Contacts of the helix formed by residues 193 - 210 (chain A) in PDB entry 6AGF
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 TRP 193 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191A ASP* 2.9 15.0 + - - +
192A PRO* 1.3 85.1 - - + +
194A ASN* 1.3 63.0 + - - +
195A TRP 3.3 1.1 - - - -
196A LEU* 3.8 22.6 + - + +
197A ASP* 3.3 19.2 + - - +
227A LEU* 5.2 6.7 - - + -
230A ILE* 3.7 31.0 - - + -
231A THR* 3.9 28.0 - - + +
237A LYS* 3.6 54.3 - - + +
240A VAL* 4.0 24.5 - - + -
241A GLY* 5.4 2.5 - - - -
244A ILE* 6.1 1.3 - - + -
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Residues in contact with ASN 194 (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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175A LYS* 3.3 27.6 + - - +
179A ARG* 5.9 2.6 - - - +
188A PHE* 3.3 48.5 + - + +
189A LEU* 4.3 2.9 - - - +
191A ASP* 2.7 32.2 + - - +
193A TRP* 1.3 77.0 - - - +
195A TRP* 1.3 59.3 + - - +
196A LEU 3.2 1.8 - - - -
197A ASP* 3.2 19.0 + - - +
198A PHE* 3.0 29.8 + - - +
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Residues in contact with TRP 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A LEU* 2.4 56.2 + - + +
190A ARG* 5.2 3.8 - - - -
191A ASP 4.2 0.7 - - - -
192A PRO* 3.7 38.3 - - + +
193A TRP 3.3 0.6 - - - -
194A ASN* 1.3 78.7 - - - +
196A LEU* 1.3 57.9 + - - +
198A PHE* 3.5 3.2 + - - +
199A SER* 3.0 28.1 + - - -
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Residues in contact with LEU 196 (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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192A PRO 4.5 2.2 + - - +
193A TRP* 3.8 21.9 + - + +
194A ASN 3.2 0.2 - - - -
195A TRP* 1.3 78.7 - - - +
197A ASP* 1.3 64.6 + - - +
198A PHE 3.2 0.4 - - - -
199A SER* 3.5 6.8 + - - +
200A VAL* 3.2 30.8 + - + +
224A LEU* 3.3 37.9 - - + +
227A LEU* 3.8 40.2 - - + +
228A LYS* 4.2 18.6 - - + -
231A THR* 6.1 1.6 - - + -
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Residues in contact with ASP 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A TYR 5.6 0.7 - - - +
171A GLU* 5.1 6.1 - - - +
172A SER* 5.3 6.6 - - - -
175A LYS* 5.3 4.6 - - + +
188A PHE* 5.2 6.7 - - + -
193A TRP 3.3 16.7 - - - +
194A ASN* 3.2 24.5 + - + +
196A LEU* 1.3 79.3 - - - +
198A PHE* 1.3 60.0 + - - +
200A VAL* 3.9 11.6 + - - +
201A ILE* 4.2 14.0 - - - +
228A LYS* 3.3 43.9 + - - +
231A THR* 4.4 14.2 + - - +
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Residues in contact with PHE 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A SER* 5.1 5.6 - - - +
176A ILE* 6.0 5.2 - - + -
185A ASP* 5.9 2.7 - - - -
188A PHE* 4.8 10.3 - + + -
189A LEU* 4.3 32.1 - - + -
194A ASN 3.0 15.2 + - - +
195A TRP 4.0 4.0 - - - +
197A ASP* 1.3 77.5 - - - +
199A SER* 1.3 64.3 + - - +
200A VAL 3.2 3.2 + - - -
201A ILE* 3.6 16.3 - - + +
202A MET* 3.3 60.7 + - + +
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Residues in contact with SER 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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195A TRP 3.0 18.2 + - - -
196A LEU* 3.5 7.6 + - - -
198A PHE* 1.3 78.2 - - - +
200A VAL* 1.3 66.1 + - - +
202A MET* 4.1 2.5 - - - -
203A MET* 3.2 36.8 + - - +
224A LEU* 5.2 10.7 - - - +
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Residues in contact with VAL 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A TYR* 5.0 8.5 - - + -
196A LEU* 3.2 21.4 + - + +
197A ASP* 4.0 9.2 - - - +
198A PHE 3.2 0.8 - - - -
199A SER* 1.3 80.7 - - - +
201A ILE* 1.3 67.9 + - + +
202A MET 3.3 0.3 + - - -
203A MET* 3.4 1.8 + - - +
204A ALA* 3.1 25.5 + - - +
221A PHE 5.4 3.1 - - - +
224A LEU* 4.5 19.1 - - + +
225A ARG* 3.4 51.1 - - + +
228A LYS* 4.9 7.0 - - + -
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Residues in contact with ILE 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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165A THR* 5.4 3.1 - - + -
168A TYR* 4.2 19.1 - - + +
169A THR* 3.7 31.9 - - + +
172A SER* 3.8 29.2 - - - +
197A ASP 4.2 11.2 + - - +
198A PHE* 3.6 23.1 - - + +
200A VAL* 1.3 82.5 - - + +
202A MET* 1.3 75.9 + - + +
204A ALA* 4.0 6.4 - - - +
205A TYR* 2.8 37.0 + - + -
225A ARG* 6.2 0.4 - - - +
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Residues in contact with MET 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 PHE* 3.3 54.2 + - + +
199A SER* 4.3 1.8 - - - +
200A VAL 3.2 0.6 - - - -
201A ILE* 1.3 91.8 - - + +
203A MET* 1.3 83.4 + - + +
205A TYR* 3.3 19.9 + - + +
206A LEU* 3.3 23.3 + - + +
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Residues in contact with MET 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 SER* 3.2 31.0 - - - +
200A VAL* 3.4 4.2 + - - +
202A MET* 1.3 93.2 - - + +
204A ALA* 1.3 66.9 + - - +
206A LEU* 3.4 34.6 + - + +
207A THR* 3.4 13.5 + - - -
218A LEU* 5.0 3.9 - - + +
221A PHE* 5.0 26.7 - - + -
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Residues in contact with ALA 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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165A THR* 4.5 14.8 - - + +
200A VAL 3.1 17.9 + - - +
201A ILE* 4.1 8.3 - - - +
202A MET 3.3 0.2 - - - -
203A MET* 1.3 76.9 - - - +
205A TYR* 1.3 59.8 + - + +
207A THR* 3.1 12.7 + - - +
208A GLU* 3.0 23.4 + - - +
222A ARG* 4.9 12.3 - - + +
225A ARG* 3.7 24.0 - - - +
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Residues in contact with TYR 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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165A THR* 4.3 16.1 - - + +
169A THR* 3.1 35.9 + - + +
201A ILE* 2.8 28.4 + - + +
202A MET* 3.3 16.6 + - + +
203A MET 3.2 0.4 - - - -
204A ALA* 1.3 77.7 - - - +
206A LEU* 1.3 63.3 + - + +
208A GLU* 3.1 19.9 + - + +
209A PHE* 2.8 29.6 + - - +
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Residues in contact with LEU 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 MET* 3.3 19.7 - - + +
203A MET* 3.7 31.6 - - + +
204A ALA 3.3 0.6 - - - -
205A TYR* 1.3 77.8 - - + +
207A THR* 1.3 60.5 + - - +
209A PHE* 3.2 8.6 + - + +
210A VAL 2.4 36.5 + - - +
211A ASP* 5.4 0.7 - - - -
218A LEU* 5.5 5.2 - - + -
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Residues in contact with THR 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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161A GLU* 4.9 12.6 - - - +
203A MET 3.4 7.3 + - - -
204A ALA* 3.1 13.0 + - - +
206A LEU* 1.3 77.9 - - - +
208A GLU* 1.3 64.7 + - - +
210A VAL* 3.4 15.0 + - - -
211A ASP* 4.5 9.4 - - - +
218A LEU* 3.0 27.0 + - + +
219A ARG* 4.5 17.5 + - - +
222A ARG* 5.8 7.3 - - - +
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Residues in contact with GLU 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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162A TYR* 3.4 36.0 + - - -
204A ALA 3.0 12.1 + - - +
205A TYR* 3.3 26.5 - - + +
207A THR* 1.3 78.7 - - - +
209A PHE* 1.3 68.2 + - + +
210A VAL* 3.4 2.1 + - - +
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Residues in contact with PHE 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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205A TYR 2.8 18.5 + - - +
206A LEU* 3.2 11.2 + - + +
208A GLU* 1.3 77.9 - - + +
210A VAL* 1.3 75.9 + - - +
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Residues in contact with VAL 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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206A LEU* 2.4 26.3 + - - +
207A THR 3.7 9.6 - - - -
208A GLU 3.2 3.6 - - - +
209A PHE* 1.3 87.8 - - - +
211A ASP* 1.3 85.9 + - - +
212A LEU* 4.0 1.7 + - - -
214A ASN* 5.6 1.6 - - - +
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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