Contacts of the helix formed by residues 426 - 431 (chain B) in PDB entry 1ZJA
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 SER 426 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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424B ASP* 2.7 28.6 + - - -
425B ASP* 1.3 83.7 + - - +
427B ALA* 1.3 67.8 + - - +
428B ASN 3.3 0.5 + - - -
429B ALA 3.0 12.0 + - - -
430B GLY* 3.3 14.4 + - - -
444B TYR* 3.4 6.4 - - - -
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Residues in contact with ALA 427 (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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426B SER* 1.3 74.1 + - - +
428B ASN* 1.3 75.2 + - - +
430B GLY* 3.2 9.7 + - - -
432B THR 3.5 13.9 - - - +
433B THR* 6.1 2.2 - - - -
444B TYR* 4.9 3.4 - - - -
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Residues in contact with ASN 428 (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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426B SER 3.3 1.0 + - - -
427B ALA* 1.3 76.5 - - - +
429B ALA* 1.3 67.1 + - - +
431B PHE* 3.1 19.9 + - - +
432B THR* 4.0 16.0 + - + +
434B GLY 3.4 22.8 + - - -
435B LYS* 4.9 0.2 - - - +
436B PRO* 3.5 25.8 - - - +
440B VAL* 3.6 27.7 + - + +
444B TYR* 4.4 9.7 + - - -
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Residues in contact with ALA 429 (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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421B PHE 4.4 1.8 - - - +
422B GLN* 3.7 19.2 - - + -
423B TRP 2.9 22.3 + - - -
424B ASP* 3.0 28.1 + - - +
426B SER 3.0 9.0 + - - -
428B ASN* 1.3 76.0 - - - +
430B GLY* 1.3 59.2 + - - +
431B PHE 3.1 1.6 + - - -
440B VAL* 4.0 7.0 - - + -
444B TYR* 3.5 31.4 - - + -
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Residues in contact with GLY 430 (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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21B LYS* 3.4 21.8 - - - +
423B TRP* 3.8 7.9 - - - +
424B ASP* 3.2 13.3 + - - -
426B SER* 3.3 17.8 + - - -
427B ALA 3.2 8.5 + - - -
428B ASN 3.1 2.4 + - - -
429B ALA* 1.3 76.4 - - - +
431B PHE* 1.3 62.8 + - - +
432B THR 3.4 2.7 - - - -
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Residues in contact with PHE 431 (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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18B ARG 3.6 8.1 - - - -
19B SER* 3.6 25.1 - - - -
20B PHE 3.3 24.7 - - - -
21B LYS* 3.8 4.6 - - - +
22B ASP* 3.0 41.4 + - + +
27B GLY 3.5 24.2 - - - -
28B ILE 4.1 1.3 - - - -
29B GLY* 3.6 20.6 - - - -
420B PRO* 3.4 33.7 - - + -
421B PHE 3.7 15.5 - - - +
423B TRP* 3.9 7.2 - - - -
428B ASN 3.1 12.4 + - - +
429B ALA 3.1 2.0 + - - -
430B GLY* 1.3 80.9 - - - +
432B THR* 1.3 76.3 + - + +
436B PRO* 4.2 4.9 - - + -
437B TRP* 4.6 0.9 - + - -
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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