Contacts of the helix formed by residues 207 - 221 (chain A) in PDB entry 1GQF
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 207 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205A ASP 3.8 1.4 + - - -
206A CYS* 1.3 75.8 - - - +
208A CYS* 1.3 57.9 + - - +
209A ALA* 3.1 12.3 + - - +
210A LYS* 2.8 25.0 + - - +
211A MET* 2.7 31.8 + - - +
245A GLY* 4.5 0.2 - - - -
246A LYS* 3.7 11.8 - - - +
247A ASP* 3.4 22.6 + - - -
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Residues in contact with CYS 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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207A SER* 1.3 71.3 - - - +
209A ALA* 1.3 57.0 + - - +
211A MET* 3.9 2.6 - - - +
212A GLN* 3.0 31.4 + - - +
245A GLY* 4.1 3.3 - - - -
247A ASP* 2.8 23.5 + - - +
254A GLY* 3.1 39.3 - - - -
255A VAL 3.6 16.8 - - - +
256A THR* 3.8 27.6 + - - -
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Residues in contact with ALA 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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207A SER* 3.0 8.2 + - - +
208A CYS* 1.3 80.0 - - - +
210A LYS* 1.3 53.2 + - - +
212A GLN* 3.4 4.6 + - - +
213A ASP* 2.7 35.8 + - - +
247A ASP* 4.5 3.0 + - - +
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Residues in contact with LYS 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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203A TYR* 4.4 14.0 - - - +
204A ASN 4.9 4.8 + - - +
206A CYS* 3.4 30.9 - - + +
207A SER* 2.8 26.3 + - - +
209A ALA* 1.3 74.1 - - - +
211A MET* 1.3 64.2 + - - +
213A ASP* 2.8 23.2 + - + +
214A LEU* 2.9 37.1 + - + +
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Residues in contact with MET 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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168A ILE* 3.3 37.7 - - + -
170A ASN* 3.4 18.6 - - - +
206A CYS* 3.5 17.3 - - + -
207A SER 2.7 20.2 + - - +
208A CYS* 3.9 3.4 - - - +
210A LYS* 1.3 73.5 - - - +
212A GLN* 1.3 64.3 + - - +
214A LEU* 3.0 28.8 - - - +
215A LEU* 3.2 11.7 + - - +
234A LEU* 4.7 8.1 - - + -
235A LEU 6.1 0.2 - - - +
236A SER* 5.4 0.4 - - - -
243A ILE* 4.3 24.0 - - + -
244A TYR 4.1 1.1 - - - +
245A GLY* 3.9 19.1 - - - -
256A THR* 4.1 17.7 - - + -
261A LEU* 4.9 9.0 - - + -
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Residues in contact with GLN 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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208A CYS 3.0 19.0 + - - +
209A ALA* 3.7 5.2 - - - +
211A MET* 1.3 77.7 - - - +
213A ASP* 1.3 64.9 + - - +
215A LEU* 4.7 0.4 - - - -
216A LYS* 3.0 21.1 + - + +
256A THR* 3.7 7.5 + - - +
260A ASP* 3.2 30.7 + - - +
261A LEU* 3.1 32.7 - - - +
263A ALA* 5.3 0.2 - - - +
264A HIS* 2.8 39.4 + - - +
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Residues in contact with ASP 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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209A ALA 2.7 20.1 + - - +
210A LYS* 2.8 19.5 + - + +
212A GLN* 1.3 72.5 - - - +
214A LEU* 1.3 60.9 + - - +
216A LYS* 3.0 11.9 + - - +
217A LYS* 2.9 61.6 + - - +
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Residues in contact with LEU 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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166A ILE* 4.3 9.7 - - + +
168A ILE* 3.7 13.0 - - + -
203A TYR* 3.5 52.0 - - + +
206A CYS* 4.5 4.3 - - - -
210A LYS* 2.9 40.2 + - + +
211A MET 3.0 14.1 - - - +
213A ASP* 1.3 72.2 - - - +
215A LEU* 1.3 101.0 + - + +
217A LYS* 3.0 11.6 + - - +
218A ALA* 2.7 25.1 + - - +
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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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166A ILE* 4.3 6.1 - - + -
168A ILE* 3.8 15.9 - - + -
211A MET 3.2 11.6 + - - +
214A LEU* 1.3 105.9 - - + +
216A LYS* 1.3 63.1 + - - +
218A ALA* 3.1 5.2 + - - +
219A SER* 3.0 21.5 + - - -
230A PHE* 4.4 10.5 - - + -
232A CYS* 4.1 23.1 - - - -
261A LEU* 3.7 26.5 - - + +
264A HIS* 3.1 18.8 + - + +
265A PHE* 3.6 34.4 - - + -
280A PHE* 4.5 4.0 - - + -
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Residues in contact with LYS 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 GLN* 3.0 11.4 + - + +
213A ASP* 3.4 14.4 - - - +
215A LEU* 1.3 74.9 - - - +
217A LYS* 1.3 63.1 + - + +
219A SER* 2.4 20.8 + - - +
220A GLU* 3.0 39.6 + - - +
264A HIS* 2.9 30.7 + - + +
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Residues in contact with LYS 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 ASP* 2.9 47.5 + - - +
214A LEU* 3.0 11.4 + - - +
216A LYS* 1.3 82.5 - - + +
218A ALA* 1.3 60.6 + - - +
220A GLU* 2.9 38.1 + - + +
221A GLU* 3.1 15.2 + - - +
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Residues in contact with ALA 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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164A LYS* 4.7 8.7 - - - +
166A ILE* 3.5 31.0 - - + -
214A LEU 2.7 10.3 + - - +
215A LEU 3.5 7.6 - - - +
217A LYS* 1.3 74.1 - - - +
219A SER* 1.3 59.9 + - - +
221A GLU* 3.2 17.3 + - - +
224A HIS* 2.8 27.5 + - - -
230A PHE* 4.0 18.8 - - + -
265A PHE* 4.4 1.8 - - + -
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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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215A LEU 3.0 5.3 + - - -
216A LYS* 2.4 29.1 + - - +
218A ALA* 1.3 74.7 - - - +
220A GLU* 1.3 65.5 + - - +
221A GLU 3.4 7.3 + - - +
264A HIS* 3.2 46.1 + - - +
265A PHE* 3.7 17.9 - - - -
270A CYS* 3.7 21.8 - - - +
272A THR* 5.3 0.2 - - - +
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Residues in contact with GLU 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 LYS* 3.0 48.8 + - - +
217A LYS* 2.9 26.4 + - + +
219A SER* 1.3 86.1 + - - +
221A GLU* 1.3 61.5 + - + +
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Residues in contact with GLU 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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164A LYS* 2.7 41.1 + - - -
217A LYS* 3.1 16.2 + - - +
218A ALA* 3.2 12.2 + - - +
219A SER 3.5 5.5 - - - +
220A GLU* 1.3 82.0 - - + +
222A ASP* 1.3 61.9 + - - +
224A HIS* 3.5 21.6 + - + +
272A THR* 3.6 10.2 - - - +
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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