Contacts of the helix formed by residues 211 - 221 (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 PHE 211 (chain A).
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Specific contacts
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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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Residues in contact with ASN 212 (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* 3.5 17.3 - - - +
211A PHE* 1.3 64.9 - - - +
213A THR* 1.3 58.0 + - - +
214A VAL 3.2 0.2 - - - -
215A SER* 3.1 13.0 - - - +
216A ARG* 2.9 49.3 + - + +
274A ALA 3.2 19.2 - - - +
275A ARG* 3.7 5.2 - - - -
276A ILE 2.7 30.0 + - - -
277A VAL 3.0 16.0 - - - +
278A ALA* 4.0 6.0 - - + +
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Residues in contact with THR 213 (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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211A PHE* 3.4 19.7 - - + -
212A ASN* 1.3 81.2 - - - +
214A VAL* 1.3 66.5 + - + +
216A ARG* 3.8 17.5 + - - +
217A THR* 3.0 27.4 + - - -
234A GLN* 3.1 25.5 + - + +
237A GLN* 4.7 8.3 + - + +
238A VAL* 5.2 3.4 - - + -
275A ARG 4.1 3.1 - - - -
276A ILE* 3.3 38.6 + - + +
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Residues in contact with VAL 214 (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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203A VAL* 3.6 27.6 - - + +
207A GLU* 3.6 15.5 - - + +
208A GLY* 3.8 8.5 - - - -
211A PHE* 3.2 11.3 + - + +
212A ASN 3.2 0.2 - - - -
213A THR* 1.3 80.0 - - + +
215A SER* 1.3 55.2 + - - +
216A ARG 3.2 1.6 - - - -
217A THR* 3.2 1.2 + - - -
218A VAL* 2.7 53.8 + - + +
230A LEU* 3.7 24.2 - - + -
234A GLN* 5.3 0.7 - - + +
238A VAL* 3.7 30.7 - - + -
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Residues in contact with SER 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A TYR* 3.6 18.6 - - - -
37A SER* 5.8 0.6 - - - -
40A ILE* 4.0 15.5 - - - -
44A ARG* 3.0 22.1 + - - -
208A GLY 3.4 18.6 + - - -
211A PHE 3.1 2.2 + - - -
212A ASN* 3.1 14.4 + - - +
214A VAL* 1.3 79.2 - - - +
216A ARG* 1.3 57.5 + - - +
219A ASP* 2.9 32.7 + - - +
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Residues in contact with ARG 216 (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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212A ASN* 2.9 52.6 + - + +
213A THR* 3.8 16.7 + - - +
215A SER* 1.3 81.3 + - - +
217A THR* 1.3 57.9 + - - +
219A ASP* 4.0 2.4 - - - +
220A ALA* 3.0 29.8 + - - +
275A ARG* 2.9 69.0 + - - +
276A ILE* 5.7 0.6 - - - +
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Residues in contact with THR 217 (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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144A MET* 5.7 0.2 - - + -
213A THR 3.0 18.1 + - - -
214A VAL 3.2 4.3 + - - -
216A ARG* 1.3 76.4 - - - +
218A VAL* 1.3 65.2 + - + +
220A ALA* 3.5 4.8 + - - +
221A GLY 3.4 16.3 + - - -
228A VAL* 3.6 16.1 - - + +
229A THR 3.6 24.9 - - - +
230A LEU* 4.0 13.2 - - + -
234A GLN* 3.0 19.0 + - - +
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Residues in contact with VAL 218 (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 29.8 - - + +
144A MET* 3.7 37.5 - - + -
204A MET* 4.1 16.4 - - + -
214A VAL* 2.7 38.4 + - + +
217A THR* 1.3 73.2 - - - +
219A ASP* 1.3 57.2 + - - +
221A GLY 3.8 0.5 - - - -
222A PHE* 2.9 42.8 + - + +
228A VAL* 4.3 7.9 - - + +
230A LEU* 4.6 1.1 - - + -
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Residues in contact with ASP 219 (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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35A PRO* 4.4 3.5 - - - +
36A TYR* 3.6 20.8 + - + +
37A SER* 2.8 46.2 + - - -
215A SER 2.9 20.6 + - - +
216A ARG* 4.1 2.9 - - - +
218A VAL* 1.3 75.7 - - - +
220A ALA* 1.3 69.2 + - - +
221A GLY 3.3 0.3 + - - -
222A PHE* 3.4 13.4 + - - +
223A ASN* 5.1 2.1 + - - -
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Residues in contact with ALA 220 (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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216A ARG 3.0 19.5 + - - +
217A THR* 3.8 6.5 - - - +
218A VAL 3.4 0.2 - - - -
219A ASP* 1.3 80.6 + - - +
221A GLY* 1.3 57.3 + - - +
222A PHE 3.9 0.3 + - - -
223A ASN 5.2 0.5 + - - -
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Residues in contact with GLY 221 (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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145A GLY* 4.6 1.9 - - - -
217A THR 3.4 7.5 + - - -
218A VAL 3.8 2.0 - - - -
219A ASP 3.2 0.4 - - - -
220A ALA* 1.3 79.0 - - - +
222A PHE* 1.3 65.0 + - - +
223A ASN 3.2 3.4 - - - -
224A SER* 2.8 35.3 + - - +
227A GLY 4.6 1.2 - - - -
228A VAL* 3.9 24.0 - - - +
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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