Contacts of the helix formed by residues 225 - 240 (chain B) 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 PRO 225 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223B GLY 3.4 6.7 - - - +
224B SER* 1.3 88.7 - - - +
226B TYR* 1.3 74.5 + - + +
227B ARG 3.3 0.9 + - - -
228B ASP* 3.9 6.2 + - - +
229B LYS* 3.5 38.2 + - - +
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Residues in contact with TYR 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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2B ALA 5.6 1.9 + - - -
4B ARG* 6.0 0.2 - - - -
6B LEU* 3.7 42.2 - - + +
47B LEU* 5.2 10.3 - - + -
49B PHE* 4.5 19.0 - + + +
83B ASP* 5.5 7.0 - - + -
84B LEU* 4.0 23.3 - - + -
220B THR* 4.6 0.7 - - + -
224B SER* 3.1 16.0 + - - +
225B PRO* 1.3 89.7 - - + +
227B ARG* 1.3 64.8 + - - +
229B LYS* 3.3 20.9 + - + +
230B ILE* 2.8 34.1 + - + +
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Residues in contact with ARG 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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100B ASP* 3.7 38.6 + - + +
101B PHE* 3.0 44.8 + - - +
102B SER* 3.8 6.3 - - - +
220B THR* 3.8 25.9 - - + +
224B SER 3.4 10.6 + - - +
225B PRO 3.3 1.8 - - - -
226B TYR* 1.3 78.3 - - - +
228B ASP* 1.3 83.6 + - - +
230B ILE* 3.3 3.6 + - - +
231B THR* 3.0 24.4 + - - -
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Residues in contact with ASP 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A PRO* 6.5 0.4 - - - -
27A TYR* 4.8 11.2 + - - +
224B SER 4.8 1.5 + - - -
225B PRO 3.9 6.5 + - - +
226B TYR 3.4 0.2 - - - -
227B ARG* 1.3 104.8 + - - +
229B LYS* 1.3 61.9 + - + +
231B THR* 3.4 7.4 + - - -
232B ILE* 3.2 28.0 + - - +
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Residues in contact with LYS 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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47B LEU* 3.9 27.7 - - + +
225B PRO* 3.5 33.4 - - - +
226B TYR* 3.3 25.2 + - + +
227B ARG 3.3 0.6 - - - -
228B ASP* 1.3 78.2 - - + +
230B ILE* 1.3 57.8 + - - +
232B ILE* 3.3 8.5 + - - +
233B ALA* 3.0 26.7 + - - +
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Residues in contact with ILE 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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43B LEU* 4.2 14.1 - - + -
47B LEU* 3.7 21.8 - - + -
49B PHE* 5.6 1.3 - - + -
84B LEU* 3.6 37.9 - - + -
102B SER* 3.8 11.0 - - - -
218B VAL* 3.9 24.7 - - + -
220B THR* 4.7 2.0 - - + -
226B TYR* 2.8 27.6 + - + +
227B ARG* 3.8 3.4 - - - +
229B LYS* 1.3 75.4 - - - +
231B THR* 1.3 60.0 + - - +
233B ALA* 3.2 3.2 + - - +
234B ILE* 2.8 49.2 + - + +
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Residues in contact with THR 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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23A ASP 6.0 1.3 - - - +
24A LYS* 6.1 0.2 - - - -
25A PRO* 4.6 21.5 - - + -
102B SER* 3.4 11.5 - - - -
103B LYS* 2.9 50.3 + - + +
227B ARG* 3.0 14.5 + - - -
228B ASP* 3.6 11.9 - - - +
229B LYS 3.4 0.2 - - - -
230B ILE* 1.3 78.6 - - - +
232B ILE* 1.3 66.6 + - + +
234B ILE* 3.3 6.4 + - - +
235B LEU* 3.1 22.0 + - + +
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Residues in contact with ILE 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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24A LYS* 4.6 26.0 - - + -
25A PRO* 4.6 15.0 - - + -
228B ASP* 3.2 15.0 + - + +
229B LYS* 3.7 9.2 - - - +
230B ILE 3.3 0.2 - - - -
231B THR* 1.3 78.9 - - + +
233B ALA* 1.3 63.9 + - - +
235B LEU* 3.3 11.5 + - + +
236B GLN* 3.1 22.4 + - + +
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Residues in contact with ALA 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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43B LEU* 3.6 23.1 - - + -
46B ILE* 3.9 29.3 - - + +
47B LEU* 4.2 7.6 - - + -
229B LYS 3.0 14.7 + - - +
230B ILE 3.2 3.3 + - - +
232B ILE* 1.3 76.4 - - - +
234B ILE* 1.3 59.2 + - - +
236B GLN* 3.2 9.5 + - - +
237B LEU* 2.9 33.5 + - - +
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Residues in contact with ILE 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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39B LEU* 5.0 7.2 - - + -
43B LEU* 4.3 9.0 - - + -
102B SER* 3.3 27.1 - - - +
103B LYS* 3.6 11.9 - - + +
104B PRO 3.9 18.4 - - - +
105B PHE* 4.1 25.4 - - + -
218B VAL* 4.4 7.6 - - + -
230B ILE* 2.8 35.8 + - + +
231B THR* 3.6 6.1 - - - +
233B ALA* 1.3 71.7 - - - +
235B LEU* 1.3 59.5 + - - +
237B LEU* 3.2 8.8 + - + +
238B GLN* 2.9 28.4 + - + +
243B LEU* 4.1 8.2 - - + +
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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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23A ASP* 3.6 56.8 - - + +
24A LYS* 4.0 24.0 - - + -
231B THR* 3.1 14.2 + - + +
232B ILE* 3.5 14.1 - - + +
233B ALA 3.2 0.2 - - - -
234B ILE* 1.3 77.6 - - - +
236B GLN* 1.3 62.1 + - - +
238B GLN* 3.3 13.3 + - + -
239B GLU* 2.9 30.8 + - + +
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Residues in contact with GLN 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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46B ILE* 3.6 40.2 - - - +
232B ILE* 3.1 14.4 + - + +
233B ALA* 3.2 9.1 + - - +
235B LEU* 1.3 77.0 - - - +
237B LEU* 1.3 63.4 + - - +
239B GLU* 3.2 11.5 + - - +
240B GLU* 3.0 53.4 + - + +
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Residues in contact with LEU 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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39B LEU* 3.8 28.0 - - + -
42B GLU* 3.8 32.1 - - + +
43B LEU* 4.2 13.5 - - + -
46B ILE* 3.8 16.4 - - + -
233B ALA 2.9 18.3 + - - +
234B ILE* 3.6 7.0 - - - +
236B GLN* 1.3 75.8 - - - +
238B GLN* 1.3 61.8 + - - +
240B GLU* 3.6 7.3 + - - +
241B GLY 3.3 2.3 + - - -
242B LYS* 2.9 56.5 + - + +
243B LEU* 3.5 17.7 + - + -
246B MET* 5.5 1.1 - - - -
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Residues in contact with GLN 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* 2.9 14.3 + - + +
235B LEU* 3.5 18.6 - - + +
237B LEU* 1.3 77.1 - - - +
239B GLU* 1.3 64.3 + - - +
241B GLY* 3.0 14.7 + - - -
243B LEU* 3.5 31.5 - - + +
244B HIS* 5.3 3.2 + - - +
259B SO4 4.9 9.0 + - - -
131C LYS* 5.7 5.3 - - - +
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Residues in contact with GLU 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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235B LEU* 2.9 25.0 + - + +
236B GLN* 3.2 9.9 + - - +
238B GLN* 1.3 77.7 - - - +
240B GLU* 1.3 60.3 + - + +
241B GLY 3.4 0.7 + - - -
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Residues in contact with GLU 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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46B ILE* 5.2 0.2 - - - +
236B GLN* 3.0 46.7 + - + +
237B LEU* 3.9 12.0 - - - +
239B GLU* 1.3 77.0 - - + +
241B GLY* 1.3 59.3 + - - +
242B LYS* 3.7 37.8 + - + +
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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