Contacts of the helix formed by residues 203 - 219 (chain A) in PDB entry 4GFU
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 203 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170A ASP* 3.5 22.7 - - - -
192A TYR* 2.9 17.3 + - - -
201A PRO* 4.1 2.5 - - - -
202A SER* 1.3 80.1 - - - +
204A PRO* 1.3 65.4 - - - +
205A ASP* 3.6 5.9 + - - +
206A HIS* 3.0 37.3 + - - -
207A MET* 3.1 6.6 + - - +
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Residues in contact with PRO 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 VAL* 6.0 1.1 - - + -
201A PRO* 3.7 11.0 - - + +
202A SER 4.0 3.8 - - - +
203A SER* 1.3 85.4 - - - +
205A ASP* 1.3 63.9 + - - +
207A MET* 3.4 11.9 + - + +
208A LEU* 3.3 28.1 + - + +
283A PHE* 3.8 32.3 - - + -
287A THR* 5.4 2.0 - - + +
290A GLN* 6.0 2.5 - - - +
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Residues in contact with ASP 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A SER* 3.2 6.4 - - - +
204A PRO* 1.3 81.7 - - - +
206A HIS* 1.3 65.4 + - + +
208A LEU* 3.3 12.0 + - - +
209A ALA* 3.0 26.3 + - - +
290A GLN* 4.2 17.0 + - - -
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Residues in contact with HIS 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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168A ASN* 3.4 40.0 + - + +
169A GLU* 3.4 30.0 + - + -
170A ASP* 2.5 31.0 + - - +
171A ILE* 3.1 12.5 - - + +
192A TYR* 3.9 10.8 - - + +
203A SER* 3.0 28.7 + - - +
205A ASP* 1.3 81.9 - - + +
207A MET* 1.3 64.2 + - - +
209A ALA* 3.3 4.1 + - + +
210A MET 3.0 17.0 + - - -
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Residues in contact with MET 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A TYR* 3.7 11.8 - - + -
195A TRP* 4.0 19.1 - - + -
201A PRO* 3.9 19.5 - - + -
203A SER 3.1 6.0 + - - +
204A PRO* 3.6 13.7 - - + +
206A HIS* 1.3 77.6 - - - +
208A LEU* 1.3 75.5 + - + +
210A MET* 2.9 22.5 + - + +
211A VAL* 3.1 8.9 + - + +
238A VAL* 4.4 5.4 - - - -
239A LEU* 3.8 21.8 - - + -
242A VAL* 4.0 23.3 - - + -
283A PHE* 3.7 37.9 - - + -
287A THR* 4.3 5.8 - - + -
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Residues in contact with LEU 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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204A PRO* 3.3 15.0 + - + +
205A ASP* 3.3 12.8 + - - +
207A MET* 1.3 85.2 - - + +
209A ALA* 1.3 58.8 + - - +
211A VAL* 3.2 7.6 + - + +
212A GLU* 2.9 43.8 + - - +
242A VAL* 3.8 28.0 - - + -
246A ARG* 5.3 6.5 - - - -
287A THR* 4.4 11.0 - - + +
290A GLN* 4.5 19.7 - - - +
291A MET* 3.9 26.5 - - + -
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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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167A LEU* 4.2 11.6 - - + +
168A ASN* 4.0 17.7 - - - +
205A ASP 3.0 14.1 + - - +
206A HIS* 3.6 9.4 - - + +
208A LEU* 1.3 76.4 - - - +
210A MET* 1.3 63.9 + - - +
212A GLU* 3.7 15.9 - - - +
213A GLU* 3.0 26.7 + - - +
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Residues in contact with MET 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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128A LEU* 3.9 17.3 - - + -
129A MET 3.6 23.6 - - - +
167A LEU* 5.6 0.4 - - - -
171A ILE* 3.4 22.1 - - + +
190A LEU* 3.2 50.0 - - + +
191A GLN 4.2 0.7 - - - +
192A TYR* 3.9 26.7 - - + +
195A TRP* 5.7 0.4 - - - -
206A HIS 3.0 5.8 + - - +
207A MET* 2.9 12.2 + - - +
209A ALA* 1.3 77.0 - - - +
211A VAL* 1.3 57.9 + - + +
213A GLU* 3.8 2.9 - - - -
214A ALA* 2.9 29.7 + - - +
239A LEU* 4.2 22.2 - - + -
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Residues in contact with VAL 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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128A LEU* 4.8 5.8 - - + -
207A MET* 3.1 12.0 + - + +
208A LEU* 3.2 7.8 + - - +
210A MET* 1.3 74.4 - - - +
212A GLU* 1.3 59.0 + - - +
214A ALA* 3.4 8.4 + - + +
215A ARG* 3.0 27.5 + - - +
239A LEU* 4.1 28.5 - - + +
242A VAL* 4.2 20.2 - - + -
243A ASP* 3.5 35.9 - - + +
246A ARG* 4.0 20.2 - - - +
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Residues in contact with GLU 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 LEU* 2.9 38.7 + - + +
209A ALA* 3.7 12.1 - - - +
211A VAL* 1.3 76.6 - - - +
213A GLU* 1.3 58.0 + - - +
215A ARG* 3.3 4.5 + - - +
216A ARG* 3.1 25.5 + - - +
246A ARG* 3.5 40.2 + - - +
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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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165A LYS* 5.1 1.2 + - - -
167A LEU* 3.9 30.9 - - + +
173A LEU* 3.7 15.7 - - + +
190A LEU* 4.2 13.2 - - + -
209A ALA 3.0 17.9 + - - +
210A MET* 3.8 3.6 - - - +
212A GLU* 1.3 74.8 - - - +
214A ALA* 1.3 67.6 + - - +
216A ARG* 2.9 44.4 + - - +
217A LEU* 3.0 37.2 + - + +
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Residues in contact with ALA 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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126A VAL* 3.8 12.1 - - + +
128A LEU* 4.0 33.4 - - + -
190A LEU* 3.8 10.2 - - + +
210A MET 2.9 18.8 + - - +
211A VAL* 3.5 7.0 - - + +
213A GLU* 1.3 76.1 - - - +
215A ARG* 1.3 57.0 + - + +
217A LEU* 3.4 2.8 + - - +
218A GLN* 2.8 30.9 + - - +
225A LEU* 4.7 10.1 - - + -
243A ASP* 6.1 0.2 - - - +
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Residues in contact with ARG 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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100A ALA* 4.9 9.1 + - - +
101A TYR* 4.2 7.3 + - - -
211A VAL 3.0 20.1 + - - +
212A GLU 3.7 4.9 - - - +
213A GLU 3.2 0.2 - - - -
214A ALA* 1.3 77.4 - - + +
216A ARG* 1.3 57.3 + - - +
218A GLN* 3.7 23.2 - - - +
219A GLY* 3.0 29.0 + - - +
221A GLY 6.0 0.2 + - - -
225A LEU* 3.8 20.4 - - + +
243A ASP* 2.8 42.4 + - - +
246A ARG* 3.8 13.2 - - - +
247A GLN* 3.4 38.7 - - - +
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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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165A LYS* 5.9 1.4 - - - +
173A LEU* 5.5 1.2 - - - +
212A GLU 3.1 14.5 + - - +
213A GLU* 2.9 42.8 + - - +
215A ARG* 1.3 76.5 - - - +
217A LEU* 1.3 80.5 + - - +
219A GLY* 3.4 12.7 + - - -
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Residues in contact with LEU 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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125A LYS* 4.5 5.9 - - - +
126A VAL* 3.8 12.9 - - + +
173A LEU* 3.8 29.4 - - + -
188A TYR* 3.9 48.5 - - + +
190A LEU* 4.5 6.5 - - + -
213A GLU* 3.0 37.4 + - + +
214A ALA* 3.7 3.4 - - - +
216A ARG* 1.3 97.9 - - - +
218A GLN* 1.3 65.3 + - - +
219A GLY* 3.3 0.7 + - - -
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Residues in contact with GLN 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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125A LYS* 3.1 54.9 + - - +
126A VAL* 3.7 11.6 + - - +
214A ALA 2.8 21.2 + - - +
215A ARG* 3.7 26.9 - - - +
216A ARG 3.4 0.2 - - - -
217A LEU* 1.3 73.1 - - - +
219A GLY* 1.3 71.8 + - - +
220A SER 3.2 4.9 - - - +
221A GLY 3.3 14.7 + - - +
223A GLU 2.7 29.7 + - - +
224A PRO 4.7 2.3 - - - +
225A LEU* 3.5 25.7 - - + +
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Residues in contact with GLY 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 ARG* 3.0 19.9 + - - +
216A ARG* 3.4 9.1 + - - -
217A LEU 3.2 4.1 - - - -
218A GLN* 1.3 89.2 - - - +
220A SER* 1.3 60.6 + - - -
221A GLY 4.6 0.7 - - - +
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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