Contacts of the helix formed by residues 205 - 211 (chain B) in PDB entry 2PQG
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 VAL 205 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36B TYR* 5.8 1.3 - - + -
39B PHE* 5.1 12.8 - - + -
40B ILE* 4.8 3.5 - - + +
75B THR* 4.3 15.9 - - + +
77B LEU* 4.7 13.2 - - + -
86B LEU* 4.5 14.4 - - + -
88B ILE* 3.9 23.6 - - + -
149B MET* 4.3 20.0 - - + -
201B LEU* 2.9 19.0 + - - +
204B MET* 1.3 79.6 - - + +
206B CYS* 1.3 65.6 + - - +
207B GLU 3.5 0.2 - - - -
208B GLY* 3.8 0.2 - - - -
209B LEU* 3.0 38.9 + - + +
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Residues in contact with CYS 206 (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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86B LEU* 6.0 1.1 - - - -
88B ILE* 3.8 20.4 - - - -
93B LEU* 3.2 21.7 - - - +
94B TYR* 4.4 12.1 - - + -
95B LEU* 3.5 37.9 - - - -
202B VAL* 3.1 20.2 + - + +
205B VAL* 1.3 78.7 - - - +
207B GLU* 1.3 64.1 + - + +
209B LEU* 3.1 18.4 + - - +
210B ARG* 3.2 18.6 + - - +
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Residues in contact with GLU 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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94B TYR* 4.0 6.3 - - - -
130B TYR* 2.8 34.3 + - - +
202B VAL* 3.0 12.9 + - + +
203B VAL* 3.3 22.2 - - + +
206B CYS* 1.3 76.4 - - - +
208B GLY* 1.3 58.7 + - - +
210B ARG* 3.3 27.9 + - - +
211B PHE* 2.9 59.9 + - - +
214B VAL* 3.8 7.4 - - + +
238B VAL* 3.1 23.7 - - + +
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Residues in contact with GLY 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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36B TYR* 3.7 9.6 - - - -
40B ILE* 4.1 7.7 - - - +
44B ARG* 2.8 25.5 + - - -
203B VAL 3.0 8.7 + - - -
204B MET 3.5 17.7 - - - -
205B VAL 3.4 2.3 + - - -
206B CYS 3.1 1.2 - - - -
207B GLU* 1.3 77.6 - - - +
209B LEU* 1.3 57.2 + - - +
211B PHE 3.3 4.1 - - - +
214B VAL* 3.8 12.8 - - - -
215B SER* 3.4 6.5 - - - -
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Residues in contact with LEU 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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39B PHE* 6.1 2.0 - - + -
40B ILE* 3.9 19.1 - - + +
43B VAL* 3.8 26.7 - - + -
44B ARG* 3.1 38.5 + - + +
47B VAL* 5.1 1.8 - - + -
73B LEU* 3.8 28.5 - - + -
75B THR* 5.6 0.2 - - + -
88B ILE* 5.0 3.4 - - + -
93B LEU* 4.2 20.6 - - + -
205B VAL* 3.0 36.2 + - + +
206B CYS* 3.1 10.5 + - - +
208B GLY* 1.3 77.6 - - - +
210B ARG* 1.3 61.8 + - - +
278B ALA* 3.7 1.6 - - - +
279B LEU* 3.4 15.2 - - + +
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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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92B ASN* 2.6 32.7 + - - +
93B LEU* 4.1 14.6 + - + -
94B TYR* 3.4 31.2 - - - +
206B CYS 3.2 12.2 + - - +
207B GLU* 3.3 35.5 + - - +
209B LEU* 1.3 78.0 - - - +
211B PHE* 1.3 63.9 + - + +
238B VAL 4.9 1.4 + - - -
241B TRP* 3.3 58.2 - - + +
277B VAL* 3.5 4.7 - - - +
278B ALA 2.6 30.4 + - - -
279B LEU* 3.1 15.5 + - - +
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Residues in contact with PHE 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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44B ARG* 3.9 3.1 - - - -
207B GLU* 2.9 39.7 + - - +
208B GLY 3.3 6.8 - - - +
210B ARG* 1.3 83.1 - - + +
212B ASN* 1.3 63.8 + - - +
213B THR* 3.5 15.3 - - + -
214B VAL* 3.2 6.5 + - + +
215B SER* 3.1 18.4 + - - -
237B GLN* 3.6 15.7 - - + -
238B VAL* 3.4 33.4 - - + -
241B TRP* 3.6 36.8 - + + -
244B ILE* 5.1 2.9 - - + -
276B ILE* 3.2 35.9 - - + +
277B VAL* 3.6 17.9 - - + -
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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