Contacts of the helix formed by residues 225 - 234 (chain B) in PDB entry 4GWF
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 GLU 225 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221B ILE* 4.4 4.6 - - + +
222B ASN* 2.9 25.9 + - + +
224B ALA* 1.4 78.5 - - + +
226B ILE* 1.4 60.5 + - - +
227B GLU 3.5 2.5 - - - +
228B SER* 3.5 19.8 + - - +
229B ARG* 3.3 19.8 + - - +
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Residues in contact with ILE 226 (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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221B ILE* 3.8 23.8 - - + -
222B ASN 4.0 0.6 + - - -
223B ALA 3.3 19.1 + - - +
224B ALA 3.3 3.2 - - - +
225B GLU* 1.4 72.9 - - - +
227B GLU* 1.4 58.2 + - + +
229B ARG* 3.1 4.0 + - - +
230B VAL* 2.8 34.4 + - + +
488B ILE* 4.2 5.2 - - + -
490B VAL* 5.6 0.4 - - + -
515B TYR* 3.9 27.8 - - + +
518B VAL* 4.1 21.5 - - + -
519B GLN* 3.8 38.8 - - + +
522B ILE* 3.8 20.6 - - + -
523B GLU* 5.8 1.1 - - + +
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Residues in contact with GLU 227 (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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224B ALA 4.9 1.0 + - - -
225B GLU 3.5 0.6 - - - -
226B ILE* 1.4 81.2 - - + +
228B SER* 1.4 52.7 + - - +
230B VAL* 3.8 0.7 - - - +
231B ARG* 2.9 55.0 + - + +
519B GLN* 3.4 22.9 - - + +
523B GLU* 3.1 25.1 - - + +
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Residues in contact with SER 228 (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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225B GLU* 3.5 28.5 + - - +
226B ILE 3.2 0.2 - - - -
227B GLU* 1.4 77.7 - - - +
229B ARG* 1.4 59.1 + - - +
231B ARG* 3.3 43.9 + - - +
232B GLU* 3.2 23.1 + - - +
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Residues in contact with ARG 229 (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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129B LYS* 5.2 6.3 - - - +
218B THR* 2.9 31.5 + - - -
219B THR* 4.1 5.5 + - - +
220B ARG 4.5 2.2 + - - -
221B ILE* 3.5 44.0 - - + +
225B GLU 3.3 9.2 + - - +
226B ILE 3.1 7.4 + - - +
228B SER* 1.4 75.9 - - - +
230B VAL* 1.4 64.8 + - - +
232B GLU* 3.3 27.2 + - - +
233B LEU* 3.0 51.6 + - + +
250B GLU* 4.0 13.9 + - - -
515B TYR* 4.4 10.3 - - + +
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Residues in contact with VAL 230 (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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226B ILE* 2.8 35.8 + - + +
227B GLU 3.9 0.7 - - - +
229B ARG* 1.4 70.5 - - - +
231B ARG* 1.4 53.8 + - - +
233B LEU* 3.2 4.7 + - - +
234B SER* 2.8 38.4 + - - +
247B PHE* 3.8 10.0 - - + -
515B TYR* 3.9 30.1 - - + +
516B MET* 3.9 31.6 - - + -
519B GLN* 3.4 28.3 - - - +
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Residues in contact with ARG 231 (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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227B GLU* 2.9 42.3 + - + +
228B SER* 3.3 42.6 + - - +
230B VAL* 1.4 73.4 - - - +
232B GLU* 1.4 57.3 + - + +
234B SER* 3.2 23.6 + - - -
235B LYS* 3.5 15.1 + - - +
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Residues in contact with GLU 232 (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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228B SER* 3.2 29.6 + - - +
229B ARG* 3.4 36.1 + - - +
231B ARG* 1.4 76.9 - - + +
233B LEU* 1.4 61.7 + - + +
235B LYS* 3.6 19.6 + - - +
246B GLY* 4.8 3.3 - - - -
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Residues in contact with LEU 233 (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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229B ARG* 3.0 40.4 + - + +
230B VAL 3.2 4.9 + - - +
232B GLU* 1.4 76.2 - - + +
234B SER* 1.4 58.3 + - - +
235B LYS 3.3 1.1 - - - -
246B GLY* 3.3 37.3 + - - +
247B PHE* 3.0 51.3 + - + +
250B GLU* 3.9 21.5 - - + +
515B TYR* 3.8 32.3 - - + +
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Residues in contact with SER 234 (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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230B VAL* 2.8 26.0 + - - +
231B ARG* 3.2 11.5 + - - -
233B LEU* 1.4 77.5 - - - +
235B LYS* 1.3 60.8 + - - +
247B PHE* 3.5 15.7 - - - -
516B MET* 4.6 5.7 - - - +
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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