Contacts of the helix formed by residues 224 - 234 (chain B) in PDB entry 2GH0
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 224 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160B ASP* 3.4 17.7 - - - +
220B CYS* 4.5 2.9 - - - +
221B ALA* 3.5 27.7 + - + +
222B PRO 3.4 5.6 + - - -
223B ASN* 1.3 75.4 - - - +
225B ARG* 1.3 61.1 + - - +
226B GLY* 3.6 5.0 + - - -
227B CYS* 3.2 33.8 + - + +
228B GLY* 3.0 18.2 + - - -
307B ASN 4.3 3.0 - - - +
308B VAL* 6.2 0.2 - - - -
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Residues in contact with ARG 225 (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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223B ASN* 3.3 16.2 + - - +
224B ASP* 1.3 72.7 + - - +
226B GLY* 1.3 53.2 + - - +
228B GLY* 3.7 0.5 - - - -
229B GLU* 2.8 39.5 + - - +
307B ASN* 2.8 48.0 + - - +
308B VAL* 2.9 34.1 - - - +
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Residues in contact with GLY 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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160B ASP* 4.4 3.8 - - - -
224B ASP* 3.2 5.0 + - - -
225B ARG* 1.3 76.7 - - - +
227B CYS* 1.3 64.0 + - - +
229B GLU* 3.9 9.6 - - - +
230B ARG* 3.0 24.9 + - - +
203D SER* 4.3 2.4 + - - -
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Residues in contact with CYS 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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160B ASP* 3.6 28.9 + - - -
162B CYS* 3.5 15.7 - - - -
219B PRO 3.6 4.9 - - - -
220B CYS* 2.1 54.0 - - + -
224B ASP* 3.2 33.3 + - - +
226B GLY* 1.3 75.8 - - - +
228B GLY* 1.3 56.5 + - - +
230B ARG* 3.3 5.4 + - - +
231B ARG* 3.0 24.3 + - - +
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Residues in contact with GLY 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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220B CYS* 3.5 11.3 - - - -
224B ASP 3.0 11.5 + - - -
227B CYS* 1.3 74.6 - - - +
229B GLU* 1.3 60.0 + - - +
231B ARG* 3.5 11.0 + - - +
232B ARG* 2.9 30.0 + - - +
304B PHE* 5.8 0.2 - - - +
306B SER 4.3 1.4 - - - +
307B ASN* 3.3 29.3 - - - +
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Residues in contact with GLU 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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225B ARG* 2.8 22.6 + - - +
226B GLY* 3.9 9.1 - - - +
228B GLY* 1.3 71.4 - - - +
230B ARG* 1.3 59.6 + - - +
232B ARG* 3.4 9.5 + - - +
233B ASN* 2.9 48.1 + - - +
307B ASN* 3.4 22.9 + - - +
201D VAL 5.1 2.3 - - - +
202D ASN* 3.1 29.7 - - - +
203D SER* 3.5 9.1 + - - +
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Residues in contact with ARG 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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160B ASP* 4.5 4.5 - - - -
162B CYS* 3.9 14.7 + - + -
163B LEU* 3.7 45.2 - - - +
166B ALA* 3.2 25.9 - - - +
179B ARG* 3.3 7.1 - - - +
215B LEU* 5.7 0.4 - - - +
226B GLY 3.0 18.2 + - - +
227B CYS 3.5 4.3 - - - +
229B GLU* 1.3 72.9 - - - +
231B ARG* 1.3 59.5 + - - +
233B ASN 3.1 2.3 + - - -
234B THR* 2.7 38.4 + - - +
142D ASP* 6.0 1.6 - - - +
143D GLU* 2.4 38.3 + - - +
199D MET* 3.8 24.9 + - + +
200D ASP 5.3 2.4 + - - -
203D SER* 3.2 17.4 + - - +
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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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162B CYS* 3.9 9.6 - - - -
216B LEU* 3.4 33.0 - - - +
218B CYS* 3.0 34.8 + - - -
220B CYS* 3.8 27.5 + - - +
227B CYS 3.0 16.5 + - - +
228B GLY* 3.7 12.7 + - - +
229B GLU 3.4 0.2 - - - -
230B ARG* 1.3 78.3 - - - +
232B ARG* 1.3 62.7 + - - +
233B ASN 3.3 0.3 + - - -
234B THR* 3.5 17.8 + - - -
235B ILE 5.0 0.2 + - - -
303B ASN* 4.6 0.9 - - - +
304B PHE* 3.5 27.8 - - + +
306B SER 4.6 2.6 + - - -
307B ASN 5.0 1.2 + - - -
308B VAL 5.2 0.8 - - - -
309B ASN* 3.2 34.1 + - - +
310B THR* 3.8 12.7 - - - +
349B MET* 3.5 14.9 - - - +
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Residues in contact with ARG 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 GLY 2.9 19.3 + - - +
229B GLU* 3.6 14.0 + - - +
231B ARG* 1.3 77.6 - - - +
233B ASN* 1.3 86.4 + - - +
234B THR 3.5 0.4 + - - -
237B PRO* 3.5 14.1 - - - +
238B ASN* 5.6 2.6 + - - -
303B ASN* 2.9 28.2 + - - +
304B PHE* 3.4 33.6 + - + +
305B VAL 4.0 8.7 - - - -
306B SER* 3.8 25.6 - - - +
307B ASN* 4.4 16.8 - - - +
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Residues in contact with ASN 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 GLU* 2.9 37.2 + - - +
230B ARG 3.1 0.4 + - - -
232B ARG* 1.3 105.5 + - - +
234B THR* 1.3 60.7 + - - +
235B ILE 3.2 2.7 - - - -
236B ALA* 2.8 22.4 + - - -
237B PRO* 3.5 20.8 - - - +
238B ASN* 4.8 11.6 + - - +
199D MET* 3.5 11.8 - - + +
202D ASN 5.0 0.8 + - - -
203D SER* 3.2 25.4 - - - +
205D TRP* 3.6 4.7 + - - -
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Residues in contact with THR 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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179B ARG* 6.0 0.2 - - - +
182B TYR* 2.6 37.5 + - - +
204B PHE* 6.3 0.9 - - + -
215B LEU* 3.7 36.4 + - + +
216B LEU* 4.0 16.2 - - + -
230B ARG* 2.7 27.7 + - - +
231B ARG* 3.5 15.6 + - - -
233B ASN* 1.3 77.7 - - - +
235B ILE* 1.3 58.0 + - + +
199D MET* 4.0 12.3 - - - -
205D TRP* 3.1 15.0 + - + -
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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