Contacts of the helix formed by residues 188 - 206 (chain A) in PDB entry 1D0L
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 ARG 188 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A MET* 3.7 22.0 - - - -
181A LEU 4.3 0.2 - - - -
185A TYR* 3.3 16.5 + - + -
187A ARG* 1.3 113.8 - - - +
189A ALA* 1.3 64.2 + - - +
190A GLU 3.3 2.7 - - - -
191A TYR* 3.3 30.1 + - + +
192A PHE* 3.0 53.7 + - + -
401A BLG 3.3 31.5 + - - -
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Residues in contact with ALA 189 (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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59A ASN* 6.4 0.9 - - - -
181A LEU 3.6 8.7 - - - -
182A SER* 3.5 22.0 - - - +
185A TYR 2.9 17.5 + - - +
186A PRO* 3.3 16.3 + - + +
188A ARG* 1.3 77.5 - - - +
190A GLU* 1.3 59.1 + - + +
192A PHE 3.9 0.5 - - - -
193A SER* 2.9 31.0 + - - -
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Residues in contact with GLU 190 (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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186A PRO 4.9 0.8 + - - +
188A ARG 3.3 0.6 - - - -
189A ALA* 1.3 76.0 - - + +
191A TYR* 1.3 65.5 + - - +
193A SER* 3.5 6.7 + - - -
194A GLY* 3.2 17.7 + - - -
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Residues in contact with TYR 191 (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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188A ARG* 3.3 38.3 + - + +
190A GLU* 1.3 78.2 - - - +
192A PHE* 1.3 93.1 + + - +
194A GLY* 3.1 12.0 + - - -
195A GLU* 3.1 41.5 + - + +
227A MET* 3.7 19.7 - - + +
229A SER* 4.5 2.3 + - - -
401A BLG 3.3 42.1 + - - -
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Residues in contact with PHE 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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95A MET* 4.4 9.4 - - + -
178A LEU* 3.9 18.2 - - + +
181A LEU* 3.5 52.0 - - + +
182A SER* 3.0 13.8 + - - +
185A TYR* 5.1 0.2 - + - -
188A ARG* 3.0 67.0 + - + +
191A TYR* 1.3 98.6 - + - +
193A SER* 1.3 58.9 + - - +
195A GLU* 3.1 4.8 + - + +
196A LEU* 2.8 24.6 + - - +
218A ALA* 3.6 24.2 - - + -
227A MET* 3.9 6.1 - - + -
401A BLG 5.7 0.2 - - - -
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Residues in contact with SER 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A PHE* 3.2 29.1 - - - +
66A LYS* 5.5 5.8 + - - +
182A SER* 3.2 16.9 + - - -
183A PHE* 5.1 1.6 - - - -
189A ALA 2.9 20.3 + - - -
190A GLU* 3.8 7.0 - - - -
191A TYR 3.3 0.2 - - - -
192A PHE* 1.3 72.5 - - - +
194A GLY* 1.3 61.6 + - - +
196A LEU* 3.4 1.5 + - - -
197A GLU* 2.9 29.9 + - - +
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Residues in contact with GLY 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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66A LYS* 6.0 1.1 - - - -
190A GLU 3.2 7.9 + - - -
191A TYR 3.1 8.6 + - - -
193A SER* 1.3 81.5 - - - +
195A GLU* 1.3 56.0 + - - +
197A GLU* 3.4 15.2 + - - +
198A THR* 3.0 33.6 + - - -
229A SER* 6.1 0.9 - - - -
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Residues in contact with GLU 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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178A LEU* 3.9 17.9 - - + -
191A TYR* 3.1 46.0 + - + +
192A PHE* 3.1 9.6 + - - +
194A GLY* 1.3 74.5 - - - +
196A LEU* 1.3 60.1 + - - +
198A THR* 3.4 1.8 + - - -
199A PHE* 2.8 29.1 + - - +
227A MET* 3.6 15.9 - - + +
228A PRO* 3.1 22.2 - - + +
229A SER* 2.6 50.7 + - - -
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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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63A PHE* 3.6 21.3 - - + -
82A LEU* 4.9 3.4 - - + -
175A LEU* 4.0 26.5 - - + -
178A LEU* 3.8 24.8 - - + +
179A ALA* 4.2 11.0 - - + +
182A SER* 3.7 12.1 - - - +
183A PHE* 3.5 35.2 - - + -
192A PHE 2.8 16.9 + - - +
193A SER 3.7 4.7 - - - +
194A GLY 3.3 0.2 - - - -
195A GLU* 1.3 72.3 - - - +
197A GLU* 1.3 65.2 + - - +
199A PHE* 3.2 7.4 + - + +
200A LEU* 3.0 37.3 + - + +
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Residues in contact with GLU 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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63A PHE* 3.7 12.3 - - + -
66A LYS* 3.6 24.7 + - - -
67A MET* 3.8 23.1 - - - +
70A LYS* 2.8 25.7 + - - +
71A HIS* 2.8 29.0 + - - +
193A SER 2.9 16.1 + - - +
194A GLY* 3.5 14.9 - - - +
196A LEU* 1.3 78.3 - - - +
198A THR* 1.3 63.3 + - - +
200A LEU 3.4 0.5 + - - -
201A LEU* 3.1 31.3 + - + +
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Residues in contact with THR 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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194A GLY 3.0 18.1 + - - -
195A GLU* 3.7 4.4 - - - -
197A GLU* 1.3 77.7 - - - +
199A PHE* 1.3 58.0 + - - +
201A LEU* 3.2 12.6 + - + +
202A MET* 2.9 30.9 + - + +
228A PRO* 3.4 33.0 - - + +
229A SER* 4.2 5.4 - - - +
231A TYR* 5.4 1.3 - - + -
232A LYS* 3.8 35.7 + - + +
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Residues in contact with PHE 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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174A ILE* 3.6 35.7 - - + -
175A LEU* 4.1 15.9 - - + -
178A LEU* 3.8 13.2 - - + -
195A GLU 2.8 18.3 + - - +
196A LEU* 3.2 10.7 + - + +
198A THR* 1.3 76.5 - - - +
200A LEU* 1.3 67.5 + - + +
202A MET* 3.2 13.0 + - + +
203A ALA* 2.9 28.9 + - + +
210A PRO* 3.3 44.9 - - + -
213A LEU* 3.7 28.7 - - + -
221A MET* 4.3 12.6 - - + -
228A PRO* 3.9 7.1 - - + +
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Residues in contact with LEU 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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63A PHE* 3.7 31.2 - - + -
67A MET* 4.2 6.5 - - + -
73A PHE* 3.9 19.0 - - + -
78A LEU* 3.9 21.5 - - + -
81A ILE* 4.8 10.5 - - + -
82A LEU* 5.6 2.9 - - + -
175A LEU* 4.1 24.5 - - + -
196A LEU* 3.0 26.9 + - + +
197A GLU 3.9 3.4 - - - +
199A PHE* 1.3 77.5 - - + +
201A LEU* 1.3 58.0 + - - +
203A ALA* 3.8 4.4 - - - +
204A ARG* 2.9 28.9 + - - +
210A PRO* 4.2 18.8 - - + -
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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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67A MET* 4.4 2.7 - - + -
71A HIS* 3.7 37.7 - - + +
73A PHE* 3.6 25.4 - - + -
197A GLU* 3.1 26.2 + - + +
198A THR* 3.5 12.1 - - + +
199A PHE 3.2 0.2 - - - -
200A LEU* 1.3 76.5 - - - +
202A MET* 1.3 58.6 + - - +
204A ARG* 3.3 22.0 + - - +
205A ASP* 2.9 40.9 + - - +
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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 THR* 2.9 11.9 + - + +
199A PHE* 3.2 19.7 + - - +
201A LEU* 1.3 77.4 - - - +
203A ALA* 1.3 57.4 + - - +
205A ASP* 3.3 6.0 + - - +
206A GLU* 2.9 34.6 + - + +
208A ASP* 5.4 3.4 - - - +
213A LEU* 5.1 7.6 - - - -
221A MET* 3.7 35.9 - - + +
228A PRO* 4.0 15.7 - - + +
231A TYR* 3.5 63.3 - - + +
246A LEU* 5.0 2.5 - - - -
247A TRP* 5.9 2.0 - - - -
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Residues in contact with ALA 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 PHE* 2.9 22.6 + - + +
200A LEU* 3.8 5.6 - - - +
202A MET* 1.3 73.5 - - - +
204A ARG* 1.3 61.9 + - - +
207A GLN* 3.0 8.7 + - - -
208A ASP* 2.8 55.9 + - + +
210A PRO* 4.1 26.9 - - + -
213A LEU* 5.4 1.6 - - + -
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Residues in contact with ARG 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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71A HIS* 3.0 29.9 + - - +
72A GLY 4.3 3.8 + - - -
73A PHE* 3.3 41.8 - - + +
200A LEU 2.9 18.1 + - - +
201A LEU* 3.6 22.4 - - - +
203A ALA* 1.3 77.4 - - - +
205A ASP* 1.3 72.0 + - - +
207A GLN* 3.2 16.9 + - - +
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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
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201A LEU* 2.9 26.6 + - - +
202A MET* 3.7 6.1 - - - +
204A ARG* 1.3 89.9 + - - +
206A GLU* 1.3 66.1 + - + +
207A GLN* 3.1 12.1 + - - +
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Residues in contact with GLU 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* 2.9 22.8 + - + +
205A ASP* 1.3 78.3 - - + +
207A GLN* 1.3 68.4 + - - +
208A ASP* 3.2 24.3 + - - +
231A TYR* 3.3 24.7 + - + +
242A GLY 5.1 0.9 - - - +
243A HIS* 3.1 33.1 + - - +
244A ILE* 3.3 31.8 + - - +
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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