Contacts of the helix formed by residues 283 - 292 (chain A) in PDB entry 1WZ9
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 283 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A LEU* 6.0 0.8 - - - +
281A MET* 5.8 2.2 - - + +
282A ILE* 1.3 73.5 - - - +
284A PRO* 1.3 66.4 - - - +
285A LYS* 3.3 24.7 + - - +
286A ALA* 3.9 15.3 + - + +
287A CYS* 4.3 9.4 + - - -
317A ASN* 4.0 9.8 - - - +
318A VAL 3.8 9.0 - - - +
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Residues in contact with PRO 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LEU* 5.5 2.5 - - + -
19A LEU* 6.4 0.7 - - + -
35A LEU* 4.1 15.7 - - + -
282A ILE* 3.2 24.2 - - + +
283A ASP* 1.3 81.7 - - - +
285A LYS* 1.3 56.8 + - - +
286A ALA 3.3 0.2 - - - -
287A CYS* 3.0 10.0 + - + +
288A LEU* 2.6 54.4 + - + +
318A VAL* 3.5 38.1 - - + +
320A HIS* 3.9 17.3 - - + -
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Residues in contact with LYS 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A ASP* 3.3 19.7 + - - +
284A PRO* 1.3 76.7 - - - +
286A ALA* 1.3 55.4 + - - +
288A LEU* 3.1 2.2 + - - +
289A GLU* 2.8 55.9 + - - +
297A PHE* 3.6 59.1 + - + +
315A LEU 5.6 0.2 + - - -
316A SER 4.6 14.9 + - - +
317A ASN* 5.4 6.7 - - - +
318A VAL* 4.8 6.3 - - + +
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Residues in contact with ALA 286 (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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283A ASP* 3.9 14.1 + - - +
284A PRO 3.3 0.6 - - - -
285A LYS* 1.3 77.7 - - - +
287A CYS* 1.3 65.8 + - - +
289A GLU* 3.5 16.2 + - - +
290A ASN* 3.2 30.3 + - - +
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Residues in contact with CYS 287 (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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15A LEU* 3.7 20.0 - - + -
18A GLN* 3.8 29.7 - - + +
19A LEU* 4.0 23.3 - - - -
22A LYS* 5.2 8.3 - - - -
283A ASP 4.3 6.7 + - - -
284A PRO* 3.0 11.4 + - + +
286A ALA* 1.3 82.4 - - - +
288A LEU* 1.3 61.4 + - - +
290A ASN* 3.2 12.4 + - - +
291A LEU* 2.9 29.7 + - - +
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Residues in contact with LEU 288 (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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11A PHE* 4.0 33.0 - - + -
15A LEU* 4.7 7.2 - - + -
35A LEU* 4.1 10.3 - - + -
39A LEU* 4.0 24.7 - - + -
57A VAL* 4.8 1.6 - - + -
284A PRO* 2.6 39.3 + - + +
285A LYS 3.7 3.4 - - - +
287A CYS* 1.3 69.2 - - - +
289A GLU* 1.3 66.3 + - - +
291A LEU* 3.1 15.9 + - + +
292A GLY 3.3 0.5 + - - -
293A LEU* 3.0 45.1 + - + +
297A PHE* 4.1 18.2 - - + -
315A LEU* 5.6 0.2 - - + -
318A VAL* 4.7 4.9 - - + -
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Residues in contact with GLU 289 (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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285A LYS* 2.8 39.9 + - - +
286A ALA* 3.6 20.3 + - - +
288A LEU* 1.3 75.0 - - - +
290A ASN* 1.3 62.8 + - - +
292A GLY* 3.0 16.5 + - - -
293A LEU 3.5 20.6 + - - +
294A LYS* 5.5 3.1 - - - +
297A PHE* 4.0 12.5 - - + +
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Residues in contact with ASN 290 (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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18A GLN* 3.0 34.1 + - - +
286A ALA* 3.2 20.7 + - - +
287A CYS* 3.2 8.1 + - - +
289A GLU* 1.3 79.4 - - - +
291A LEU* 1.3 61.8 + - - +
292A GLY* 3.4 0.9 + - - -
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Residues in contact with LEU 291 (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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11A PHE* 5.2 2.5 - - + -
14A ASP* 4.2 30.1 - - + +
15A LEU* 4.2 16.6 - - + -
18A GLN* 3.6 33.4 - - + +
57A VAL* 3.6 31.8 - - + +
287A CYS 2.9 31.0 + - - +
288A LEU* 3.1 16.1 + - + +
290A ASN* 1.3 77.9 - - - +
292A GLY* 1.3 56.8 + - - +
293A LEU 3.8 0.4 - - - -
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Residues in contact with GLY 292 (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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53A GLU* 2.9 28.1 - - - +
57A VAL* 4.1 7.9 - - - -
289A GLU 3.0 11.4 + - - -
290A ASN 3.2 1.9 + - - -
291A LEU* 1.3 79.5 - - - +
293A LEU* 1.3 58.2 + - - +
294A LYS* 3.0 6.3 + - - +
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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