Contacts of the helix formed by residues 211 - 222 (chain D) in PDB entry 4CQM
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 211 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209D LYS 3.7 4.9 - - - +
210D VAL* 1.3 94.6 - - + +
212D GLN* 1.3 63.4 + - - +
213D LYS* 4.3 9.9 - - + +
214D VAL* 3.1 21.5 + - + +
215D VAL* 3.2 11.1 + - - +
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Residues in contact with GLN 212 (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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210D VAL 3.8 0.8 + - - -
211D PRO* 1.3 70.2 - - - +
213D LYS* 1.3 65.3 + - - +
215D VAL* 3.1 19.5 + - + +
216D ASP* 2.8 50.7 + - - +
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Residues in contact with LYS 213 (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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211D PRO* 3.2 6.8 - - + +
212D GLN* 1.3 78.2 - - - +
214D VAL* 1.3 60.5 + - - +
216D ASP* 4.2 5.7 - - - +
217D LYS* 3.7 18.0 + - - +
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Residues in contact with VAL 214 (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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210D VAL* 3.9 13.7 - - + -
211D PRO* 3.1 22.3 + - + +
213D LYS* 1.3 79.4 - - - +
215D VAL* 1.3 58.9 + - - +
217D LYS* 3.2 8.5 + - - +
218D ILE* 3.0 37.5 + - + +
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Residues in contact with VAL 215 (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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207D THR* 4.6 7.9 - - - +
210D VAL* 3.7 19.3 - - + +
211D PRO 3.2 16.8 + - - +
212D GLN* 3.1 25.9 + - + +
214D VAL* 1.3 77.8 - - - +
216D ASP* 1.3 58.1 + - - +
218D ILE* 3.1 12.2 + - + +
219D THR* 2.6 40.1 + - - +
227D LEU* 3.8 28.4 - - + +
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Residues in contact with ASP 216 (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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212D GLN* 2.8 37.3 + - - +
213D LYS* 4.3 6.8 - - - +
215D VAL* 1.3 79.3 - - - +
217D LYS* 1.3 61.8 + - - +
219D THR* 3.2 10.4 + - - -
220D GLU* 3.2 30.6 + - - +
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Residues in contact with LYS 217 (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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213D LYS 3.7 12.3 + - - +
214D VAL* 3.2 11.4 + - - +
215D VAL 3.2 0.4 - - - -
216D ASP* 1.3 77.4 - - - +
218D ILE* 1.3 62.4 + - + +
220D GLU* 3.5 16.1 + - - +
221D MET* 3.3 28.3 + - - +
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Residues in contact with ILE 218 (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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201D PHE* 3.5 59.9 - - + -
210D VAL* 5.0 9.6 - - + -
214D VAL* 3.0 26.6 + - + +
215D VAL* 3.4 11.4 - - + +
217D LYS* 1.3 75.7 - - + +
219D THR* 1.3 65.1 + - - +
221D MET* 3.0 14.9 + - + +
222D ILE* 3.0 35.1 + - + +
227D LEU* 4.2 5.6 - - + -
259D LEU* 4.8 4.0 - - + -
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Residues in contact with THR 219 (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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168C ARG* 3.7 0.3 + - - -
215D VAL* 2.6 27.1 + - - +
216D ASP* 3.2 13.1 + - - -
218D ILE* 1.3 76.2 - - - +
220D GLU* 1.3 61.3 + - - +
222D ILE* 3.5 18.0 + - - +
225D GLY* 3.3 34.4 - - - +
226D HIS* 3.9 8.3 - - - -
227D LEU* 3.5 18.0 - - + +
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Residues in contact with GLU 220 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168C ARG* 2.8 25.6 + - - +
216D ASP* 3.2 16.6 + - - +
217D LYS* 3.7 14.0 - - - +
218D ILE 3.2 0.6 - - - -
219D THR* 1.3 76.0 - - - +
221D MET* 1.3 64.8 + - + +
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Residues in contact with MET 221 (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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185A ARG* 5.9 4.0 - - - +
236B ILE* 4.2 35.0 - - + +
217D LYS* 3.3 18.1 + - - +
218D ILE* 3.0 15.1 + - - +
220D GLU* 1.3 75.5 - - + +
222D ILE* 1.3 64.5 + - - +
223D PRO* 3.2 10.9 - - - +
259D LEU* 3.7 16.4 - - + +
260D PHE* 4.2 19.1 - - + -
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Residues in contact with ILE 222 (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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168C ARG* 2.9 15.1 + - - -
221C TYR* 3.5 22.2 - - - +
201D PHE* 4.7 6.7 - - + +
218D ILE* 3.0 27.3 + - + +
219D THR* 3.7 7.9 - - - +
221D MET* 1.3 75.1 - - - +
223D PRO* 1.3 65.7 - - + +
224D MET* 3.6 13.9 - - + +
225D GLY* 2.8 24.5 + - - +
226D HIS 3.6 22.4 - - - +
227D LEU* 3.8 27.1 - - + -
256D THR 4.2 4.7 - - - +
257D GLY 4.0 6.3 - - - +
259D LEU* 4.1 16.6 - - + -
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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