Contacts of the helix formed by residues 211 - 220 (chain A) in PDB entry 2QFZ
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 ASP 211 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204A LEU* 3.8 13.4 - - + +
209A ASN 3.4 3.9 + - - +
210A THR* 1.3 72.0 - - - +
212A LEU* 1.3 56.0 + - - +
213A GLU* 3.2 23.5 + - - +
214A GLU* 3.3 29.8 + - + +
215A LEU* 3.0 24.9 + - - +
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Residues in contact with LEU 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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210A THR* 3.2 19.4 + - + +
211A ASP* 1.3 68.9 + - - +
213A GLU* 1.3 59.6 + - - +
215A LEU* 3.7 16.6 - - + +
216A ARG* 2.9 60.2 + - - +
234A LEU* 4.0 41.7 - - + +
235A LEU* 4.3 3.0 - - + +
239A LEU 6.1 0.4 - - - +
241A ALA* 4.2 20.4 - - + +
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Residues in contact with GLU 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 ASP* 3.2 11.8 + - - +
212A LEU* 1.3 79.2 - - - +
214A GLU* 1.3 68.0 + - - +
216A ARG* 3.3 17.2 + - - +
217A ARG* 3.0 28.9 + - + +
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Residues in contact with GLU 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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204A LEU* 3.9 17.7 - - + -
211A ASP* 3.3 30.2 + - + +
213A GLU* 1.3 90.9 - - - +
215A LEU* 1.3 61.8 + - - +
217A ARG* 3.5 17.1 + - - +
218A LEU* 3.1 29.8 + - - +
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Residues in contact with LEU 215 (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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201A PHE* 4.1 22.4 - - + -
204A LEU* 3.7 21.4 - - + +
205A LEU* 3.7 29.2 - - + -
210A THR* 4.5 3.6 - - + -
211A ASP 3.0 14.8 + - - +
212A LEU* 3.7 25.6 - - + +
213A GLU 3.3 0.4 - - - -
214A GLU* 1.3 75.3 - - - +
216A ARG* 1.3 49.5 - - - +
218A LEU* 3.2 3.9 + - - +
219A SER* 2.8 39.9 + - - +
231A THR* 4.0 16.6 - - + -
234A LEU* 4.1 14.6 - - + -
235A LEU* 4.0 21.5 - - + -
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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 LEU* 2.9 60.3 + - - +
213A GLU* 3.5 14.5 - - - +
215A LEU* 1.3 72.8 - - - +
217A ARG* 1.3 64.7 + - - +
219A SER 3.3 0.2 + - - -
220A TRP* 3.2 20.8 + - - +
235A LEU* 3.3 32.0 + - + +
443A GLN 4.7 3.2 + - - -
444A SER* 3.2 43.4 + - - +
445A GLU 5.7 1.6 - - - -
446A PRO* 6.0 0.4 - - - -
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Residues in contact with ARG 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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213A GLU* 3.0 17.3 + - + +
214A GLU* 3.8 19.7 - - - +
215A LEU 3.4 0.2 - - - -
216A ARG* 1.3 76.0 - - - +
218A LEU* 1.3 64.3 + - + +
220A TRP* 3.9 10.4 + - - +
1009A UNX 2.8 20.3 - - - -
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Residues in contact with LEU 218 (chain A).
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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197A ARG* 2.5 45.8 + - + +
200A LYS* 4.0 41.5 - - + -
201A PHE* 3.9 25.4 - - + +
204A LEU* 4.0 21.1 - - + -
214A GLU* 3.1 18.7 + - + +
215A LEU* 3.6 7.4 - - - +
217A ARG* 1.3 81.2 - - + +
219A SER* 1.3 61.4 + - - +
220A TRP 3.2 1.1 + - - -
221A SER 3.5 2.8 + - - -
1009A UNX 3.8 1.5 - - - -
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Residues in contact with SER 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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201A PHE* 3.6 7.9 - - - -
215A LEU 2.8 23.0 + - - -
216A ARG 3.3 0.6 + - - -
218A LEU* 1.3 74.8 - - - +
220A TRP* 1.3 59.6 + - - +
221A SER 3.1 0.4 - - - -
222A GLY* 2.8 23.2 + - - -
223A ILE* 3.8 15.9 - - - -
231A THR* 3.4 25.3 - - - +
235A LEU* 3.5 13.0 - - - +
440A ASP* 3.7 12.0 - - - +
444A SER* 3.1 19.2 + - - -
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Residues in contact with TRP 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 3.2 12.4 + - - +
217A ARG* 3.9 11.9 - - - +
218A LEU 3.2 0.6 - - - -
219A SER* 1.3 77.8 - - - +
221A SER* 1.3 70.0 + - - +
222A GLY 3.3 2.4 + - - -
437A ARG* 3.6 4.5 + - - -
441A THR* 2.7 48.2 + - + +
444A SER* 3.8 14.8 - - - -
445A GLU* 2.8 32.9 + - + -
452A PHE* 4.2 4.7 - + - -
495A SER 5.6 1.6 - - - -
498A LEU* 3.7 35.9 - - + -
499A ALA* 4.4 5.8 - - + -
502A TYR* 3.6 34.8 - + + -
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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