Contacts of the helix formed by residues 206 - 213 (chain B) in PDB entry 2C1H
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 TYR 206 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200B LYS* 4.1 2.4 - - - +
201B TYR 2.7 30.6 + - - -
203B SER* 3.6 27.6 - - - +
204B SER 3.3 2.2 - - - -
205B PHE* 1.3 79.8 - - - +
207B GLY* 1.3 64.9 + - - +
208B PRO* 3.6 1.6 - - - -
209B PHE* 3.3 4.1 + - + +
210B ARG* 3.2 27.9 + - - +
226B GLN* 3.6 17.5 - - - -
253B LYS* 3.6 31.5 + - + +
254B PRO* 3.4 23.4 - - + +
278B VAL* 3.7 13.0 - - + -
279B SER* 3.9 2.0 - - - -
1330B DSB 3.4 55.9 - - + +
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Residues in contact with GLY 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293A TRP 4.1 9.4 - - - -
294A ILE* 5.8 0.9 - - - -
204B SER 4.4 6.0 + - - -
205B PHE 3.3 1.8 - - - -
206B TYR* 1.3 74.5 - - - +
208B PRO* 1.3 66.4 - - - +
210B ARG* 3.0 29.3 + - - +
211B ASP* 3.6 6.6 + - - +
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Residues in contact with PRO 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293A TRP* 3.6 20.6 - - + +
294A ILE* 4.6 2.9 - - + -
52B VAL* 4.0 0.2 - - - +
54B SER* 3.2 24.2 + - - +
55B MET* 3.2 34.0 - - + +
205B PHE 4.0 5.8 - - - +
207B GLY* 1.3 87.2 - - - +
209B PHE* 1.3 57.4 + - - +
211B ASP* 2.9 15.3 - - - +
212B ALA* 3.3 5.2 - - - +
279B SER* 3.4 17.5 - - - +
280B GLY* 4.0 5.4 - - - +
283B ALA* 3.9 22.9 - - + -
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Residues in contact with PHE 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B PHE* 3.6 17.3 - + - -
55B MET* 4.2 0.9 - - - -
84B PHE* 3.4 34.8 - + - -
127B ASP* 5.8 2.9 - - + -
206B TYR 3.6 4.3 - - - +
207B GLY 3.2 0.4 - - - -
208B PRO* 1.3 74.8 - - - +
210B ARG* 1.3 63.1 + - - +
212B ALA* 3.4 3.9 + - - +
213B LEU* 3.3 51.8 + - + +
279B SER* 2.8 12.1 + - - +
318B TYR* 3.3 19.7 - - - -
1330B DSB 3.1 80.1 - - + +
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Residues in contact with ARG 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B ASP* 3.3 3.2 + - - -
133B GLY 3.2 18.4 + - - -
203B SER 5.8 0.8 + - - -
206B TYR* 3.2 18.7 + - - +
207B GLY* 3.0 13.8 + - - +
209B PHE* 1.3 82.8 - - - +
211B ASP* 1.3 60.5 + - - +
213B LEU* 3.8 1.5 + - - -
214B HIS* 3.4 2.4 + - - -
215B SER* 3.2 50.9 + - - +
218B GLN* 3.5 35.9 - - + +
222B LYS* 3.1 43.8 - - - +
1330B DSB 2.7 29.2 + - - +
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Residues in contact with ASP 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B VAL* 4.0 4.3 - - - +
53B SER* 3.5 18.0 + - - -
54B SER* 2.5 30.3 + - - -
60B ARG* 3.5 7.8 + - - -
207B GLY 3.6 3.2 + - - +
208B PRO* 2.9 21.1 - - - +
210B ARG* 1.3 77.6 - - - +
212B ALA* 1.3 64.7 + - - +
213B LEU 3.3 0.4 - - - -
214B HIS* 3.3 27.4 + - - +
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Residues in contact with ALA 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B PHE* 4.1 14.0 - - + -
52B VAL* 3.7 23.6 - - + -
55B MET* 4.1 2.2 - - - -
60B ARG* 2.8 39.0 + - - +
86B ILE* 3.6 3.3 - - - +
208B PRO 3.3 17.5 - - - +
209B PHE 3.4 8.0 + - - +
210B ARG 3.2 0.2 - - - -
211B ASP* 1.3 82.7 + - - +
213B LEU* 1.3 66.2 + - + +
214B HIS 3.2 0.4 - - - -
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Residues in contact with LEU 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B PHE* 3.6 24.2 - - + -
84B PHE* 3.7 22.9 - - + -
85B GLY 4.5 3.1 - - - +
86B ILE* 3.8 30.4 - - + +
90B LYS* 4.6 2.4 + - - -
123B ASP* 5.7 0.2 - - - +
128B PRO* 4.2 32.7 - - + +
209B PHE* 3.3 57.8 + - + +
210B ARG* 3.8 1.7 + - - +
212B ALA* 1.3 76.7 - - - +
214B HIS* 1.3 58.5 + - - +
215B SER* 2.8 21.8 + - - +
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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