Contacts of the helix formed by residues 172 - 185 (chain D) in PDB entry 2C11
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 LEU 172 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86D ALA* 3.7 24.5 - - + +
89D ALA* 4.0 22.7 - - + +
90D ARG 5.0 4.9 - - - +
91D PRO 5.7 0.2 - - - -
95D CYS* 4.1 16.8 - - - -
97D PHE* 3.7 13.2 - - + -
129D PHE* 3.6 32.5 - - + -
166D TYR* 6.1 0.7 - - - +
169D ARG* 5.1 4.9 - - - +
170D PRO 3.3 2.2 + - - +
171D VAL* 1.3 75.4 - - - +
173D PHE* 1.3 65.5 + - - +
174D GLN 4.0 2.2 - - - +
175D GLU* 3.3 29.7 + - + +
176D TYR* 3.0 19.8 + - - -
418D GLU* 3.6 16.8 - - + +
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Residues in contact with PHE 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87D ALA* 3.9 22.0 - - + +
172D LEU* 1.3 71.7 - - - +
174D GLN* 1.3 70.9 + - - +
176D TYR* 3.1 25.7 + - - +
177D LEU* 3.4 38.2 + - + +
418D GLU* 2.6 25.3 + - + +
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Residues in contact with GLN 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86D ALA 4.7 0.4 + - - +
87D ALA 3.5 7.2 + - - +
88D GLN* 3.2 37.5 - - - +
89D ALA 3.0 27.4 - - - +
90D ARG* 3.1 40.2 - - - +
172D LEU* 4.0 4.0 - - + +
173D PHE* 1.3 85.6 - - - +
175D GLU* 1.3 63.0 - - - +
177D LEU* 3.0 34.2 + - - +
178D ASP* 3.3 17.7 + - - +
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Residues in contact with GLU 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89D ALA 4.7 1.9 + - - +
91D PRO* 5.0 6.5 - - + +
169D ARG* 2.9 26.6 + - - -
171D VAL* 3.3 16.9 - - + +
172D LEU* 3.3 29.1 + - + +
173D PHE 3.2 0.4 - - - -
174D GLN* 1.3 79.9 - - - +
176D TYR* 1.3 61.1 + - - +
178D ASP* 3.6 12.5 + - - +
179D ILE* 3.2 25.6 + - + +
223D ARG* 2.8 35.0 + - - -
251D HIS* 3.3 14.4 + - - +
259D TRP* 3.9 20.0 - - + -
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Residues in contact with TYR 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171D VAL* 3.3 36.6 + - + +
172D LEU 3.0 19.9 + - - -
173D PHE* 3.1 13.3 + - - +
174D GLN 3.1 0.2 + - - -
175D GLU* 1.3 74.9 - - - +
177D LEU* 1.3 68.4 + - + +
179D ILE* 2.8 19.0 + - + +
180D ASP* 3.0 21.8 + - - +
212D THR* 3.7 34.5 - - + +
216D ARG* 3.1 24.9 + - - -
227D PHE* 4.5 14.8 - + - -
389D PHE* 4.2 11.0 - + - -
394D TYR* 5.5 7.0 - - - -
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Residues in contact with LEU 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173D PHE* 3.4 44.0 - - + +
174D GLN* 3.0 26.4 + - - +
176D TYR* 1.3 77.2 - - + +
178D ASP* 1.3 53.7 + - - +
180D ASP* 2.9 17.8 + - - +
181D GLN* 2.4 38.9 + - - +
206D ARG* 5.2 5.7 + - - +
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Residues in contact with ASP 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89D ALA 5.2 0.2 - - - +
90D ARG* 2.4 44.9 + - - +
91D PRO* 5.1 1.6 - - - +
174D GLN* 3.3 16.6 + - - +
175D GLU* 3.6 8.2 - - - +
176D TYR 3.2 0.6 - - - -
177D LEU* 1.3 76.9 - - - +
179D ILE* 1.3 57.2 + - - +
181D GLN* 3.1 13.4 - - + +
182D MET* 2.8 31.0 + - - +
256D PRO* 4.3 9.9 - - + +
259D TRP* 3.2 33.0 - - + -
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Residues in contact with ILE 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171D VAL* 4.9 4.5 - - + -
175D GLU* 3.2 17.0 - - + +
176D TYR* 2.8 19.3 + - + +
178D ASP* 1.3 75.9 - - - +
180D ASP* 1.3 66.0 + - - +
182D MET* 3.0 7.8 + - - +
183D ILE* 2.8 43.6 + - + +
227D PHE* 3.5 40.6 - - + -
249D VAL* 4.2 16.2 - - + -
251D HIS* 4.3 24.7 - - + +
259D TRP* 4.0 16.8 - - + -
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Residues in contact with ASP 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448C TYR* 5.0 7.3 + - - -
176D TYR* 3.2 19.5 - - - +
177D LEU* 2.9 20.5 + - - +
179D ILE* 1.3 77.6 - - - +
181D GLN* 1.3 57.0 + - - +
183D ILE* 2.8 7.5 + - - -
184D PHE* 2.7 37.6 + - + +
206D ARG* 3.1 34.8 + - - +
210D THR* 3.0 27.2 + - - +
227D PHE* 5.4 1.6 - - - -
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Residues in contact with GLN 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177D LEU 2.4 17.7 + - - +
178D ASP* 3.1 21.1 - - + +
180D ASP* 1.3 71.5 - - - +
182D MET* 1.3 59.1 - - + +
184D PHE* 5.6 0.2 - - - -
185D ASN* 2.8 67.1 + - - +
186D ARG* 6.3 1.5 - - + +
206D ARG* 4.9 2.9 - - - +
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Residues in contact with MET 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178D ASP 2.8 20.0 + - - +
179D ILE* 3.5 5.6 - - - +
181D GLN* 1.3 76.5 - - + +
183D ILE* 1.3 58.2 + - + +
186D ARG* 3.2 43.9 + - - +
187D GLU* 2.8 40.4 + - + +
249D VAL* 4.7 10.8 - - + -
256D PRO 5.1 0.9 - - - +
259D TRP* 3.6 27.1 - - + +
260D THR* 3.4 39.0 - - - +
261D ILE* 3.7 23.3 - - + -
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Residues in contact with ILE 183 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179D ILE* 2.8 35.8 + - + +
180D ASP* 2.8 7.8 + - - +
182D MET* 1.3 77.8 - - + +
184D PHE* 1.3 71.6 + - + +
185D ASN 3.1 1.3 - - - -
187D GLU* 3.2 10.0 + - + -
188D LEU* 2.5 60.7 + - + -
210D THR* 4.2 19.7 - - + -
227D PHE* 4.8 9.0 - - + -
229D LEU* 4.8 1.8 - - + -
247D LEU* 4.0 25.1 - - + -
249D VAL* 4.3 14.4 - - + -
261D ILE* 5.0 2.7 - - + -
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Residues in contact with PHE 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180D ASP* 2.7 16.1 + - + +
181D GLN* 5.6 0.2 - - - -
183D ILE* 1.3 77.8 - - + +
185D ASN* 1.3 66.6 + - - +
188D LEU* 3.7 24.7 - - + -
189D PRO* 3.6 7.0 - - - +
201D TYR* 3.0 26.4 + + - +
205D GLY* 6.2 0.4 - - - -
206D ARG* 2.8 68.0 - - - +
207D ASN 4.7 0.2 - - - -
208D LEU* 3.0 46.9 - - + -
209D VAL* 4.0 6.1 - - - -
210D THR* 3.6 26.2 - - + -
229D LEU* 5.8 0.9 - - + -
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Residues in contact with ASN 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181D GLN* 2.8 54.2 + - - +
184D PHE* 1.3 90.9 + - - +
186D ARG* 1.3 62.9 + - + +
187D GLU 3.5 0.2 - - - -
189D PRO* 2.8 21.9 - - - +
206D ARG* 5.9 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