Contacts of the helix formed by residues 229 - 238 (chain C) in PDB entry 3GHG
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 GLY 229 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211C TYR 3.2 12.1 - - - -
212C LYS 3.0 13.5 - - - -
214C GLY* 3.5 6.3 - - - -
227C TRP* 3.4 7.5 - - - +
228C LEU* 1.3 81.9 - - - +
230C ASN* 1.3 67.9 + - - -
231C GLU 2.8 5.0 + - - -
232C LYS* 2.8 15.9 + - - +
233C ILE* 2.9 16.0 + - - +
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Residues in contact with ASN 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208C TRP* 5.4 0.5 - - - -
211C TYR* 3.1 12.5 + - - +
212C LYS* 3.0 6.4 + - - -
227C TRP* 2.9 39.4 - - - +
229C GLY* 1.3 71.3 - - - -
231C GLU* 1.3 63.3 + - - +
233C ILE* 3.0 11.9 + - - +
234C HIS* 2.8 25.6 + - - +
267C VAL* 4.3 2.7 - - + +
274C TYR* 3.3 37.8 - - + +
312C PHE* 3.3 34.6 - - - -
335C TRP* 5.0 4.5 - - - -
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Residues in contact with GLU 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212C LYS* 2.9 30.9 + - + +
213C GLU* 4.8 7.2 - - - +
229C GLY 2.8 1.6 + - - -
230C ASN* 1.3 81.1 - - - +
232C LYS* 1.3 64.8 + - + +
234C HIS* 3.1 23.2 + - - +
235C LEU* 3.2 28.1 + - + +
270C GLU* 4.7 3.1 + - - +
274C TYR* 2.2 45.3 + - - +
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Residues in contact with LYS 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B VAL* 3.2 19.8 + - - +
206B VAL* 5.2 2.2 - - - +
207B SER* 5.6 3.2 - - - +
217B LYS* 6.3 0.9 - - - +
178C PHE* 3.3 55.8 - - + +
179C LEU 4.1 7.3 + - - +
212C LYS 4.8 1.8 - - - +
213C GLU* 3.6 16.8 - - - +
218C LEU* 5.8 0.2 - - - +
228C LEU* 3.3 43.5 - - + +
229C GLY 2.8 10.9 + - - +
231C GLU* 1.3 76.7 - - + +
233C ILE* 1.3 63.4 + - - +
234C HIS 2.9 1.6 + - - -
235C LEU* 3.1 7.7 + - - +
236C ILE* 2.9 28.0 + - - +
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Residues in contact with ILE 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194C PHE* 2.6 65.1 - - + +
227C TRP* 4.3 15.5 - - + -
228C LEU* 5.0 0.4 - - + -
229C GLY 2.9 21.9 + - - +
230C ASN* 3.5 9.9 - - - +
232C LYS* 1.3 76.0 - - + +
234C HIS* 1.3 58.0 + - - +
236C ILE* 4.0 9.0 - - - +
237C SER* 3.0 25.7 + - - -
265C PHE* 4.5 17.0 - - + -
267C VAL* 4.4 14.9 - - + +
335C TRP* 5.4 2.5 - - + -
386C ILE* 4.8 5.3 - - + +
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Residues in contact with HIS 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173C LYS* 5.4 4.1 + - - -
230C ASN 2.8 12.4 + - - +
231C GLU* 3.4 24.0 - - - +
232C LYS 2.9 0.4 + - - -
233C ILE* 1.3 77.4 - - - +
235C LEU* 1.3 66.0 + - + +
237C SER* 2.8 18.2 + - - -
238C THR* 2.8 53.4 + - + +
267C VAL* 2.9 23.1 + - + -
268C GLY 3.1 17.2 + - - +
269C PRO* 3.5 36.8 - - + +
274C TYR* 4.2 4.0 - - + -
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Residues in contact with LEU 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171C PRO* 4.0 12.1 - - + +
173C LYS* 3.9 16.4 - - + +
174C ALA* 3.3 49.6 - - + +
178C PHE* 4.8 8.3 - - + -
231C GLU* 3.2 31.2 + - + +
232C LYS* 3.5 8.3 - - - +
234C HIS* 1.3 86.0 - - + +
236C ILE* 1.3 68.6 + - - +
238C THR* 3.7 6.3 + - - +
239C GLN* 3.5 18.9 + - - +
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Residues in contact with ILE 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C LYS 5.8 0.7 - - - +
152C ASP* 5.5 5.6 - - + -
169C ILE* 4.7 6.5 - - + -
171C PRO* 4.3 6.3 - - + +
178C PHE* 4.0 27.1 - - + -
192C THR* 4.5 18.6 - - + -
194C PHE* 5.8 2.0 - - + -
228C LEU* 4.4 14.4 - - + -
232C LYS 2.9 27.6 + - - +
233C ILE* 4.0 7.9 - - - +
235C LEU* 1.3 81.9 - - - +
237C SER* 1.3 65.7 + - - +
238C THR 2.9 0.5 + - - -
239C GLN* 3.0 23.2 - - - +
244C TYR* 3.2 30.3 - - + +
386C ILE* 4.2 18.6 - - + -
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Residues in contact with SER 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233C ILE 3.0 15.8 + - - -
234C HIS 2.8 18.7 + - - -
236C ILE* 1.3 81.6 - - - +
238C THR* 1.3 64.8 + - - +
239C GLN 3.6 4.0 + - - +
242C ILE 4.6 2.9 - - - +
243C PRO* 5.6 0.3 - - - +
244C TYR* 3.3 28.3 + - - +
265C PHE* 4.3 10.9 - - - +
266C LYS* 3.6 32.5 - - - +
267C VAL 3.2 11.6 + - - -
386C ILE* 5.0 3.4 - - - -
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Residues in contact with THR 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173C LYS* 2.9 28.9 + - - -
234C HIS* 2.8 44.0 + - + +
235C LEU* 3.8 5.8 + - - +
236C ILE 2.9 0.2 + - - -
237C SER* 1.3 88.9 - - - +
239C GLN* 1.3 59.7 + - - +
241C ALA 5.4 0.4 - - - -
266C LYS* 4.4 20.6 - - + +
267C VAL 3.4 16.4 - - - +
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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