Contacts of the helix formed by residues 205 - 211 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A TYR* 5.5 1.6 - - + -
39A PHE* 5.1 13.0 - - + -
40A ILE* 5.0 3.3 - - + +
75A THR* 4.3 14.6 - - + +
77A LEU* 4.6 13.0 - - + -
86A LEU* 4.2 16.6 - - + -
88A ILE* 4.0 24.5 - - + -
149A MET* 4.3 19.1 - - + -
201A LEU* 2.8 23.6 + - - +
204A MET* 1.3 75.3 - - - +
206A CYS* 1.3 68.7 + - - +
208A GLY* 3.6 0.2 - - - -
209A LEU* 2.8 38.3 + - + +
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Residues in contact with CYS 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A LEU* 6.3 0.9 - - - -
88A ILE* 4.2 14.6 - - - -
93A LEU* 3.2 20.1 - - - +
94A TYR* 3.9 13.5 - - + -
95A LEU* 3.4 41.3 - - - -
201A LEU 5.0 0.2 - - - -
202A VAL* 3.2 20.0 + - + +
205A VAL* 1.3 80.1 - - - +
207A GLU* 1.3 62.0 + - + +
209A LEU* 3.1 11.2 + - - +
210A ARG* 3.0 30.0 + - - +
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Residues in contact with GLU 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A TYR* 4.1 6.0 - - - -
130A TYR* 2.7 44.1 + - - +
202A VAL* 3.0 13.0 + - + +
203A VAL* 3.2 19.7 - - + +
206A CYS* 1.3 77.8 - - + +
208A GLY* 1.3 58.4 - - - +
210A ARG* 3.1 39.2 + - - -
211A PHE* 3.0 44.5 + - + +
214A VAL* 3.6 7.2 - - + +
238A VAL* 3.4 23.0 - - + +
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Residues in contact with GLY 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A TYR* 3.5 10.8 - - - -
40A ILE* 4.2 4.8 - - - +
44A ARG* 2.8 31.2 + - - -
203A VAL 3.0 10.8 + - - -
204A MET 3.5 17.9 - - - -
205A VAL 3.1 2.6 + - - -
206A CYS 3.1 0.6 - - - -
207A GLU* 1.3 76.7 - - - +
209A LEU* 1.3 50.1 + - - +
211A PHE 3.1 6.5 - - - +
214A VAL* 3.8 10.3 - - - -
215A SER* 3.4 7.6 - - - -
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Residues in contact with LEU 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A PHE* 6.0 1.3 - - + -
40A ILE* 4.3 16.4 - - + +
43A VAL* 3.6 29.6 - - + -
44A ARG* 3.0 39.5 + - + +
47A VAL* 5.4 1.8 - - + -
73A LEU* 4.0 26.7 - - + -
75A THR* 5.7 0.2 - - + -
88A ILE* 4.9 3.8 - - + -
93A LEU* 3.8 23.8 - - + -
205A VAL* 2.8 37.1 + - + +
206A CYS* 3.4 9.9 - - - +
208A GLY* 1.3 75.9 - - - +
210A ARG* 1.3 65.2 + - - +
278A ALA* 3.8 1.0 - - - +
279A LEU* 3.8 10.4 - - + +
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Residues in contact with ARG 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A ASN* 2.6 32.9 + - - +
93A LEU* 4.0 17.3 + - + -
94A TYR* 3.4 32.9 - - - +
206A CYS 3.0 15.9 + - - +
207A GLU* 3.1 33.2 + - - +
209A LEU* 1.3 77.0 - - - +
211A PHE* 1.3 64.6 + - + +
238A VAL 5.0 0.6 + - - -
241A TRP* 3.4 61.5 - - + +
277A VAL* 3.7 3.5 - - - +
278A ALA 2.7 30.0 + - - -
279A LEU 3.2 12.2 + - - +
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Residues in contact with PHE 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A ARG* 3.7 3.4 - - - -
207A GLU* 3.0 36.3 + - - +
208A GLY 3.1 14.9 - - - +
210A ARG* 1.3 84.1 - - + +
212A ASN* 1.3 57.6 + - - +
213A THR* 3.0 21.8 - - + -
214A VAL* 3.2 5.1 + - + -
215A SER 3.1 13.7 + - - -
237A GLN* 3.7 16.8 - - + -
238A VAL* 3.4 40.2 - - + -
241A TRP* 3.4 31.4 - + + -
244A ILE* 5.0 2.0 - - + -
276A ILE* 3.3 24.2 - - + +
277A VAL* 3.5 21.3 - - + -
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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