Contacts of the helix formed by residues 218 - 231 (chain F) in PDB entry 1G2D
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 GLN 218 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62D A 3.5 19.2 + - - +
63D A 3.0 49.3 + - - -
64D G 4.7 0.7 - - - +
70E C 4.2 8.0 + - - -
205F TYR* 3.8 4.8 - - - -
216F PHE* 3.5 12.1 - - - +
217F SER* 1.3 87.4 - - - +
219F LYS* 1.3 64.8 + - - +
220F THR* 4.2 8.6 + - - +
221F ASN* 3.6 21.1 + - - +
222F LEU* 3.5 13.9 + - - +
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Residues in contact with LYS 219 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69E C 4.9 24.8 + - - +
70E C 4.6 13.5 + - - -
205F TYR* 3.6 41.1 - - + +
218F GLN* 1.3 72.7 - - - +
220F THR* 1.3 66.7 + - - +
222F LEU* 3.1 8.0 + - + +
223F ASP* 3.0 57.1 + - - +
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Residues in contact with THR 220 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70E C 3.1 34.0 + - - -
71E T 3.1 40.4 - - + +
72E T 4.6 5.2 - - + +
218F GLN* 3.4 9.5 + - - +
219F LYS* 1.3 78.3 - - - +
221F ASN* 1.3 65.7 - - - +
223F ASP* 3.1 12.3 + - - +
224F THR* 2.9 38.9 + - - +
227F ARG* 6.1 0.4 - - - +
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Residues in contact with ASN 221 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D A 3.8 23.4 + - - +
62D A 2.9 52.0 + - - -
216F PHE* 3.7 25.0 - - + +
217F SER* 5.7 0.8 - - - +
218F GLN* 3.6 27.3 + - - +
219F LYS 3.2 0.6 - - - -
220F THR* 1.3 81.3 - - - +
222F LEU* 1.3 62.9 + - - +
224F THR* 3.5 7.4 + - - -
225F HIS* 3.0 24.3 + - - +
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Residues in contact with LEU 222 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205F TYR* 3.7 36.1 - - + +
206F ALA 3.8 11.2 - - - +
207F CYS* 3.8 33.0 - - - +
208F PRO* 4.5 2.9 - - + -
216F PHE* 3.6 24.6 - - + -
218F GLN 3.5 3.9 + - - +
219F LYS* 3.1 11.3 + - + +
221F ASN* 1.3 77.0 - - - +
223F ASP* 1.3 66.0 + - - +
225F HIS* 3.1 3.6 + - - +
226F ILE* 3.0 43.9 + - + +
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Residues in contact with ASP 223 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219F LYS* 3.0 47.5 + - - +
220F THR* 3.4 9.7 - - - +
222F LEU* 1.3 83.7 - - - +
224F THR* 1.3 62.6 + - - +
226F ILE* 3.3 17.9 + - - +
227F ARG* 3.6 21.6 + - - +
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Residues in contact with THR 224 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D A 6.1 1.6 - - - +
220F THR* 2.9 25.1 + - - +
221F ASN* 3.9 8.9 + - - -
223F ASP* 1.3 76.1 - - - +
225F HIS* 1.3 60.3 + - - +
227F ARG* 3.2 55.6 + - - +
228F ILE* 4.3 5.5 + - - +
245F SER* 4.4 2.4 - - - +
246F GLN* 3.6 35.9 - - + +
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Residues in contact with HIS 225 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D A 3.1 35.7 + - - +
207F CYS* 3.6 14.1 - - + +
212F CYS* 3.4 10.2 - - - -
214F ARG* 3.8 9.9 - - + +
216F PHE* 3.3 28.8 - + + -
221F ASN 3.0 18.3 + - - +
222F LEU* 3.4 3.6 - - + +
224F THR* 1.3 76.1 - - - +
226F ILE* 1.3 68.1 + - + +
227F ARG 3.0 2.2 - - - -
228F ILE* 3.0 45.0 + - + +
229F HIS* 4.0 0.7 - - - -
304F ZN 2.1 36.6 - - - -
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Residues in contact with ILE 226 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207F CYS* 3.9 16.2 - - - -
208F PRO* 3.4 35.0 - - + -
209F VAL* 5.7 1.6 - - + -
222F LEU* 3.0 29.7 + - + +
223F ASP* 3.3 11.1 + - - +
225F HIS* 1.3 76.9 - - + +
227F ARG* 1.3 57.4 + - - +
228F ILE 3.1 0.2 - - - -
229F HIS* 3.0 25.6 + - + +
230F THR* 3.1 26.7 + - + -
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Residues in contact with ARG 227 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220F THR* 6.1 0.4 - - - +
223F ASP* 3.6 13.4 + - - +
224F THR* 3.2 51.9 + - - +
225F HIS 3.0 0.4 - - - -
226F ILE* 1.3 77.5 - - - +
228F ILE* 1.3 55.9 + - - +
229F HIS 3.2 1.3 - - - -
230F THR* 3.3 11.4 - - - +
231F GLY* 2.8 28.2 + - - -
232F GLN* 3.3 29.9 + - + +
234F PRO* 3.6 23.1 - - - +
235F PHE* 3.8 13.5 - - - -
245F SER* 2.6 40.3 + - - -
246F GLN* 4.7 0.2 - - - +
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Residues in contact with ILE 228 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D T 3.7 49.5 + - + +
60D A 3.9 20.0 - - - +
224F THR 4.4 6.3 - - - +
225F HIS* 3.0 48.7 - - + +
226F ILE 3.1 1.0 - - - -
227F ARG* 1.3 77.8 - - + +
229F HIS* 1.3 74.8 + - + +
231F GLY* 4.2 3.4 + - - -
245F SER* 5.5 3.4 - - - +
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Residues in contact with HIS 229 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207F CYS* 3.3 11.5 - - - -
209F VAL* 3.7 23.6 - - + +
212F CYS* 3.8 14.6 - - + -
225F HIS* 3.5 13.7 + - - -
226F ILE* 3.0 15.2 + - + +
228F ILE* 1.3 92.0 + - + +
230F THR* 1.3 65.8 + - + +
231F GLY 3.3 1.7 + - - -
304F ZN 2.1 37.3 - - - -
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Residues in contact with THR 230 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226F ILE* 3.1 30.9 + - + +
227F ARG* 3.3 12.3 - - - +
229F HIS* 1.3 79.0 - - + +
231F GLY* 1.3 62.8 + - - +
232F GLN* 3.4 25.9 + - - +
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Residues in contact with GLY 231 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227F ARG 2.8 14.0 + - - -
228F ILE 4.9 3.4 - - - -
229F HIS 3.3 3.8 - - - -
230F THR* 1.3 78.8 - - - +
232F GLN* 1.3 65.0 + - - +
233F LYS* 3.7 17.5 + - - +
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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