Contacts of the helix formed by residues 191 - 209 (chain A) in PDB entry 5A5J
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 191 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185A LYS* 3.7 12.6 + - - -
187A PHE* 3.5 30.3 - - + -
188A ASP* 3.5 22.7 + - + +
190A LYS* 1.3 72.4 - - - +
192A GLN* 1.3 56.8 + - - +
193A GLN* 3.4 20.9 + - - +
194A PHE* 2.7 33.1 + - + +
195A LEU 3.4 2.4 + - - -
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Residues in contact with GLN 192 (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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190A LYS 3.0 8.8 + - - +
191A ASP* 1.3 72.5 + - - +
193A GLN* 1.3 64.4 + - - +
194A PHE 2.9 0.5 + - - -
195A LEU* 3.0 24.6 + - - +
196A ASN* 2.9 50.0 + - - +
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Residues in contact with GLN 193 (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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185A LYS* 5.5 2.2 - - - +
187A PHE* 4.2 15.9 - - + -
191A ASP* 3.4 19.1 + - - +
192A GLN* 1.3 76.5 - - - +
194A PHE* 1.3 60.8 + - - +
196A ASN* 3.8 9.4 - - - +
197A LEU* 3.4 20.5 + - - +
243A TYR* 3.1 32.4 + - + +
246A GLU* 5.2 5.3 - - - +
247A LYS* 2.3 38.5 - - - +
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Residues in contact with PHE 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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168A PHE* 6.0 0.9 - + - -
172A CYS* 3.4 35.2 - - + -
175A CYS* 4.0 14.6 - - + -
176A ASN* 3.5 37.7 - - - -
179A CYS* 4.1 6.7 - - - -
187A PHE* 3.7 31.1 - + + -
188A ASP 4.2 12.6 - - - +
189A TYR* 4.4 13.5 - + - -
190A LYS 5.5 0.2 - - - +
191A ASP* 2.7 19.7 + - - +
193A GLN* 1.3 68.1 - - - +
195A LEU* 1.4 55.5 + - + +
196A ASN 2.7 16.4 + - - -
197A LEU* 2.7 21.0 + - + +
198A MET* 3.0 41.2 + - + +
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Residues in contact with LEU 195 (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 PHE* 4.1 26.5 - - + -
189A TYR 4.3 7.2 - - - +
190A LYS* 3.2 41.1 - - + +
191A ASP 3.4 2.9 + - - +
192A GLN* 3.0 30.8 + - - +
194A PHE* 1.4 76.1 - - + +
196A ASN* 1.3 57.4 + - - +
198A MET* 4.7 6.7 - - - +
199A GLU* 3.2 28.0 + - - +
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Residues in contact with ASN 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 GLN* 2.9 41.8 + - - +
193A GLN* 3.8 8.5 - - - +
194A PHE 2.7 4.8 + - - -
195A LEU* 1.3 72.2 - - - +
197A LEU* 1.3 66.3 + - - +
198A MET 3.1 1.1 - - - -
199A GLU* 3.2 11.2 + - - +
200A LYS* 3.0 35.3 + - - +
239A PHE* 4.1 21.1 - - + -
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Residues in contact with LEU 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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175A CYS* 5.2 3.8 - - - -
179A CYS* 4.2 24.5 - - - -
183A PHE* 4.9 0.2 - - + -
187A PHE* 5.4 1.3 - - + -
193A GLN 3.4 11.1 + - - +
194A PHE* 2.7 19.3 + - + +
196A ASN* 1.3 76.7 - - - +
198A MET* 1.3 58.7 + - + +
200A LYS* 3.3 7.6 + - - +
201A LEU* 3.2 31.8 + - + +
239A PHE* 4.6 7.5 - - + -
240A MET* 3.6 27.3 - - + +
243A TYR* 4.3 31.6 - - + +
244A ILE* 5.9 1.1 - - + -
295A PHE* 4.3 26.2 - - + -
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Residues in contact with MET 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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168A PHE* 4.2 17.7 - - + +
171A GLY* 3.5 13.5 - - - +
172A CYS* 3.1 52.3 - - - -
175A CYS* 3.6 25.1 - - + -
194A PHE* 3.0 34.4 + - + +
195A LEU* 4.7 4.0 - - - +
197A LEU* 1.3 74.4 - - + +
199A GLU* 1.3 64.5 + - - +
200A LYS 3.3 0.4 - - - -
201A LEU* 3.9 10.2 - - + +
202A ASN* 3.0 42.1 + - - +
299A THR* 5.5 1.3 - - + -
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Residues in contact with GLU 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 LEU 3.2 22.1 + - - +
196A ASN* 3.2 12.0 + - - +
198A MET* 1.3 77.4 - - - +
200A LYS* 1.3 77.0 + - - +
202A ASN* 3.5 7.6 + - - +
203A GLU* 3.2 34.0 + - - +
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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 ASN* 3.0 29.3 + - - +
197A LEU 3.6 5.6 - - - +
198A MET 3.3 0.2 - - - -
199A GLU* 1.3 95.1 + - - +
201A LEU* 1.3 60.4 + - - +
203A GLU* 3.4 9.1 + - - -
204A ASN* 3.2 28.8 + - - +
232A LYS* 6.1 1.6 - - - +
235A LYS* 4.9 12.7 - - - +
236A ASN* 3.5 33.7 + - + +
239A PHE* 3.6 47.0 - - + -
240A MET* 4.6 15.7 - - + -
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Residues in contact with LEU 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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175A CYS* 4.1 20.9 - - - -
197A LEU* 3.2 20.8 + - + +
198A MET* 3.9 10.8 - - + +
199A GLU 3.4 0.2 - - - -
200A LYS* 1.3 73.7 - - - +
202A ASN* 1.3 61.7 + - - +
204A ASN* 3.2 8.5 + - + +
205A ILE* 3.0 34.1 + - + +
240A MET* 4.0 24.2 - - + +
295A PHE* 4.2 18.6 - - + +
296A GLY* 4.4 4.9 - - - -
299A THR* 4.1 25.1 - - + +
1494A 6YF 3.4 33.9 - - + +
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Residues in contact with ASN 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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168A PHE* 5.5 10.9 - - - -
198A MET* 3.0 30.8 + - - +
199A GLU* 3.8 7.6 - - - +
201A LEU* 1.3 79.9 - - - +
203A GLU* 1.3 59.0 + - - +
205A ILE* 3.5 11.5 - - - +
206A LYS* 3.1 26.9 + - - +
300A GLU* 4.5 11.6 - - - +
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Residues in contact with GLU 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 GLU* 3.2 29.3 + - - +
200A LYS* 3.6 10.1 + - - +
201A LEU 3.2 0.8 - - - -
202A ASN* 1.3 74.3 - - - +
204A ASN* 1.3 63.1 + - - +
205A ILE 3.1 0.2 - - - -
206A LYS* 3.4 4.1 + - - +
207A ILE* 3.0 38.4 + - + +
232A LYS* 3.1 40.3 - - + +
236A ASN* 3.4 24.8 + - - +
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Residues in contact with ASN 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 3.3 8.5 + - - -
201A LEU* 3.2 12.6 + - + +
203A GLU* 1.3 75.3 - - - +
205A ILE* 1.3 60.9 + - + +
207A ILE* 3.9 1.0 - - - +
208A LEU* 3.0 39.2 + - + +
232A LYS 4.4 0.9 - - - +
233A LEU* 4.0 22.7 + - + +
236A ASN* 3.2 34.8 + - - +
237A VAL* 4.5 16.4 - - - +
240A MET* 4.6 13.1 - - - +
1494A 6YF 3.9 27.0 + - - +
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Residues in contact with ILE 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 LEU* 3.0 17.7 + - + +
202A ASN* 3.5 18.4 - - - +
203A GLU 3.1 0.2 - - - -
204A ASN* 1.3 75.6 - - - +
206A LYS* 1.4 83.7 + - - +
207A ILE 3.0 1.3 + - - -
208A LEU 3.1 0.7 + - - -
209A SER* 3.0 32.1 + - - +
300A GLU* 3.8 28.7 - - + +
1494A 6YF 3.1 66.2 - - + +
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Residues in contact with LYS 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 ASN 3.1 13.8 + - - +
203A GLU* 3.4 4.5 + - - +
205A ILE* 1.4 89.7 - - - +
207A ILE* 1.3 68.5 + - + +
209A SER* 3.4 14.9 + - - -
210A SER* 3.7 5.7 + - - -
225A TYR* 5.3 3.5 - - - -
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Residues in contact with ILE 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 GLU* 3.0 29.0 + - + +
204A ASN* 3.9 1.8 - - - +
205A ILE 3.0 1.0 - - - -
206A LYS* 1.3 82.7 - - + +
208A LEU* 1.3 62.0 + - + +
210A SER* 2.9 27.6 + - - +
225A TYR* 4.4 24.8 - - + -
229A THR* 3.8 33.0 - - + +
230A HIS* 6.3 1.6 - - + -
232A LYS* 4.7 9.0 - - + +
233A LEU* 3.3 48.7 - - + +
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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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100A PHE* 5.3 14.1 - - + -
204A ASN* 3.0 34.9 + - + +
205A ILE 3.1 0.8 + - - +
207A ILE* 1.3 73.1 - - + +
209A SER* 1.3 56.0 + - - +
210A SER* 3.0 17.3 + - - -
223A ILE* 4.3 7.8 - - - +
233A LEU* 4.0 18.4 - - + -
475A GLY* 4.0 9.5 - - - -
476A PHE* 4.2 16.1 + - + +
1494A 6YF 3.2 73.4 - - + +
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Residues in contact with SER 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 ILE* 3.0 23.8 + - - +
206A LYS* 3.4 12.8 + - - -
208A LEU* 1.3 74.1 - - - +
210A SER* 1.3 57.6 + - - +
211A PRO* 3.5 5.2 - - - +
473A VAL 4.3 1.2 - - - +
474A ASN* 3.0 41.9 + - - -
475A GLY 3.0 15.8 + - - +
476A PHE 4.4 0.9 - - - +
1494A 6YF 3.2 20.4 + - - -
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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