Contacts of the helix formed by residues 198 - 210 (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 ASP 198 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199X PRO* 1.3 66.6 - - - +
200X HIS* 2.5 39.2 + - - +
201X ARG* 3.0 44.2 + - + +
202X LEU* 3.1 28.4 + - - +
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Residues in contact with PRO 199 (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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216A PTR 6.2 0.4 - - - +
261A SER* 3.8 30.3 - - - +
262A GLY 4.9 3.9 + - - +
263A VAL* 5.0 4.3 - - + +
198X ASP* 1.3 85.8 - - - +
200X HIS* 1.3 70.8 + - + +
201X ARG 3.3 1.6 - - - -
202X LEU* 3.6 15.9 - - + +
203X LEU* 2.7 30.1 + - - +
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Residues in contact with HIS 200 (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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216A PTR 4.0 40.4 + + + -
198X ASP* 2.5 28.3 + - - +
199X PRO* 1.3 82.9 - - + +
201X ARG* 1.3 57.8 + - - +
203X LEU* 3.2 8.6 + - - +
204X GLN* 2.7 35.8 + - - +
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Residues in contact with ARG 201 (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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198X ASP* 3.0 39.3 + - + +
200X HIS* 1.3 79.8 - - - +
202X LEU* 1.3 53.2 + - - +
204X GLN* 2.9 20.1 + - - +
205X GLN* 2.7 41.5 + - + +
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Residues in contact with LEU 202 (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* 4.7 4.0 - - + -
198X ASP 3.1 16.8 + - - +
199X PRO* 3.6 15.9 - - + +
201X ARG* 1.3 78.6 - - - +
203X LEU* 1.3 57.1 + - - +
205X GLN* 3.4 6.7 + - + +
206X LEU* 3.0 52.0 + - + +
215X GLU* 5.9 2.0 - - - +
219X ARG* 3.3 27.1 - - - +
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Residues in contact with LEU 203 (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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216A PTR 5.1 16.2 - - + -
223A ARG* 6.0 0.7 - - - +
227A LEU 5.8 0.2 - - - +
228A ILE* 4.0 35.4 - - + +
262A GLY* 4.1 21.8 - - - -
263A VAL* 4.0 17.5 - - + +
199X PRO 2.7 21.3 + - - +
200X HIS* 3.5 7.2 - - - +
202X LEU* 1.3 70.4 - - - +
204X GLN* 1.3 61.4 + - - +
206X LEU* 3.1 2.1 + - - +
207X VAL* 2.9 40.2 + - + +
212X LEU* 3.8 27.4 - - + -
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Residues in contact with GLN 204 (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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200X HIS 2.7 18.8 + - - +
201X ARG* 3.3 20.0 - - + +
203X LEU* 1.3 75.5 - - - +
205X GLN* 1.3 56.9 + - + +
207X VAL* 3.9 6.0 - - - +
208X LEU* 2.9 43.7 + - + +
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Residues in contact with GLN 205 (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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201X ARG* 2.7 23.7 + - + +
202X LEU* 3.8 8.7 - - + +
204X GLN* 1.3 73.2 - - + +
206X LEU* 1.3 54.6 + - + +
207X VAL 3.1 1.8 - - - -
208X LEU* 3.8 19.2 - - - +
209X SER* 2.6 51.9 + - - -
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Residues in contact with LEU 206 (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* 3.8 22.0 - - + -
202X LEU* 3.0 46.6 + - + +
203X LEU 3.6 4.0 - - - +
205X GLN* 1.3 76.9 - - + +
207X VAL* 1.3 59.0 + - - +
209X SER* 3.4 3.6 - - - +
210X GLY* 2.9 7.6 + - - -
211X ASN* 2.8 58.3 + - + +
212X LEU* 3.4 22.0 + - + -
215X GLU* 3.8 25.1 - - + +
219X ARG* 5.2 0.2 - - - +
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Residues in contact with VAL 207 (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 20.4 - - - +
229A PHE 3.8 21.3 - - - +
230A GLY* 4.6 6.5 - - - +
285A ASN* 5.4 1.3 - - - +
288A TYR* 3.6 27.7 - - + -
289A THR 5.3 0.5 + - - +
203X LEU* 2.9 32.8 + - + +
204X GLN* 3.9 6.1 - - - +
206X LEU* 1.3 77.2 - - - +
208X LEU* 1.3 67.6 + - + +
210X GLY* 3.6 2.1 + - - -
212X LEU* 4.2 10.8 - - + -
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Residues in contact with LEU 208 (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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204X GLN* 2.9 38.6 + - + +
205X GLN* 3.8 21.1 - - - +
207X VAL* 1.3 80.1 - - + +
209X SER* 1.3 60.7 + - - +
210X GLY 3.5 0.2 + - - -
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Residues in contact with SER 209 (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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291A PHE* 5.6 5.9 - - - -
205X GLN* 2.6 38.1 + - - +
206X LEU* 3.2 12.5 + - - +
208X LEU* 1.3 75.1 - - - +
210X GLY* 1.3 60.5 + - - +
211X ASN* 3.1 26.5 + - - +
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Residues in contact with GLY 210 (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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288A TYR* 3.3 16.6 - - - -
289A THR 3.1 24.0 - - - -
290A GLU* 3.1 22.5 - - - +
291A PHE* 4.8 2.3 + - - -
206X LEU 2.9 7.8 + - - -
207X VAL 3.6 1.5 + - - -
208X LEU 3.3 3.2 - - - -
209X SER* 1.3 79.4 - - - +
211X ASN* 1.3 65.7 + - - +
214X LYS* 3.5 1.0 + - - -
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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