Contacts of the helix formed by residues 210 - 222 (chain G) in PDB entry 3Q3G
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 HIS 210 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C TYR 5.4 0.8 + - - -
99C SER* 5.6 0.8 - - - -
100C TYR* 4.6 16.8 - + - -
61D LYS* 4.7 5.4 + - - -
176G TYR* 3.5 5.0 - - - -
177G SER 2.8 16.4 + - - +
178G GLU* 3.7 29.6 + - + -
180G PHE* 3.3 20.4 - - + -
208G ARG* 4.3 11.5 - - - +
209G THR* 1.3 76.2 - - - +
211G THR* 1.3 61.0 + - - +
213G THR* 4.4 1.1 + - - -
214G GLY 3.2 16.1 + - - -
246G PHE 3.2 23.4 + - - -
247G GLY* 3.4 19.0 + - - -
248G ASP* 3.0 32.0 - - - +
249G PRO* 4.1 11.4 - - + +
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Residues in contact with THR 211 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138G LEU* 4.4 1.0 - - + +
176G TYR* 2.8 36.4 + - + +
209G THR* 3.4 11.1 - - - +
210G HIS* 1.3 68.9 - - - +
212G ALA* 1.4 59.7 + - - +
214G GLY* 3.1 3.1 + - - -
215G ILE* 2.9 45.0 + - + +
239G VAL* 4.4 14.4 - - + -
241G THR* 4.7 2.9 + - - +
243G GLY 4.8 1.0 + - - -
245G LYS* 3.6 11.0 + - - +
248G ASP* 3.2 1.8 + - - -
252G TYR* 3.4 23.0 + - + +
283G GLU* 4.9 0.2 + - - -
287G ILE* 4.4 7.0 - - + -
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Residues in contact with ALA 212 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211G THR* 1.4 71.0 - - - +
213G THR* 1.4 57.1 + - - +
215G ILE* 3.1 5.2 + - - -
216G ARG 3.0 24.6 + - - -
245G LYS* 3.8 11.7 - - + +
248G ASP* 2.9 14.3 + - - +
250G LEU* 3.6 19.3 - - + +
251G GLY 3.8 20.0 - - - +
252G TYR* 3.9 13.8 - - + -
255G VAL* 3.3 19.5 - - + +
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Residues in contact with THR 213 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180G PHE* 3.6 31.6 - - + -
210G HIS* 4.0 2.0 - - - -
211G THR 3.4 0.2 - - - -
212G ALA* 1.4 74.9 - - - +
214G GLY* 1.3 57.0 - - - +
216G ARG* 3.5 2.6 + - - +
217G LYS* 3.0 43.5 + - + +
248G ASP* 2.5 27.1 + - - -
249G PRO* 3.9 11.3 - - + +
250G LEU* 3.6 26.0 - - + +
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Residues in contact with GLY 214 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138G LEU* 3.7 13.7 - - - -
174G MET* 3.5 9.6 - - - +
176G TYR* 4.4 1.8 - - - -
180G PHE* 3.5 21.9 - - - -
210G HIS 3.2 8.2 + - - -
211G THR 3.1 7.5 + - - -
213G THR* 1.3 74.0 - - - +
215G ILE* 1.4 57.5 + - - +
217G LYS 3.3 1.2 + - - -
218G VAL* 3.0 32.2 + - - +
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Residues in contact with ILE 215 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138G LEU* 3.7 19.1 - - + -
211G THR* 2.9 27.5 + - + +
212G ALA* 3.1 1.8 + - - +
214G GLY* 1.4 70.0 - - - +
216G ARG* 1.4 65.9 + - - +
218G VAL* 3.3 5.1 + - - +
219G VAL* 3.0 31.7 + - + +
237G LEU* 4.5 13.2 - - + -
239G VAL* 4.8 5.6 - - + -
252G TYR* 3.8 28.7 - - + -
255G VAL* 3.5 19.5 - - + -
256G ILE* 4.5 14.4 - - + -
259G ALA* 4.8 7.2 - - + -
266G ARG* 4.8 3.6 - - - -
287G ILE* 3.9 20.0 - - + -
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Residues in contact with ARG 216 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212G ALA 3.0 13.3 + - - +
213G THR* 3.7 8.1 - - - +
215G ILE* 1.4 74.2 - - - +
217G LYS* 1.3 56.4 + - + +
219G VAL* 3.3 5.6 + - - +
220G ARG* 2.8 84.0 + - - +
250G LEU* 3.6 33.5 - - + +
254G ASP* 2.8 39.2 + - - +
255G VAL* 3.4 14.0 - - + +
258G GLU* 3.8 9.3 + - - +
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Residues in contact with LYS 217 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174G MET* 3.8 15.2 - - + +
180G PHE* 3.6 36.1 - - + -
213G THR* 3.0 30.9 + - + +
214G GLY 3.3 4.7 + - - +
216G ARG* 1.3 75.5 - - + +
218G VAL* 1.3 57.6 + - - +
220G ARG* 4.6 2.0 - - - +
221G GLU* 2.8 55.2 + - - +
703G GOL 2.5 45.2 + - - +
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Residues in contact with VAL 218 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136G ALA* 4.3 0.4 - - + -
138G LEU* 3.7 32.3 - - + -
174G MET* 4.1 6.7 - - + -
214G GLY 3.0 17.2 + - - +
215G ILE* 3.3 9.6 + - - +
217G LYS* 1.3 75.3 - - - +
219G VAL* 1.3 60.9 + - + +
222G LEU* 3.0 53.9 + - + +
223G PHE* 3.2 27.2 + - + -
237G LEU* 3.6 30.3 - - + -
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Residues in contact with VAL 219 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215G ILE* 3.0 25.3 + - + +
216G ARG* 3.7 6.3 - - - +
218G VAL* 1.3 80.1 - - + +
220G ARG* 1.3 60.9 + - - +
223G PHE* 3.5 28.6 - - + +
237G LEU* 5.6 0.2 - - + -
255G VAL 5.5 1.6 - - - +
258G GLU* 4.3 24.9 - - + +
259G ALA* 3.9 26.2 - - + +
262G GLU* 4.2 31.1 - - + +
264G VAL* 4.0 18.2 - - + -
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Residues in contact with ARG 220 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216G ARG* 2.8 70.2 + - + +
217G LYS* 4.5 2.5 - - - +
219G VAL* 1.3 74.3 - - + +
221G GLU* 1.3 61.6 + - + +
223G PHE 4.9 0.3 - - - +
224G ASN* 3.6 19.6 + - - +
258G GLU* 2.8 38.4 + - - +
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Residues in contact with GLU 221 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182G ILE* 3.6 18.8 - - + +
217G LYS* 2.8 45.0 + - - +
220G ARG* 1.3 76.2 - - + +
222G LEU* 1.4 63.5 + - - +
223G PHE 3.4 1.1 - - - -
224G ASN* 3.3 6.0 - - - +
227G ASN* 2.7 31.9 + - - +
703G GOL 2.7 45.0 + - - -
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Residues in contact with LEU 222 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136G ALA* 4.1 17.7 - - + -
137G PHE 4.2 2.0 - - - +
172G SER* 3.1 29.6 - - - +
173G LEU 4.2 3.1 - - - +
174G MET* 3.9 20.4 - - + +
182G ILE* 3.8 39.5 - - + -
185G THR* 5.1 2.9 - - + -
186G PHE* 3.1 27.6 - - + -
217G LYS 3.7 0.9 + - - +
218G VAL* 3.0 45.1 + - + +
221G GLU* 1.4 75.2 - - - +
223G PHE* 1.3 59.7 + - + +
224G ASN 3.2 7.7 + - - +
227G ASN* 4.2 6.3 - - + +
229G ALA* 3.8 1.7 - - - +
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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