.5 7.6 - - + -
417J VAL* 3.5 31.6 - - + -
431J VAL* 3.3 40.8 - - + -
438J LYS 2.9 16.0 + - - +
439J ALA 4.2 0.9 - - - +
441J TYR* 1.3 76.8 - - + +
443J SER* 1.3 59.9 + - - +
445J ALA* 4.4 0.9 - - - +
446J LEU* 2.9 47.7 + - + +
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Residues in contact with SER 443 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153I TYR* 4.1 11.3 + - - -
155I ARG* 4.4 1.0 + - - -
489I LYS* 3.1 28.4 + - - +
491I VAL* 4.1 26.6 - - - +
431J VAL* 4.9 0.8 - - - +
439J ALA 3.0 18.0 + - - -
440J ASN* 3.1 15.9 + - - -
442J LEU* 1.3 76.1 - - - +
444J GLN* 1.3 63.1 + - - +
451J VAL* 3.8 23.9 - - - +
453J VAL* 4.6 5.2 - - - -
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Residues in contact with GLN 444 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72I LEU* 4.9 4.7 - - - +
155I ARG* 3.7 27.6 + - - +
157I GLU* 4.4 1.2 - - - +
489I LYS* 3.1 17.7 + - - -
440J ASN* 2.9 33.0 + - - +
441J TYR* 3.6 11.7 + - - +
442J LEU 3.1 0.4 - - - -
443J SER* 1.3 81.2 - - - +
445J ALA* 1.3 58.7 + - + +
446J LEU 4.5 0.2 - - - -
151L PHE* 5.5 1.4 - - - +
495L VAL* 3.5 29.9 - - - +
496L PRO* 5.0 1.6 - - - +
497L GLN 3.7 28.1 + - - +
498L LYS* 4.9 2.7 - - - +
499L ASN* 5.5 6.3 - - + +
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Residues in contact with ALA 445 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72I LEU* 4.1 24.3 - - + +
417J VAL* 3.9 28.8 - - + +
421J ASN* 3.0 21.0 + - - -
441J TYR* 3.0 29.2 + - + +
442J LEU 4.2 0.9 - - - +
444J GLN* 1.3 75.9 - - + +
446J LEU* 1.3 61.8 + - - +
447J GLN* 3.4 6.6 + - - +
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Residues in contact with LEU 446 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489I LYS* 2.7 32.4 + - - -
274J PRO* 4.9 0.9 - - + -
276J ILE* 3.8 24.2 - - + -
417J VAL* 4.8 5.8 - - - -
420J ALA* 3.8 18.8 - - + -
421J ASN* 3.6 9.9 - - - +
429J ALA* 4.1 25.4 - - + -
430J ALA 4.8 0.2 - - - +
431J VAL* 3.5 29.8 - - + -
442J LEU* 2.9 37.3 + - + +
443J SER 4.1 0.2 - - - +
444J GLN 3.5 0.4 - - - -
445J ALA* 1.3 70.2 - - - +
447J GLN* 1.3 58.4 + - - +
448J ALA 3.2 3.9 + - - -
451J VAL* 4.2 16.5 - - + +
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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