Contacts of the helix formed by residues 212 - 223 (chain C) in PDB entry 1G59
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 SER 212 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187C TYR* 5.4 1.2 - - - -
188C HIS* 4.0 18.2 - - - -
208C GLU 5.2 0.4 + - - -
209C TRP* 2.7 36.4 + - - +
210C LEU 3.0 1.4 + - - -
211C VAL* 1.3 79.1 - - - +
213C THR* 1.3 65.3 + - - +
214C PRO 3.3 0.4 - - - -
215C ILE* 3.1 28.0 + - - +
216C HIS* 3.1 24.0 + - - -
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Residues in contact with THR 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158C VAL* 3.1 29.8 - - + -
205C ARG* 3.5 2.1 + - - -
209C TRP 3.3 0.9 + - - -
210C LEU* 2.8 21.1 + - - +
212C SER* 1.3 79.6 + - - +
214C PRO* 1.3 52.2 - - - +
216C HIS* 2.7 30.5 + - - +
217C VAL* 2.7 25.3 + - + +
230C PHE* 4.1 31.2 - - + -
232C HIS* 3.2 29.0 + - - +
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Residues in contact with PRO 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156C THR* 4.0 5.6 - - + +
158C VAL* 3.5 7.2 - - + -
168C TYR* 3.3 40.4 - - + -
173C ILE* 3.6 31.4 - - + -
210C LEU 3.5 2.2 - - - +
211C VAL 2.9 23.3 - - - +
212C SER 3.3 0.4 - - - -
213C THR* 1.3 95.5 - - - +
215C ILE* 1.3 60.0 + - - +
217C VAL* 3.3 11.8 - - + +
218C LEU* 3.0 26.2 + - - +
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Residues in contact with ILE 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148C LEU* 4.3 9.8 - - + +
173C ILE* 3.8 21.1 - - + -
174C PRO* 4.7 6.3 - - + +
176C VAL* 3.3 40.4 - - + -
188C HIS* 3.4 43.5 - - + +
211C VAL 5.5 1.1 - - - +
212C SER* 3.1 17.4 + - - +
213C THR 3.0 0.4 - - - -
214C PRO* 1.3 79.4 - - - +
216C HIS* 1.3 62.6 + - - +
218C LEU* 3.2 7.8 + - - +
219C LEU* 2.8 36.1 + - + +
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Residues in contact with HIS 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187C TYR* 3.9 5.7 - + - -
188C HIS* 3.2 40.5 + + - -
191C ASN* 3.1 22.4 + - - +
192C VAL* 3.9 14.3 - - + +
205C ARG* 3.3 39.7 + - - -
212C SER* 3.1 27.2 + - - -
213C THR* 2.7 15.5 + - - +
215C ILE* 1.3 72.5 - - - +
217C VAL* 1.3 60.7 + - - +
219C LEU* 3.1 3.5 + - - +
220C TYR* 2.8 36.9 + - + -
230C PHE* 4.6 13.0 - - + -
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Residues in contact with VAL 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156C THR* 3.7 18.4 - - + -
157C GLU 3.9 11.7 - - - +
158C VAL* 3.5 14.8 - - + -
213C THR* 2.7 28.5 + - + +
214C PRO* 3.3 17.7 - - + +
216C HIS* 1.3 72.4 - - - +
218C LEU* 1.3 58.8 + - + +
220C TYR* 3.4 12.9 + - - +
221C ARG* 3.0 30.9 + - - +
227C ALA* 5.2 6.5 - - + -
230C PHE* 5.1 7.3 - - + -
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Residues in contact with LEU 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C TRP* 4.7 8.2 + - - +
148C LEU* 4.2 14.1 - - + -
150C VAL* 3.8 39.5 - - + -
151C PRO* 4.5 15.5 - - + -
156C THR* 2.9 34.8 - - + +
170C ASN* 4.9 0.2 - - - +
173C ILE* 4.4 11.2 - - + -
214C PRO 3.0 16.7 + - - +
215C ILE* 3.3 5.8 - - - +
216C HIS 3.0 0.2 - - - -
217C VAL* 1.3 76.6 - - - +
219C LEU* 1.3 60.1 + - - +
221C ARG* 2.9 28.9 - - - +
222C ALA* 2.9 26.7 + - - +
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Residues in contact with LEU 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C LEU* 4.2 21.5 - - + -
148C LEU* 4.0 19.3 - - + -
178C LEU* 3.7 24.2 - - + -
188C HIS 2.8 37.2 - - - +
189C LEU* 4.2 3.6 - - + +
192C VAL* 3.9 17.7 - - + -
215C ILE* 2.8 27.8 + - + +
216C HIS* 3.5 6.7 - - - +
218C LEU* 1.3 72.9 - - - +
220C TYR* 1.3 65.0 + - - +
221C ARG 2.9 1.6 - - - -
222C ALA* 3.1 5.6 + - - +
223C PHE* 3.0 35.3 + - + -
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Residues in contact with TYR 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191C ASN* 4.6 1.6 + - - -
192C VAL* 3.8 33.3 - - + +
195C ASP* 3.4 29.6 + - - +
196C HIS* 4.5 6.9 + - + -
200C VAL 5.4 0.2 + - - -
216C HIS* 2.8 29.7 + - + -
217C VAL* 3.6 8.7 - - - +
219C LEU* 1.3 73.2 - - - +
221C ARG* 1.3 61.6 + - - +
223C PHE 3.6 0.7 + - - -
224C GLY 3.2 3.1 + - - -
225C TRP* 3.1 66.2 + + - +
226C GLU 3.7 12.3 - - - -
227C ALA* 3.8 20.6 - - + -
228C PRO* 3.2 30.7 - - + +
230C PHE* 4.0 11.9 - + - -
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Residues in contact with ARG 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C TRP* 3.8 29.6 - - + -
151C PRO* 5.1 10.3 - - - +
155C THR 4.3 15.4 + - - -
156C THR* 4.5 13.3 + - - +
157C GLU 5.5 1.6 - - - +
217C VAL* 3.0 18.9 + - - +
218C LEU* 2.9 30.6 - - - +
220C TYR* 1.3 75.3 - - - +
222C ALA* 1.3 58.1 + - - +
224C GLY* 2.8 22.2 + - - -
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Residues in contact with ALA 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C LEU* 3.6 20.2 - - + -
99C ARG* 3.3 24.7 + - - -
101C TRP* 3.5 47.2 - - + -
148C LEU* 5.4 0.9 - - + -
218C LEU 2.9 14.3 + - - +
219C LEU* 3.5 11.2 - - + +
221C ARG* 1.3 72.7 - - - +
223C PHE* 1.3 59.9 + - - +
224C GLY* 3.1 5.0 + - - -
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Residues in contact with PHE 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C TYR* 3.4 48.2 - + + -
95C GLU* 3.9 13.9 - - + -
96C LEU* 3.3 33.7 - - + -
99C ARG* 3.4 18.8 + - - +
189C LEU* 4.5 5.2 - - + -
192C VAL* 4.0 14.6 - - + -
193C VAL* 4.2 18.4 - - + -
219C LEU* 3.0 26.1 + - + +
220C TYR 4.0 0.4 - - - +
222C ALA* 1.3 75.2 - - - +
224C GLY* 1.3 64.2 + - - +
225C TRP* 3.4 51.6 - + + +
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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