Contacts of the helix formed by residues 234 - 244 (chain B) in PDB entry 1GGT
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 ILE 234 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228B GLY 3.6 15.7 - - - +
229B GLN* 3.9 9.4 - - - +
231B GLU* 3.1 22.2 + - + +
232B ASP 5.1 0.7 - - - +
233B GLY* 1.3 74.2 - - - +
235B LEU* 1.3 59.5 + - - +
237B THR* 2.8 24.2 + - - -
238B CYS* 2.8 14.5 + - - -
296B VAL* 4.2 17.9 - - + -
299B LEU* 3.7 32.5 - - + -
300B LEU* 4.0 18.8 - - + -
323B THR* 3.6 30.3 - - + -
327B CYS* 4.1 12.1 - - - -
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Residues in contact with LEU 235 (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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69B TYR* 4.1 24.2 - - + -
71B ASN* 4.9 6.7 - - + +
75B ILE* 4.0 24.7 - - + -
181B TYR* 3.5 45.3 - - + -
183B LEU* 4.4 15.0 - - + -
229B GLN 4.6 1.0 + - - -
231B GLU 4.8 0.8 + - - -
233B GLY 5.4 0.7 - - - +
234B ILE* 1.3 75.6 - - - +
236B ASP* 1.3 65.7 + - - +
238B CYS* 3.2 3.7 + - - +
239B LEU* 3.2 31.0 + - + +
327B CYS* 3.5 19.4 - - - +
328B LEU* 4.8 4.7 - - + -
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Residues in contact with ASP 236 (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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71B ASN* 4.7 7.1 + - - -
156B LYS* 4.9 4.5 - - - +
181B TYR* 2.6 35.6 + - - -
233B GLY* 3.8 15.9 + - - +
234B ILE 3.2 0.2 - - - -
235B LEU* 1.3 83.4 - - - +
237B THR* 1.3 56.8 + - - +
239B LEU* 3.3 11.6 + - - +
240B TYR* 2.8 24.6 + - - +
303B ARG* 4.0 18.9 + - - +
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Residues in contact with THR 237 (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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233B GLY 2.7 29.6 - - - +
234B ILE* 2.8 8.8 + - - -
236B ASP* 1.3 70.3 - - - +
238B CYS* 1.3 63.4 + - - +
240B TYR* 3.0 11.9 + - - +
241B VAL* 2.7 32.3 + - - +
299B LEU* 3.8 29.9 + - + +
300B LEU* 4.3 13.0 - - + -
302B TYR* 5.4 1.6 - - - -
303B ARG* 3.4 36.1 - - + +
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Residues in contact with CYS 238 (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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234B ILE* 2.8 25.4 + - - -
235B LEU* 3.2 9.2 + - - +
237B THR* 1.3 78.4 - - - +
239B LEU* 1.3 63.4 + - - +
241B VAL* 3.2 17.6 + - - +
242B MET* 3.4 15.0 + - - +
299B LEU* 4.8 8.3 - - - -
324B PHE* 3.6 44.9 - - + -
327B CYS* 4.0 17.3 - - - -
328B LEU* 4.2 16.6 - - + -
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Residues in contact with LEU 239 (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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20B ASN* 4.2 13.9 - - + +
154B VAL* 4.8 2.9 - - + +
155B GLY* 4.1 19.3 - - - +
156B LYS* 4.1 18.6 - - + +
181B TYR* 3.8 32.1 - - + -
183B LEU* 6.0 0.7 - - + -
235B LEU* 3.2 18.5 + - + +
236B ASP* 3.4 11.2 - - - +
237B THR 3.1 0.2 - - - -
238B CYS* 1.3 74.7 - - - +
240B TYR* 1.3 64.2 + - - +
242B MET* 3.1 34.6 + - + +
243B ASP* 3.2 17.3 + - - +
252B ARG* 4.2 3.2 + - - +
328B LEU* 4.2 13.7 - - + -
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Residues in contact with TYR 240 (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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236B ASP 2.8 14.7 + - - +
237B THR* 3.1 15.7 - - - +
239B LEU* 1.3 76.2 - - - +
241B VAL* 1.3 61.0 + - - +
243B ASP* 3.1 12.5 + - + +
244B ARG* 2.8 65.0 + - + +
302B TYR* 3.4 36.6 - + - -
303B ARG* 3.2 46.0 - - + +
306B GLU* 3.0 29.1 + - + +
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Residues in contact with VAL 241 (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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237B THR* 2.7 25.1 + - - +
238B CYS* 3.4 12.1 - - - +
239B LEU 3.2 0.2 - - - -
240B TYR* 1.3 73.6 - - - +
242B MET* 1.3 64.9 + - + +
244B ARG* 3.1 9.0 + - - +
245B ALA* 3.1 19.6 + - - +
262B GLY* 5.2 5.2 - - - +
265B MET* 3.9 30.2 - - + +
274B VAL* 4.6 10.3 - - + -
299B LEU* 5.2 7.2 - - + -
302B TYR* 4.0 23.6 - - + -
324B PHE* 4.0 21.8 - - + -
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Residues in contact with MET 242 (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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154B VAL* 5.2 4.5 - - + +
238B CYS 3.4 19.4 + - - +
239B LEU* 3.1 31.9 + - + +
241B VAL* 1.3 77.5 - - + +
243B ASP* 1.3 59.6 + - - +
245B ALA* 3.1 12.6 + - - +
247B MET* 2.9 45.7 + - + +
252B ARG* 3.6 40.6 - - - +
258B VAL* 4.5 8.3 - - - +
261B VAL* 5.6 3.4 - - + -
262B GLY* 6.0 1.1 - - - -
324B PHE* 4.1 20.0 - - + -
328B LEU* 4.0 22.4 - - + -
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Residues in contact with ASP 243 (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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18B ASN 4.3 3.7 - - - +
19B SER* 3.7 10.6 - - - +
20B ASN* 3.0 20.6 + - - +
21B ALA* 3.5 26.2 + - - +
239B LEU* 3.2 11.6 + - - +
240B TYR* 3.1 16.8 + - + +
242B MET* 1.3 76.1 - - - +
244B ARG* 1.3 57.3 + - + +
245B ALA 3.0 0.2 - - - -
246B GLN* 2.7 26.6 + - - +
252B ARG* 2.7 36.3 + - - +
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Residues in contact with ARG 244 (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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240B TYR* 2.8 64.1 + - + +
241B VAL 3.1 8.9 + - - +
243B ASP* 1.3 77.3 - - + +
245B ALA* 1.3 57.9 + - - +
246B GLN* 3.2 7.1 + - - +
265B MET* 4.0 10.0 - - + +
271B ASP 3.6 10.7 + - - -
272B GLU* 3.5 23.6 + - - +
302B TYR* 3.5 23.9 + - - +
306B GLU* 3.2 35.8 + - - +
307B ASN* 4.8 0.8 - - - +
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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