Contacts of the helix formed by residues 226 - 240 (chain C) in PDB entry 3GBA
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 TYR 226 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6C LEU* 3.6 48.5 - - + +
47C LEU* 5.3 7.9 - - + -
49C PHE* 4.7 19.1 - + + +
83C ASP* 5.6 7.6 - - + -
220C THR* 5.1 0.7 - - + -
224C SER* 3.0 14.4 + - - +
225C PRO* 1.3 97.8 - - + +
227C ARG* 1.3 65.9 + - - +
228C ASP 3.3 2.0 + - - -
229C LYS* 3.3 9.2 + - + +
230C ILE* 2.9 41.6 + - + +
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Residues in contact with ARG 227 (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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100C ASP* 3.2 35.9 + - + +
101C PHE 5.4 7.2 - - - +
102C SER* 5.7 1.3 - - - -
220C THR* 4.1 18.4 - - - +
223C GLY 6.0 0.2 - - - +
224C SER* 3.4 21.6 + - - +
225C PRO 3.5 0.4 - - - -
226C TYR* 1.3 78.0 - - - +
228C ASP* 1.3 94.2 + - - +
230C ILE* 3.3 7.5 + - - +
231C THR* 3.3 22.1 + - - +
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Residues in contact with ASP 228 (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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225C PRO 5.0 2.3 + - - +
226C TYR 3.4 0.6 - - - -
227C ARG* 1.3 117.0 + - - +
229C LYS* 1.3 64.4 + - + +
231C THR* 3.3 7.7 + - - +
232C ILE* 3.1 31.6 + - + +
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Residues in contact with LYS 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C LEU* 3.5 38.9 - - + +
225C PRO 5.4 1.2 + - - +
226C TYR* 3.3 12.0 + - + +
228C ASP* 1.3 78.4 - - + +
230C ILE* 1.3 60.6 + - - +
232C ILE* 3.3 17.2 + - + +
233C ALA 2.9 23.0 + - - -
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Residues in contact with ILE 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C LEU* 4.7 9.0 - - + -
47C LEU* 3.8 19.7 - - + -
49C PHE* 5.5 2.2 - - + -
84C LEU* 4.4 14.4 - - + -
102C SER* 3.9 21.3 - - - -
218C VAL* 4.0 23.8 - - + -
220C THR* 3.7 30.1 - - + -
226C TYR* 2.9 33.1 + - + +
227C ARG* 3.6 4.9 - - - +
229C LYS* 1.3 75.2 - - - +
231C THR* 1.3 59.6 + - - +
233C ALA* 3.3 4.3 + - - +
234C ILE* 3.0 31.7 + - + +
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Residues in contact with THR 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C PHE 4.7 0.5 + - - -
102C SER* 3.3 11.8 - - - -
103C LYS* 3.2 46.1 + - + +
227C ARG* 3.3 10.8 + - - +
228C ASP* 3.7 8.7 - - - +
229C LYS 3.3 0.4 - - - -
230C ILE* 1.3 76.9 - - - +
232C ILE* 1.3 66.7 + - + +
234C ILE* 3.2 7.4 + - - +
235C LEU* 3.0 32.0 + - + +
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Residues in contact with ILE 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C LEU* 6.0 0.4 - - + -
228C ASP* 3.1 21.2 + - + +
229C LYS* 3.3 22.2 + - + +
231C THR* 1.3 75.3 - - + +
233C ALA* 1.3 59.0 + - - +
235C LEU* 3.2 13.9 + - + +
236C GLN* 2.9 33.6 + - + +
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Residues in contact with ALA 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C LEU* 3.7 19.3 - - + -
46C ILE* 3.8 30.6 - - + +
47C LEU* 4.1 7.2 - - + +
229C LYS 2.9 17.2 + - - +
230C ILE 3.6 4.7 - - - +
232C ILE* 1.3 78.9 - - - +
234C ILE* 1.3 56.7 + - - +
236C GLN* 3.2 8.7 + - - +
237C LEU* 2.9 34.9 + - - +
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Residues in contact with ILE 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C LEU* 5.0 6.7 - - + -
43C LEU* 4.3 11.7 - - + -
102C SER* 2.9 39.3 - - - +
103C LYS* 3.7 20.9 - - + +
104C PRO 4.0 12.1 - - - +
105C PHE* 4.2 18.8 - - + -
218C VAL* 3.9 19.1 - - + -
230C ILE* 3.0 20.2 + - + +
231C THR* 3.7 5.2 - - - +
233C ALA* 1.3 74.6 - - - +
235C LEU* 1.3 59.5 + - - +
237C LEU* 3.3 8.6 + - - +
238C GLN* 2.9 30.9 + - - +
243C LEU* 3.9 6.1 - - + +
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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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103C LYS* 4.3 27.1 - - + -
231C THR* 3.0 34.9 + - + +
232C ILE* 3.6 12.1 - - + +
234C ILE* 1.3 77.1 - - - +
236C GLN* 1.3 57.0 + - - +
238C GLN* 3.3 20.9 + - - +
239C GLU* 2.9 42.0 + - - +
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Residues in contact with GLN 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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46C ILE* 3.7 37.5 - - - +
232C ILE* 2.9 21.1 + - + +
233C ALA* 3.2 8.9 + - - +
235C LEU* 1.3 75.9 - - - +
237C LEU* 1.3 61.8 + - - +
239C GLU* 3.3 15.8 - - - +
240C GLU* 3.1 57.0 + - - +
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Residues in contact with LEU 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C LEU* 3.8 29.2 - - + -
42C GLU* 3.8 37.5 - - + +
43C LEU* 4.5 6.3 - - + -
46C ILE* 3.8 15.7 - - + -
233C ALA 2.9 25.0 + - - +
234C ILE* 3.6 7.4 - - - +
236C GLN* 1.3 76.0 - - - +
238C GLN* 1.3 61.4 + - - +
240C GLU* 3.6 2.8 + - - +
241C GLY 3.3 2.4 + - - -
242C LYS* 2.9 55.5 + - + +
243C LEU* 3.5 18.4 + - + -
246C MET* 5.3 1.1 - - - -
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Residues in contact with GLN 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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103C LYS* 5.7 0.9 - - - +
104C PRO 4.6 14.3 + - - +
105C PHE 6.3 0.2 - - - -
234C ILE* 2.9 18.9 + - - +
235C LEU* 3.5 26.3 - - - +
237C LEU* 1.3 77.0 - - - +
239C GLU* 1.3 63.3 + - - +
241C GLY* 3.1 15.1 + - - -
243C LEU* 3.9 23.0 - - + +
244C HIS 5.9 0.2 + - - -
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Residues in contact with GLU 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235C LEU* 2.9 28.9 + - - +
236C GLN* 3.3 23.5 - - - +
238C GLN* 1.3 77.8 - - - +
240C GLU* 1.3 66.2 + - + +
241C GLY 3.2 1.1 + - - -
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Residues in contact with GLU 240 (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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236C GLN* 3.1 45.0 + - - +
237C LEU* 4.2 3.7 - - - +
238C GLN 3.3 0.2 - - - -
239C GLU* 1.3 84.6 - - + +
241C GLY* 1.3 60.7 + - - +
242C LYS* 3.3 32.9 + - + +
245C MET* 5.2 3.5 - - - +
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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