Contacts of the helix formed by residues 196 - 207 (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 SER 196 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197A ARG* 1.3 65.6 + - - +
198A LEU* 3.6 8.1 - - - +
199A ASP* 3.5 30.6 - - - +
200A LYS* 3.3 33.3 + - - +
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Residues in contact with ARG 197 (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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196A SER* 1.3 77.9 + - - +
198A LEU* 1.3 62.5 + - - +
200A LYS* 3.1 25.0 + - + +
201A PHE* 3.1 35.6 + - + -
218A LEU* 2.5 46.8 + - + +
221A SER* 3.7 22.7 + - - -
222A GLY 2.8 24.2 + - - -
224A PRO* 4.3 12.1 - - + +
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Residues in contact with LEU 198 (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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196A SER 3.3 6.4 - - - +
197A ARG* 1.3 78.8 - - - +
199A ASP* 1.3 56.5 + - - +
201A PHE* 3.3 4.2 + - - +
202A LYS* 2.9 46.4 + - + +
224A PRO* 3.7 31.1 - - + +
226A PRO* 4.0 25.1 - - + -
227A VAL* 3.9 24.2 - - + -
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Residues in contact with ASP 199 (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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196A SER* 3.5 23.6 - - - +
197A ARG 3.4 0.2 - - - -
198A LEU* 1.3 78.1 - - - +
200A LYS* 1.3 55.9 + - - +
202A LYS* 4.0 9.4 - - - +
203A GLN* 3.1 30.4 + - - +
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Residues in contact with LYS 200 (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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196A SER* 3.3 26.1 + - - +
197A ARG* 3.1 18.0 + - - +
199A ASP* 1.3 74.8 - - - +
201A PHE* 1.3 65.2 + - - +
203A GLN* 3.3 8.3 + - + +
204A LEU* 3.0 25.4 + - + +
218A LEU* 4.0 32.5 - - + -
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Residues in contact with PHE 201 (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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197A ARG* 3.1 45.6 + - + -
198A LEU 3.5 6.3 - - - +
200A LYS* 1.3 73.9 - - - +
202A LYS* 1.3 58.4 + - - +
204A LEU* 3.2 8.0 + - - +
205A LEU* 2.8 35.1 + - + +
215A LEU* 4.1 12.6 - - + -
218A LEU* 3.8 39.7 - - + +
219A SER* 3.6 20.2 - - - -
222A GLY 3.9 6.3 - - - -
223A ILE* 3.9 12.3 - - + -
224A PRO* 3.3 28.7 - - + -
227A VAL* 3.6 27.4 - - + -
231A THR* 4.0 10.5 - - - -
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Residues in contact with LYS 202 (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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198A LEU* 2.9 37.0 + - + +
199A ASP* 4.0 8.3 - - - +
201A PHE* 1.3 77.8 - - - +
203A GLN* 1.3 60.7 + - - +
205A LEU* 3.4 8.4 + - + +
206A ALA* 3.1 24.6 + - - +
226A PRO* 6.4 0.2 - - + -
227A VAL* 3.8 19.7 - - + -
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Residues in contact with GLN 203 (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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199A ASP 3.1 19.6 + - - +
200A LYS* 3.7 9.7 - - + +
201A PHE 3.2 0.2 - - - -
202A LYS* 1.3 77.6 - - - +
204A LEU* 1.3 61.9 + - - +
206A ALA* 3.4 14.7 + - + +
207A GLY 3.7 10.0 + - - +
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Residues in contact with LEU 204 (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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200A LYS* 3.0 12.6 + - + +
201A PHE 3.2 6.9 + - - +
203A GLN* 1.3 76.2 - - - +
205A LEU* 1.3 59.9 + - - +
206A ALA 3.2 0.9 + - - -
207A GLY* 3.2 7.6 + - - -
210A THR* 2.9 26.8 + - + +
211A ASP* 3.8 33.2 - - + +
214A GLU* 3.9 18.4 - - + +
215A LEU* 3.7 41.1 - - + +
218A LEU* 4.0 21.5 - - + -
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Residues in contact with LEU 205 (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* 2.8 22.8 + - - +
202A LYS* 3.8 6.1 - - - +
204A LEU* 1.3 73.0 - - - +
206A ALA* 1.3 59.3 + - - +
207A GLY 3.3 0.6 + - - -
210A THR* 3.8 4.7 - - + -
215A LEU* 3.7 28.5 - - + -
227A VAL* 4.0 30.1 - - + -
230A MET* 3.9 27.4 - - + -
231A THR* 4.0 10.3 - - - +
234A LEU* 3.8 21.3 - - + -
243A VAL* 3.8 0.7 - - - +
246A ARG* 3.0 33.1 + - - +
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Residues in contact with ALA 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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202A LYS 3.1 16.5 + - - +
203A GLN* 3.8 8.3 - - + +
204A LEU 3.2 1.0 - - - -
205A LEU* 1.3 76.3 - - - +
207A GLY* 1.3 64.0 + - - +
208A PRO* 3.7 2.4 - - - +
243A VAL* 3.0 19.8 - - - +
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Residues in contact with GLY 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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203A GLN 3.7 6.7 + - - +
204A LEU 3.2 14.3 + - - -
205A LEU 3.3 0.8 - - - -
206A ALA* 1.3 79.9 - - - +
208A PRO* 1.4 72.9 - - - +
209A ASN 3.4 5.2 - - - -
210A THR* 3.9 7.9 - - - -
243A VAL* 3.8 3.8 - - - -
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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