Contacts of the helix formed by residues 211 - 222 (chain X) in PDB entry 1GNG
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 211 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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290A GLU* 3.6 7.6 - - - -
206X LEU* 2.8 20.0 + - + -
209X SER* 3.1 35.4 + - - +
210X GLY* 1.3 74.4 - - - +
212X LEU* 1.3 60.8 + - - +
213X ILE 3.6 1.8 - - - -
214X LYS* 2.8 38.2 + - + +
215X GLU* 2.9 31.1 + - + +
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Residues in contact with LEU 212 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A ILE* 4.0 21.5 - - + +
229A PHE* 3.9 30.7 - - + -
263A VAL* 4.5 13.7 - - + -
266A LEU* 3.4 27.8 - - + -
288A TYR* 2.9 18.5 + - + +
203X LEU* 3.8 21.1 - - + -
206X LEU* 3.4 22.0 + - + +
207X VAL* 4.2 7.9 - - + -
211X ASN* 1.3 77.7 - - - +
213X ILE* 1.3 56.8 + - - +
215X GLU* 3.7 0.5 - - - +
216X ALA* 2.9 26.7 + - - +
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Residues in contact with ILE 213 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A PHE* 3.5 30.1 - - + -
266A LEU* 4.5 4.3 - - + -
270A ILE* 4.7 3.8 - - + -
275A THR* 4.1 20.9 - - + -
276A PRO* 3.8 12.3 - - + -
281A ILE* 3.3 35.0 - - + -
288A TYR* 4.6 1.3 - - + -
290A GLU* 3.0 17.5 + - + +
293A PHE* 3.5 33.7 - - + -
212X LEU* 1.3 74.1 - - - +
214X LYS* 1.3 59.8 + - - +
216X ALA* 3.3 5.3 + - - +
217X VAL* 2.9 36.6 + - + +
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Residues in contact with LYS 214 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290A GLU* 2.8 47.4 + - - +
291A PHE 5.5 0.2 - - - +
292A LYS* 2.8 42.9 + - - +
293A PHE* 3.9 2.6 - - + +
294A PRO* 4.0 18.3 - - + +
210X GLY 3.5 6.9 + - - -
211X ASN* 2.8 34.6 + - + +
213X ILE* 1.3 75.7 - - - +
215X GLU* 1.3 61.2 + - - +
217X VAL* 3.4 3.1 + - - +
218X ARG* 3.1 21.0 + - + +
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Residues in contact with GLU 215 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A VAL* 4.5 4.3 - - + -
202X LEU* 6.0 2.0 - - - -
206X LEU* 3.8 30.8 - - + +
211X ASN* 2.9 23.8 + - + +
212X LEU 3.7 2.0 - - - +
214X LYS* 1.3 76.9 - - - +
216X ALA* 1.3 67.2 + - - +
218X ARG* 2.8 40.2 + - - +
219X ARG* 2.7 54.5 + - - +
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Residues in contact with ALA 216 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A VAL* 4.5 7.6 - - + +
266A LEU* 4.0 14.1 - - + -
267A VAL* 3.2 33.7 - - + +
270A ILE* 3.9 17.7 - - + -
212X LEU 2.9 18.5 + - - +
213X ILE 3.7 3.8 - - - +
215X GLU* 1.3 78.2 - - - +
217X VAL* 1.3 57.6 + - - +
219X ARG* 3.3 2.7 + - - -
220X LEU* 2.9 25.0 + - - +
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Residues in contact with VAL 217 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A ILE* 4.3 4.9 - - + -
275A THR* 3.8 12.3 - - + -
294A PRO* 3.2 43.3 - - + +
296A ILE* 3.3 31.6 - - + -
213X ILE 2.9 23.0 + - - +
214X LYS 3.7 1.3 - - - +
215X GLU 3.2 0.2 - - - -
216X ALA* 1.3 73.9 - - - +
218X ARG* 1.3 67.2 + - - +
220X LEU* 2.9 23.2 + - - +
221X HIS* 3.2 24.9 + - + +
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Residues in contact with ARG 218 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214X LYS 3.1 14.3 + - - +
215X GLU* 2.8 44.5 + - - +
217X VAL* 1.3 76.1 - - - +
219X ARG* 1.3 75.7 + - - +
221X HIS* 3.0 20.2 + - - +
222X SER* 3.3 29.9 + - - +
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Residues in contact with ARG 219 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A SER* 4.4 6.9 + - - -
263A VAL* 3.3 38.8 - - - +
264A ASP* 4.4 10.7 - - - +
267A VAL* 4.2 12.2 - - + +
202X LEU* 3.3 34.2 - - - +
215X GLU* 2.7 35.8 + - - +
216X ALA 3.6 6.1 - - - +
218X ARG* 1.3 89.4 - - - +
220X LEU* 1.3 61.3 + - - +
221X HIS 3.2 0.7 + - - -
222X SER* 3.4 15.6 + - - -
223X ARG 3.8 8.8 + - - -
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Residues in contact with LEU 220 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A VAL* 3.7 15.5 - - + +
270A ILE* 3.6 23.1 - - + -
271A LYS* 3.3 38.6 - - + +
296A ILE* 3.4 33.7 - - + -
216X ALA 2.9 13.1 + - - +
217X VAL* 2.9 14.3 + - - +
219X ARG* 1.3 79.0 - - - +
221X HIS* 1.3 63.2 + - + +
222X SER 5.3 0.3 - - - -
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Residues in contact with HIS 221 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294A PRO* 5.4 3.1 - - + -
296A ILE* 4.1 12.5 - - + +
217X VAL* 3.3 36.1 + - + +
218X ARG* 3.0 10.7 + - - +
220X LEU* 1.3 91.1 - - + +
222X SER* 1.3 62.5 + - - +
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Residues in contact with SER 222 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218X ARG* 3.3 27.8 + - - +
219X ARG* 3.4 9.5 + - - -
221X HIS* 1.3 80.0 - - - +
223X ARG 1.3 50.1 + - - +
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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