Contacts of the helix formed by residues 212 - 221 (chain C) in PDB entry 6GL7
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 PRO 212 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171C ASN* 5.3 4.7 - - - +
173C ASN* 5.4 7.9 - - + +
174C CYS* 5.2 5.2 - - + +
177C LEU* 5.7 0.2 - - + -
210C ARG 3.8 5.1 - - - +
211C VAL* 1.3 95.3 - - + +
213C SER* 1.3 65.4 + - - +
214C GLU* 3.1 29.6 - - - +
215C TYR* 3.0 28.9 + - + -
216C THR 3.1 8.7 + - - -
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Residues in contact with SER 213 (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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140C ARG* 4.6 16.9 + - - -
144C ILE* 6.5 1.1 - - - -
211C VAL 3.5 2.1 + - - -
212C PRO* 1.3 71.4 - - - +
214C GLU* 1.3 62.2 + - - +
215C TYR 2.9 1.9 + - - -
216C THR* 3.0 10.0 + - - -
217C TYR* 2.8 59.2 + - - +
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Residues in contact with GLU 214 (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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144C ILE* 6.5 0.7 - - - -
147C GLY 4.5 22.4 - - - +
212C PRO* 3.1 27.4 - - - +
213C SER* 1.3 76.7 + - - +
215C TYR* 1.3 77.4 + - + +
218C ARG* 3.2 30.6 + - - +
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Residues in contact with TYR 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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164C ALA 5.2 1.1 - - - -
167C ALA* 3.3 37.6 + - + -
168C CYS* 4.0 13.5 - - + -
171C ASN* 2.8 38.2 + - + +
174C CYS* 3.6 14.4 - - + -
211C VAL* 3.6 15.7 - - + -
212C PRO* 3.0 28.0 + - + -
214C GLU* 1.3 101.9 - - + +
216C THR* 1.3 63.9 + - - +
217C TYR 3.5 0.4 - - - -
218C ARG* 4.0 4.0 - - - -
219C MET* 3.1 34.6 + - + +
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Residues in contact with THR 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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207C PHE* 4.7 2.7 - - + -
208C PHE* 3.9 42.7 + - + +
211C VAL* 3.5 41.3 - - + +
212C PRO 3.1 1.0 + - - -
213C SER* 3.0 18.9 + - - -
215C TYR* 1.3 75.6 - - - +
217C TYR* 1.3 78.3 + - - -
219C MET* 4.1 4.1 - - - +
220C LEU* 2.8 34.5 + - - +
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Residues in contact with TYR 217 (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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97C ARG* 5.2 4.9 + - - -
140C ARG* 6.2 1.1 - - - -
144C ILE* 4.7 13.0 - - + -
208C PHE* 6.5 0.2 - + - -
213C SER* 2.8 36.7 + - - +
214C GLU* 5.6 0.4 - - - -
216C THR* 1.3 87.5 + - - +
218C ARG* 1.3 61.3 + - - +
220C LEU* 5.5 0.9 - - + -
221C PHE* 2.9 55.4 + + + +
291C GLN* 3.5 20.7 + - - -
294C LEU* 3.4 30.3 - - + -
295C GLY* 3.5 22.7 + - - -
298C ALA* 3.8 23.3 - - + +
355C PHE* 6.2 2.2 - - + -
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Residues in contact with ARG 218 (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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163C ASP* 3.6 25.6 + - - +
164C ALA* 3.4 21.9 - - + +
167C ALA* 3.2 27.4 - - - +
213C SER 4.0 2.0 + - - -
214C GLU* 3.2 26.5 + - - +
215C TYR* 4.0 5.1 - - - +
216C THR 3.4 0.6 - - - -
217C TYR* 1.3 80.6 - - - +
219C MET* 1.3 61.1 + - + +
221C PHE 5.4 0.2 - - - -
222C CYS* 3.3 23.7 + - - +
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Residues in contact with MET 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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161C CYS 5.3 0.4 - - - +
164C ALA* 3.4 30.7 - - + +
165C ALA* 4.0 10.8 - - + +
168C CYS* 3.5 21.8 - - + -
174C CYS* 3.5 30.1 - - - -
178C ARG* 4.2 12.8 - - - -
207C PHE* 4.1 20.4 - - + -
215C TYR* 3.1 32.9 + - + +
216C THR* 4.1 1.1 - - - +
218C ARG* 1.3 76.5 - - + +
220C LEU* 1.3 64.9 + - - +
222C CYS* 3.1 20.8 - - - -
236C THR* 3.8 16.8 + - + -
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Residues in contact with LEU 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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208C PHE* 3.9 30.7 - - + -
216C THR 2.8 24.3 + - - +
217C TYR* 5.5 0.7 - - + -
219C MET* 1.3 75.6 - - - +
221C PHE* 1.3 84.2 + - + +
222C CYS 3.9 0.3 + - - -
233C ARG* 4.1 3.1 - - - +
236C THR* 3.6 30.3 + - + -
237C ILE* 4.3 8.1 - - + -
297C TYR* 5.2 2.5 - - + -
298C ALA* 4.8 6.7 - - + -
301C ILE* 4.7 17.3 - - + -
308C ASN* 5.6 2.7 - - - +
309C TYR* 2.6 40.0 + - + +
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Residues in contact with PHE 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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217C TYR* 2.9 38.4 + + + +
218C ARG* 4.2 0.4 - - - -
220C LEU* 1.3 106.7 - - + +
222C CYS* 1.3 63.1 + - - +
294C LEU* 3.2 33.2 - - + -
297C TYR* 3.6 38.4 - + - -
298C ALA* 4.6 2.9 - - + -
309C TYR* 3.3 18.4 - + - -
348C LEU* 6.0 0.2 - - + -
352C ILE* 3.7 36.9 - - + +
355C PHE* 4.2 13.7 - - + +
356C GLY* 3.4 20.4 + - - -
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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