Contacts of the helix formed by residues 425 - 433 (chain A) in PDB entry 2ZHB
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 VAL 425 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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321A LYS* 4.4 7.2 - - + -
328A TYR* 3.5 46.4 - - + -
330A LEU* 3.7 26.7 - - + -
420A LEU* 4.0 21.3 - - + +
423A GLU* 2.7 17.4 + - + +
424A PRO* 1.3 81.7 - - - +
426A THR* 1.3 63.5 + - - +
428A GLU* 3.1 19.9 - - - +
429A LEU* 3.2 26.2 + - + +
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Residues in contact with THR 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A ILE* 4.1 22.3 + - + +
264A PRO* 4.7 10.1 - - + -
267A LEU* 3.6 27.0 - - + +
421A PHE* 3.6 28.9 - - + +
423A GLU 4.0 1.8 + - - -
424A PRO* 3.8 2.1 - - - +
425A VAL* 1.3 79.2 + - - +
427A ALA* 1.3 63.7 + - - +
429A LEU* 3.5 4.7 + - + +
430A CYS* 3.2 25.9 + - - -
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Residues in contact with ALA 427 (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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259A PRO 5.5 7.2 - - - +
260A LEU 6.0 2.0 - - - +
261A GLU* 6.6 0.4 - - - -
262A ILE* 5.7 1.6 - - - -
425A VAL 3.3 0.6 - - - -
426A THR* 1.3 80.2 + - - +
428A GLU* 1.3 77.1 + - - +
430A CYS* 3.0 18.6 + - - +
431A GLU* 3.1 12.2 + - - +
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Residues in contact with GLU 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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319A ALA* 5.2 4.5 - - + -
320A PHE 4.4 8.1 - - - +
321A LYS* 3.2 47.6 + - + +
330A LEU* 4.1 16.8 - - + -
424A PRO 4.2 1.4 - - - +
425A VAL* 3.1 25.7 - - - +
427A ALA* 1.3 82.6 + - - +
429A LEU* 1.3 57.5 + - - +
431A GLU* 3.0 11.2 + - - +
432A MET* 2.8 28.6 + - - +
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Residues in contact with LEU 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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267A LEU* 3.8 22.9 - - + -
278A VAL* 4.0 20.6 - - + -
330A LEU* 3.8 23.6 - - + -
420A LEU* 4.6 13.7 - - + +
421A PHE* 4.7 6.7 - - + -
425A VAL* 3.2 27.2 + - + +
426A THR* 3.7 7.6 - - + +
427A ALA 3.2 0.6 - - - -
428A GLU* 1.3 78.0 - - - +
430A CYS* 1.3 56.9 + - - +
432A MET* 2.9 32.9 + - + +
433A MET* 2.8 48.4 + - + +
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Residues in contact with CYS 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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262A ILE* 3.5 29.4 - - - -
267A LEU* 3.4 28.3 - - - -
426A THR 3.2 11.7 + - - -
427A ALA* 3.0 11.1 + - - +
429A LEU* 1.3 78.5 - - - +
431A GLU* 1.3 56.8 + - - +
433A MET* 4.7 0.2 - - - -
434A GLY 3.1 7.3 + - - -
435A VAL* 2.9 51.6 + - + +
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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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317A ARG* 3.4 19.4 + - - +
427A ALA 3.1 10.2 + - - +
428A GLU* 3.0 13.5 + - - +
430A CYS* 1.3 77.6 - - - +
432A MET* 1.3 63.0 + - - +
434A GLY* 3.6 8.8 + - - -
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Residues in contact with MET 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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278A VAL* 5.2 1.3 - - + -
317A ARG* 3.3 65.1 + - + +
318A SER 3.9 5.8 - - - +
319A ALA* 3.6 27.6 - - + -
330A LEU* 4.1 7.2 - - + +
331A PHE 4.2 10.1 - - - +
332A GLU* 4.0 26.6 - - + +
428A GLU 2.8 12.2 + - - +
429A LEU* 3.3 39.5 - - + +
431A GLU* 1.3 80.4 - - - +
433A MET* 1.3 65.0 + - + +
434A GLY 3.3 0.4 - - - -
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Residues in contact with MET 433 (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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267A LEU* 3.7 31.0 - - + -
270A ILE* 4.8 4.0 - - + -
271A VAL* 4.1 22.2 - - + -
274A ARG* 2.4 58.2 + - - +
278A VAL* 4.7 6.1 - - + -
332A GLU* 3.5 23.8 - - - +
429A LEU* 2.8 37.2 + - + +
432A MET* 1.3 79.5 - - + +
434A GLY* 1.3 60.7 + - - +
435A VAL* 3.0 19.6 + - + -
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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