Contacts of the helix formed by residues 434 - 446 (chain B) in PDB entry 5ZR1
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 LYS 434 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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430B PRO 3.5 19.7 + - - -
431B SER* 3.6 22.6 + - - +
432B ILE 3.1 2.7 - - - +
433B ARG* 1.3 90.4 - - + +
435B ASN* 1.3 65.7 + - - +
436B THR* 3.4 9.4 - - - +
437B PHE* 3.4 4.4 + - + +
438B GLN* 3.2 22.6 + - - +
504B SER* 5.9 1.4 + - - -
440E ASN* 4.1 37.8 + - + +
441E ILE 5.0 7.9 - - - +
442E ASP* 4.8 11.4 - - + -
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Residues in contact with ASN 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433B ARG 4.0 0.2 + - - -
434B LYS* 1.3 75.8 - - - +
436B THR* 1.3 57.8 + - + +
438B GLN* 5.0 0.2 - - - -
439B THR* 2.6 42.1 + - - -
464B LEU* 6.3 0.4 - - - -
469B LYS* 2.5 36.8 + - - +
440E ASN* 3.8 15.1 - - - +
441E ILE 5.6 3.2 + - - +
443E TYR* 5.0 18.0 + - + -
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Residues in contact with THR 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B TYR* 3.6 39.6 - - + +
398B ASN* 6.2 2.7 - - - +
401B ILE* 5.0 3.1 - - - +
434B LYS* 4.5 7.6 - - - +
435B ASN* 1.3 76.7 - - + +
437B PHE* 1.3 65.5 + - - +
439B THR* 4.1 5.7 - - - -
440B MET* 3.3 20.6 + - - +
440E ASN* 4.7 9.3 + - - +
17G T 6.0 2.2 - - - +
18G G 4.6 16.1 + - - +
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Residues in contact with PHE 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B LEU* 4.3 4.7 - - + -
370B CYS* 3.8 31.2 - - - -
371B ASN 3.8 5.4 - - - -
372B TYR* 3.5 42.4 - + + -
375B VAL* 4.1 15.7 - - + -
431B SER 3.9 16.4 - - - +
432B ILE* 3.5 37.9 - - + +
434B LYS* 3.4 6.3 + - + +
435B ASN 3.3 0.4 - - - -
436B THR* 1.3 80.7 + - - +
438B GLN* 1.3 60.2 + - - +
440B MET* 3.3 17.0 + - + +
441B LEU* 3.1 46.2 + - + +
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Residues in contact with GLN 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427B LEU* 3.0 34.1 + - - +
432B ILE* 2.9 21.4 + - - +
433B ARG 4.3 1.6 - - - +
434B LYS 3.2 17.5 + - - +
435B ASN* 5.0 0.2 - - - -
437B PHE* 1.3 74.4 - - - +
439B THR* 1.3 60.2 + - - +
441B LEU* 3.4 0.6 + - - +
442B SER* 2.8 35.4 + - - -
464B LEU* 3.9 24.2 - - + +
465B TRP* 3.2 21.5 + - - -
469B LYS* 3.5 24.5 - - + +
473B TYR* 2.9 23.3 + - - -
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Residues in contact with THR 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401B ILE* 4.3 15.0 - - + -
435B ASN* 2.6 33.7 + - - -
436B THR* 4.1 6.5 - - - -
437B PHE 3.3 0.2 - - - -
438B GLN* 1.3 74.3 - - - +
440B MET* 1.3 64.2 + - - +
442B SER* 4.1 2.6 - - - -
443B PHE* 3.1 55.3 + - + -
469B LYS* 3.6 12.7 + - - +
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Residues in contact with MET 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372B TYR* 3.4 50.7 - - + +
375B VAL* 4.1 16.6 - - + -
376B PHE* 3.9 18.4 - - + -
379B ILE* 5.4 0.4 - - + -
400B VAL* 4.1 4.7 - - + -
401B ILE* 4.2 13.4 - - + +
404B ILE* 3.7 21.7 - - + +
436B THR 3.3 12.7 + - - +
437B PHE* 3.3 28.4 + - + +
438B GLN 3.3 0.4 - - - -
439B THR* 1.3 79.0 - - - +
441B LEU* 1.3 64.2 + - + +
443B PHE* 3.9 0.3 - - - -
444B LEU* 3.0 37.8 + - + +
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Residues in contact with LEU 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363B LEU* 4.9 5.4 - - + -
375B VAL* 5.5 1.1 - - + -
422B LEU* 4.1 21.8 - - + -
424B VAL* 4.4 9.9 - - + -
427B LEU* 3.7 27.8 - - + -
432B ILE* 4.3 5.6 - - + -
437B PHE* 3.1 41.1 + - + +
438B GLN* 3.4 0.9 + - - +
440B MET* 1.3 91.6 - - + +
442B SER* 1.3 53.1 + - - +
444B LEU* 3.8 23.0 - - + +
445B SER* 2.5 36.6 + - - -
452B ILE* 5.0 2.9 - - + +
473B TYR* 3.3 15.6 - - + +
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Residues in contact with SER 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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438B GLN 2.8 23.1 + - - -
439B THR* 4.1 3.8 - - - -
441B LEU* 1.3 74.6 - - - +
443B PHE* 1.3 67.4 + - - +
445B SER* 3.1 12.8 + - - -
446B VAL* 3.4 3.5 - - - +
469B LYS* 3.7 24.0 - - - +
472B ASN* 3.3 31.7 - - - +
473B TYR* 3.1 30.3 - - - -
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Residues in contact with PHE 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401B ILE* 4.8 12.3 - - + -
404B ILE* 3.8 20.8 - - + +
405B GLN* 4.3 26.2 - - + -
408B ILE* 3.3 36.5 - - + +
439B THR* 3.1 45.1 + - + +
440B MET 4.1 0.9 - - - +
442B SER* 1.3 80.3 - - - +
444B LEU* 1.3 59.4 + - - +
446B VAL* 3.4 14.4 + - + +
447B ILE 4.2 0.7 + - - -
468B MET* 5.5 9.9 - - + -
472B ASN* 4.7 17.3 - - - -
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Residues in contact with LEU 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376B PHE* 5.3 2.7 - - + -
379B ILE* 3.7 36.6 - - + -
383B LEU* 6.0 0.2 - - + -
404B ILE* 4.0 16.8 - - + +
407B MET* 4.4 13.2 - - - -
422B LEU* 3.8 13.5 - - + -
440B MET* 3.0 27.7 + - + +
441B LEU* 3.9 20.9 - - + +
442B SER 3.2 0.2 - - - -
443B PHE* 1.3 77.4 - - - +
445B SER* 1.3 60.2 + - - +
446B VAL 3.3 0.6 + - - -
447B ILE* 3.6 21.2 + - + +
450B ILE* 3.3 45.6 - - + +
452B ILE* 4.8 1.1 - - + -
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Residues in contact with SER 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313B SER* 5.0 1.0 - - - -
441B LEU 2.5 22.6 + - - -
442B SER 3.1 9.2 + - - -
444B LEU* 1.3 74.5 - - - +
446B VAL* 1.3 62.3 + - - +
447B ILE 3.2 8.8 + - - +
448B ARG* 5.4 0.2 - - - -
450B ILE 5.1 1.0 - - - +
452B ILE* 3.3 32.1 - - - +
472B ASN 3.6 15.3 - - - +
473B TYR* 3.2 26.8 - - - +
474B ASN* 5.6 0.7 - - - +
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Residues in contact with VAL 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B ILE* 4.1 28.5 - - + -
412B LYS* 6.5 0.2 - - + -
442B SER 3.4 10.8 - - - +
443B PHE* 3.4 20.4 - - + +
444B LEU 3.3 0.6 - - - -
445B SER* 1.3 75.6 - - - +
447B ILE* 1.3 65.3 + - - +
448B ARG* 3.1 6.9 + - - +
472B ASN* 3.3 37.5 - - + +
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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