Contacts of the helix formed by residues 220 - 231 (chain B) in PDB entry 3DGR
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 THR 220 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192B ASP* 3.6 12.8 + - - -
193B PHE 4.9 0.3 - - - -
194B GLY 4.4 0.4 + - - -
195B TYR* 3.3 51.6 + - + +
204B ALA* 3.8 31.6 - - + +
208B ALA* 3.8 7.8 - - + +
218B THR* 3.0 15.4 + - - -
219B ASP* 1.3 77.5 - - - +
221B VAL* 1.3 63.5 + - - +
222B ALA* 3.2 7.4 + - + +
223B GLY* 3.2 11.1 + - - -
224B LEU* 3.3 11.3 - - - +
387B LEU* 5.2 1.2 - - + +
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Residues in contact with VAL 221 (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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13A LEU* 3.4 47.3 - - + +
15A THR 3.2 27.1 - - - +
17A SER* 3.9 12.8 - - - +
86A VAL* 4.1 17.2 - - + +
87A TYR* 4.0 16.6 - - + +
90A HIS* 5.7 3.8 - - + -
195B TYR* 4.3 1.7 - - + -
219B ASP 3.6 5.6 - - - +
220B THR* 1.3 72.7 - - - +
222B ALA* 1.3 62.1 + - - +
224B LEU* 3.2 27.9 + - + +
225B ALA* 3.7 5.5 + - - +
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Residues in contact with ALA 222 (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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13A LEU 4.7 1.7 + - - +
195B TYR* 4.2 18.5 - - + +
201B GLN* 4.9 5.4 - - - +
205B GLY* 3.8 22.2 - - - +
220B THR* 3.2 5.3 + - + +
221B VAL* 1.3 76.5 - - - +
223B GLY* 1.3 64.5 + - - +
225B ALA* 3.4 8.9 + - - +
226B LEU* 3.1 22.5 + - - +
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Residues in contact with GLY 223 (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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205B GLY* 3.5 24.0 - - - -
208B ALA* 3.9 16.3 - - - +
209B SER* 3.9 4.1 - - - -
212B LEU* 4.9 1.6 - - - -
220B THR* 3.2 7.5 + - - +
222B ALA* 1.3 79.2 - - - +
224B LEU* 1.3 62.6 + - - +
226B LEU* 3.3 4.2 + - - +
227B ILE* 3.1 31.8 + - - +
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Residues in contact with LEU 224 (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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86A VAL* 5.8 5.6 - - + -
90A HIS* 4.5 13.0 - - + +
212B LEU* 3.9 7.0 - - + -
218B THR* 3.7 13.0 - - + -
220B THR 3.3 18.2 - - - +
221B VAL* 3.2 24.2 + - + +
223B GLY* 1.3 75.2 - - - +
225B ALA* 1.3 58.1 + - - +
227B ILE* 3.3 4.5 + - - +
228B LYS* 3.0 30.6 + - - +
237B VAL* 4.2 13.7 - - + -
238B PRO* 3.4 22.3 - - + +
239B GLY* 3.0 45.1 - - - +
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Residues in contact with ALA 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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13A LEU* 6.2 4.9 - - + -
221B VAL 3.7 6.8 + - - +
222B ALA* 3.4 10.7 + - - +
223B GLY 3.3 0.4 - - - -
224B LEU* 1.3 74.7 - - - +
226B LEU* 1.3 64.6 + - - +
228B LYS* 3.7 9.0 - - - +
229B LYS* 3.1 26.7 + - - +
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Residues in contact with LEU 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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60B TYR* 4.1 8.5 - - - +
64B TYR* 3.7 41.3 - - + +
202B GLU 5.4 0.2 - - - +
205B GLY* 3.6 28.7 - - - +
206B ILE* 3.6 15.0 - - + +
209B SER* 3.7 16.6 - - - +
222B ALA 3.1 13.6 + - - +
223B GLY 3.3 8.5 + - - +
225B ALA* 1.3 74.8 - - - +
227B ILE* 1.3 61.1 + - - +
229B LYS 3.3 0.2 + - - -
230B TYR* 2.9 44.7 + - + +
231B TYR* 4.2 10.8 - - + -
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Residues in contact with ILE 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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60B TYR* 4.6 1.1 - - - +
209B SER* 3.7 18.4 - - - -
212B LEU* 3.6 22.0 - - + -
223B GLY 3.1 16.7 + - - +
224B LEU 3.3 5.6 + - - +
226B LEU* 1.3 78.8 - - - +
228B LYS* 1.3 54.2 + - - +
231B TYR* 2.8 16.8 + - + -
232B GLY 2.7 29.4 + - - +
233B THR* 3.9 9.2 - - + +
238B PRO* 3.5 31.6 - - + -
473B PHE* 3.6 55.2 - - + -
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Residues in contact with LYS 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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86A VAL* 6.3 2.7 - - - -
224B LEU 3.0 17.4 + - - +
225B ALA* 3.7 9.2 - - - +
226B LEU 3.3 0.2 - - - -
227B ILE* 1.3 79.9 - - - +
229B LYS* 1.3 61.1 + - - +
231B TYR 4.8 0.3 - - - -
232B GLY* 4.0 15.9 + - - +
233B THR* 5.5 2.0 - - - +
236B PRO 4.2 18.7 + - - +
237B VAL* 6.1 0.7 - - + -
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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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68B LYS* 6.1 0.2 - - - +
225B ALA 3.1 18.6 + - - +
228B LYS* 1.3 79.3 - - - +
230B TYR* 1.3 101.3 + - + +
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Residues in contact with TYR 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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63B GLN* 2.9 23.8 - - - +
64B TYR* 3.7 34.8 - + - -
67B ASN* 3.7 27.5 + - + +
68B LYS* 3.7 51.6 + - + +
226B LEU* 2.9 35.8 + - + +
229B LYS* 1.3 115.9 + - + +
231B TYR* 1.3 77.2 + - + +
470B SER* 5.1 0.2 + - - -
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Residues in contact with TYR 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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60B TYR* 3.3 28.7 - + - -
61B GLY* 3.3 19.9 + - - -
63B GLN* 3.2 34.6 - - + +
64B TYR* 3.3 15.3 + - + -
121B GLU* 2.8 27.2 + - - -
226B LEU* 4.2 12.3 - - + -
227B ILE* 2.8 11.3 + - - +
228B LYS 4.8 0.7 - - - -
229B LYS 3.7 0.6 - - - -
230B TYR* 1.3 95.8 - - + +
232B GLY* 1.3 61.5 + - - +
471B TYR 3.6 4.9 - - - +
472B SER* 3.5 15.1 - - - -
473B PHE* 3.8 26.0 - + + +
476B ILE* 3.2 24.2 - - + -
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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