Contacts of the helix formed by residues 422 - 433 (chain A) in PDB entry 3ZXR
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 GLN 422 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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327A TYR* 3.7 14.3 - - + -
420A PRO 3.5 1.6 - - - -
421A THR* 1.3 91.0 - - + +
423A LEU* 1.3 66.7 + - - +
424A SER* 2.9 26.5 + - - +
425A ASP* 3.1 37.5 + - - +
426A VAL* 3.6 8.3 + - - +
464A ASN* 6.2 0.2 - - - +
507A CL 3.9 12.7 - - + +
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Residues in contact with LEU 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318A ALA* 5.0 0.2 - - - -
321A ASN 4.0 6.7 - - - +
322A PRO* 3.4 37.9 - - + +
323A THR* 3.6 17.7 - - - +
324A VAL* 3.7 11.1 - - + +
327A TYR* 3.5 16.2 - - + -
422A GLN* 1.3 74.0 - - - +
424A SER* 1.3 63.5 + - - +
426A VAL* 3.1 24.4 + - + +
427A ILE* 3.0 41.0 + - + +
455A LYS* 4.4 7.0 - - + -
459A GLU* 3.9 10.5 - - + +
460A ILE* 4.0 18.6 - - + -
507A CL 3.8 9.2 - - + +
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Residues in contact with SER 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A GLN* 2.9 28.6 + - - -
423A LEU* 1.3 77.7 - - - +
425A ASP* 1.3 61.1 + - - +
427A ILE* 3.5 1.0 + - - +
428A ASP* 2.9 43.1 + - - +
460A ILE* 3.9 26.0 - - - +
464A ASN* 5.7 0.9 - - - -
507A CL 3.3 14.8 - - - +
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Residues in contact with ASP 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314A PRO 4.9 0.4 - - - -
420A PRO* 4.7 10.5 - - + +
421A THR* 4.0 12.1 + - - -
422A GLN* 3.1 37.8 + - - +
424A SER* 1.3 88.0 + - - +
426A VAL* 1.3 56.8 + - - +
428A ASP* 3.5 10.3 + - - +
429A ARG* 3.0 27.4 + - - +
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Residues in contact with VAL 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314A PRO 3.5 16.1 - - - +
315A SER* 4.3 0.3 - - - -
317A LEU* 4.1 5.4 - - + -
318A ALA* 3.6 29.2 - - + +
327A TYR* 3.3 30.5 - - + +
420A PRO* 3.5 35.9 - - + -
422A GLN 3.6 2.0 + - - +
423A LEU* 3.1 25.5 + - + +
425A ASP* 1.3 73.5 - - - +
427A ILE* 1.3 59.2 + - - +
429A ARG* 3.8 0.9 - - - +
430A LEU* 2.8 30.8 + - - +
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Residues in contact with ILE 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A ALA* 3.8 21.8 - - + -
423A LEU* 3.0 34.2 + - + +
424A SER* 3.9 4.0 - - - +
426A VAL* 1.3 75.2 - - - +
428A ASP* 1.3 64.9 + - - +
430A LEU* 3.3 6.4 + - + +
431A GLU* 2.9 23.6 + - - +
451A TRP* 4.2 12.1 - - + +
452A ILE* 3.7 26.5 - - + +
455A LYS* 4.0 23.1 - - + -
456A ARG* 3.7 29.4 - - + +
460A ILE* 4.1 9.2 - - + -
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Residues in contact with ASP 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424A SER* 2.9 31.0 + - - +
425A ASP* 3.7 9.9 - - - +
427A ILE* 1.3 76.3 - - - +
429A ARG* 1.3 57.0 + - - +
431A GLU* 3.3 5.9 + - - +
432A ALA* 3.0 26.7 + - - +
456A ARG* 2.9 28.5 + - - +
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Residues in contact with ARG 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311A HIS* 5.4 3.0 + - - -
314A PRO* 3.5 57.5 - - + +
315A SER* 3.9 7.0 - - - +
425A ASP 3.0 17.3 + - - +
426A VAL 3.8 0.2 - - - +
427A ILE 3.2 0.2 - - - -
428A ASP* 1.3 74.7 - - - +
430A LEU* 1.3 55.1 + - - +
432A ALA* 3.1 8.7 + - - +
433A ASP* 2.8 54.9 + - + +
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Residues in contact with LEU 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A SER* 3.8 21.5 - - - +
318A ALA* 3.8 20.6 - - + -
319A PHE* 3.9 14.4 - - + -
426A VAL 2.8 21.0 + - - +
427A ILE* 3.6 4.7 - - + +
429A ARG* 1.3 71.7 - - - +
431A GLU* 1.3 53.4 + - - +
433A ASP 3.3 3.3 + - - -
434A HIS* 2.7 45.7 + - + +
437A LEU* 3.6 31.4 - - + -
448A ILE* 4.1 12.8 - - + -
451A TRP* 3.9 22.2 - - + -
452A ILE* 3.9 15.3 - - + -
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Residues in contact with GLU 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427A ILE 2.9 13.6 + - - +
428A ASP* 3.4 9.2 - - - +
430A LEU* 1.3 77.8 - - - +
432A ALA* 1.3 60.2 + - - +
434A HIS* 3.5 17.9 + - - -
452A ILE* 3.6 23.5 - - + +
456A ARG* 2.9 38.6 + - - +
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Residues in contact with ALA 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428A ASP 3.0 13.5 + - - +
429A ARG* 3.1 14.5 + - - +
431A GLU* 1.3 79.4 - - - +
433A ASP* 1.3 61.9 + - + +
434A HIS* 4.3 2.1 + - - -
435A GLU* 5.7 0.5 - - - +
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Residues in contact with ASP 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A HIS* 5.8 1.0 + - - -
312A HIS* 4.6 16.2 + - - -
315A SER* 3.6 19.8 + - - -
429A ARG* 2.8 40.6 + - - +
430A LEU 3.3 3.3 + - - +
432A ALA* 1.3 79.1 - - + +
434A HIS* 1.3 63.8 + - - +
435A GLU* 4.1 13.8 + - - +
436A TYR* 4.1 4.0 - - - -
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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