Contacts of the helix formed by residues 206 - 220 (chain B) in PDB entry 1G9Y
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 ASN 206 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204B LYS 4.0 1.2 + - - -
205B TYR* 1.3 74.4 - - - +
207B LYS* 1.3 63.0 + - - +
208B GLU* 3.4 18.4 + - - +
209B PHE* 3.2 35.6 + - + +
210B LEU* 3.0 26.4 + - - +
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Residues in contact with LYS 207 (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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8A GLU* 2.8 38.2 + - - +
205B TYR 3.6 3.5 + - - -
206B ASN* 1.3 78.2 + - - +
208B GLU* 1.3 60.1 + - + +
210B LEU* 3.3 9.6 + - - +
211B LEU* 2.9 36.0 + - + +
294B PHE* 3.9 28.9 - - + -
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Residues in contact with GLU 208 (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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7A LYS* 2.8 37.1 + - + +
11A LEU* 3.5 34.8 - - + +
94A PHE* 5.0 3.1 - - - -
206B ASN* 3.4 16.5 + - - +
207B LYS* 1.3 77.4 - - + +
209B PHE* 1.3 65.2 + - - +
211B LEU* 3.8 3.5 - - + +
212B TYR* 3.2 23.9 + - - +
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Residues in contact with PHE 209 (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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96A LYS* 4.8 12.6 - - - +
205B TYR* 4.0 37.7 - + + -
206B ASN* 3.2 25.8 + - + +
207B LYS 3.2 0.2 - - - -
208B GLU* 1.3 78.3 - - - +
210B LEU* 1.3 62.8 + - + +
212B TYR* 3.8 4.4 - + - +
213B LEU* 2.9 60.4 + - + +
258B LEU* 4.2 4.3 - - + -
261B GLU* 3.3 50.0 - - + -
262B ILE* 4.1 11.9 - - + -
287B PHE* 5.0 1.1 - + - -
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Residues in contact with LEU 210 (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 TYR* 3.8 42.4 - - + +
206B ASN 3.0 13.9 + - - +
207B LYS* 3.7 8.3 - - - +
209B PHE* 1.3 84.1 - - + +
211B LEU* 1.3 58.5 + - - +
213B LEU* 4.5 0.9 - - + -
214B ALA* 2.8 33.1 + - - +
287B PHE* 4.7 6.5 - - + +
290B GLN* 3.4 32.8 - - + +
291B LEU* 3.5 30.7 - - + +
294B PHE* 3.8 20.1 - - + -
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Residues in contact with LEU 211 (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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8A GLU* 3.9 43.7 - - + +
11A LEU* 3.8 28.9 - - + -
12A TYR* 3.3 25.5 - - + +
207B LYS* 2.9 36.7 + - + +
208B GLU* 3.8 6.3 - - + +
209B PHE 3.3 0.2 - - - -
210B LEU* 1.3 78.9 - - - +
212B TYR* 1.3 64.2 + - - +
214B ALA* 3.5 2.3 + - - +
215B GLY 3.4 8.3 + - - -
294B PHE* 3.4 36.6 - - + -
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Residues in contact with TYR 212 (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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11A LEU* 3.4 23.5 + - + +
14A ALA 4.0 0.7 - - - -
15A GLY* 3.4 35.5 - - - -
18A ASP* 2.4 37.7 + - + +
94A PHE* 3.3 27.8 - - + -
96A LYS* 3.4 45.4 - - + +
208B GLU 3.2 14.6 + - - +
209B PHE* 3.8 6.3 - + - +
211B LEU* 1.3 80.0 - - - +
213B LEU* 1.3 69.9 + - + +
215B GLY 3.1 4.0 + - - -
216B PHE* 3.0 23.8 + + + -
254B PHE* 3.7 23.3 - + - -
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Residues in contact with LEU 213 (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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209B PHE* 2.9 48.6 + - + +
210B LEU* 4.0 3.4 - - + +
212B TYR* 1.3 82.1 - - + +
214B ALA* 1.3 56.1 + - - +
216B PHE* 3.0 14.7 + - + -
217B VAL* 2.6 57.7 + - + +
243B PHE* 5.1 0.2 - - + -
245B VAL* 5.0 0.7 - - + -
254B PHE* 5.7 1.6 - - + -
258B LEU* 4.0 31.6 - - + -
262B ILE* 4.2 2.9 - - + -
287B PHE* 3.7 30.1 - - + -
291B LEU* 4.3 5.8 - - + -
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Residues in contact with ALA 214 (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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12A TYR* 3.9 2.2 - - + -
210B LEU 2.8 23.2 + - - +
211B LEU 3.8 3.1 - - - +
212B TYR 3.3 0.2 - - - -
213B LEU* 1.3 73.0 - - - +
215B GLY* 1.3 56.8 + - - +
217B VAL* 3.3 0.6 + - - -
218B ASP* 2.8 31.0 + - - +
291B LEU* 3.5 14.3 - - + +
294B PHE* 3.4 40.2 - - + +
295B LEU* 3.6 14.8 - - + +
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Residues in contact with GLY 215 (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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12A TYR* 3.3 40.5 - - - -
16A PHE* 3.2 21.0 - - - -
211B LEU 3.4 4.4 + - - -
212B TYR 3.1 4.8 + - - -
214B ALA* 1.3 80.7 - - - +
216B PHE* 1.3 61.5 + - - +
218B ASP 3.3 1.0 + - - -
219B GLY 3.1 16.1 + - - -
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Residues in contact with PHE 216 (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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15A GLY* 3.2 25.4 - - - +
16A PHE* 4.5 0.2 - - - +
18A ASP* 3.7 28.7 - - + -
19A GLY* 3.8 2.9 - - - -
97A LEU* 3.8 12.1 - - + -
212B TYR* 3.0 18.8 + - + +
213B LEU* 3.0 17.9 + - + +
215B GLY* 1.3 75.1 - - - +
217B VAL* 1.3 59.0 + - - +
219B GLY* 3.0 2.1 + - - +
220B ASP* 2.8 40.6 + - + -
221B GLY 3.7 0.2 + - - -
245B VAL* 3.2 33.7 - - + -
247B GLN* 3.5 25.4 - - - -
254B PHE* 3.2 35.0 - + - -
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Residues in contact with VAL 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B LEU* 2.6 40.2 + - + +
214B ALA 3.7 3.8 - - - +
216B PHE* 1.3 68.4 - - - +
218B ASP* 1.3 61.2 + - - +
219B GLY 2.9 4.7 - - - -
221B GLY* 2.8 32.5 + - - +
222B SER 4.8 0.9 - - - +
223B ILE* 4.9 5.8 - - + -
243B PHE* 3.5 42.8 - - + -
245B VAL* 4.2 6.1 - - + -
291B LEU* 4.2 4.9 - - + -
295B LEU* 4.2 15.3 - - + -
298B LYS* 3.1 24.5 - - + -
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Residues in contact with ASP 218 (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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12A TYR* 2.6 32.7 + - - +
16A PHE* 3.6 14.7 - - + -
20A ASP* 4.1 1.9 - - - +
47A GLN* 4.8 0.5 - - - +
801A CA 4.2 1.7 - - - -
214B ALA 2.8 15.9 + - - +
215B GLY 3.3 4.0 + - - +
217B VAL* 1.3 75.8 - - - +
219B GLY* 1.3 61.6 + - - +
295B LEU* 3.6 6.9 - - - +
296B LYS 2.7 20.8 + - - -
297B LEU* 3.0 24.0 + - + +
298B LYS* 2.9 44.5 + - - +
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Residues in contact with GLY 219 (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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16A PHE* 4.0 4.9 - - - -
19A GLY* 4.5 1.8 - - - -
20A ASP* 3.3 28.9 - - - -
801A CA 2.3 28.0 - - - -
215B GLY 3.1 9.6 + - - -
216B PHE 3.0 5.9 + - - -
217B VAL 2.9 2.0 - - - -
218B ASP* 1.3 80.3 - - - +
220B ASP* 1.3 58.3 + - - -
221B GLY 3.5 0.8 - - - +
298B LYS* 5.0 0.3 - - - -
415C G 3.0 7.3 + - - +
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Residues in contact with ASP 220 (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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18A ASP 4.2 0.2 - - - +
19A GLY* 3.4 15.2 - - - +
216B PHE* 2.8 26.2 + - + +
219B GLY* 1.3 70.6 - - - -
221B GLY* 1.3 60.0 + - - -
245B VAL* 4.7 1.1 - - - -
246B THR* 3.3 35.7 + - - +
247B GLN* 2.9 18.7 + - - +
802B CA 2.4 23.3 - - - -
414C C 3.5 10.6 - - - +
415C G 3.7 14.1 - - - +
803C CA 2.2 32.7 - - - -
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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