Contacts of the helix formed by residues 230 - 236 (chain A) in PDB entry 1GWX
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 230 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222A TYR* 4.1 1.2 + - - -
229A THR* 1.3 71.7 - - - +
231A LYS* 1.3 56.4 + - - +
233A ALA 3.8 0.2 - - - -
234A ARG* 2.8 74.6 + - + +
332A SER* 3.3 35.6 - - - +
374A PHE* 5.7 2.2 - - - -
375A ASN* 3.2 30.9 + - - +
378A GLU* 4.5 2.8 - - - +
379A LEU* 2.8 42.3 + - - +
380A ASP* 4.9 1.6 - - - -
381A ASP* 2.7 19.5 + - - +
384A LEU* 4.0 10.6 - - + +
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Residues in contact with LYS 231 (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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229A THR* 3.0 7.8 - - - +
230A LYS* 1.3 75.4 - - - +
232A LYS* 1.3 81.9 + - - +
234A ARG* 4.0 4.5 - - - +
235A SER* 3.0 30.9 + - - -
381A ASP* 3.1 19.0 + - - +
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Residues in contact with LYS 232 (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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227A ASN* 3.7 20.4 + - - -
228A MET* 3.2 31.6 - - + -
229A THR* 3.0 20.4 + - - +
231A LYS* 1.3 88.0 - - - +
233A ALA* 1.3 58.4 + - - +
235A SER* 2.8 22.6 + - - +
236A ILE* 3.0 28.0 - - + +
343A ASN* 4.1 24.7 + - - +
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Residues in contact with ALA 233 (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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228A MET* 2.9 23.0 - - + +
229A THR 3.0 10.0 + - - +
230A LYS 3.8 0.9 - - - +
232A LYS* 1.3 72.8 - - - +
234A ARG* 1.3 55.4 + - - +
235A SER 3.0 1.6 - - - -
236A ILE* 2.6 22.5 + - - -
237A LEU* 2.7 30.7 + - + +
332A SER 3.1 24.9 - - - +
333A ILE* 3.9 8.5 - - + -
340A LEU* 3.8 8.1 - - + -
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Residues in contact with ARG 234 (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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230A LYS* 2.8 61.0 + - + +
231A LYS* 4.1 4.5 - - - +
233A ALA* 1.3 72.2 - - - +
235A SER* 1.3 58.0 + - - +
237A LEU* 4.0 18.2 - - - +
238A THR* 3.1 28.2 + - - -
331A ALA 3.8 2.5 + - - -
332A SER* 2.6 33.8 + - - +
334A VAL 2.7 30.7 + - - -
335A ASN* 4.7 2.2 - - - +
375A ASN* 4.4 6.2 - - - +
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Residues in contact with SER 235 (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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231A LYS* 3.0 21.6 + - - -
232A LYS* 2.8 20.5 + - - +
233A ALA 3.0 0.6 - - - -
234A ARG* 1.3 76.7 - - - +
236A ILE* 1.3 54.8 + - - +
238A THR* 3.0 19.9 - - - +
243A HIS* 2.6 24.9 + - - -
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Residues in contact with ILE 236 (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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228A MET* 3.8 18.8 - - + -
232A LYS* 3.0 31.6 - - + +
233A ALA 2.6 13.4 + - - +
235A SER* 1.3 75.2 - - - +
237A LEU* 1.3 57.2 + - - +
238A THR 3.0 7.4 + - - +
243A HIS* 2.7 28.6 - - + +
244A THR* 3.8 25.8 - - + +
246A PRO* 4.1 15.5 - - + +
340A LEU* 3.8 24.0 - - + -
343A ASN 4.8 2.5 - - - +
344A GLY* 4.0 21.5 - - - +
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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