Contacts of the helix formed by residues 184 - 196 (chain A) in PDB entry 1YDY
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 184 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A MET* 4.2 4.7 - - - +
179A HIS* 4.2 9.9 - - + -
183A LYS* 1.3 73.0 - - - +
185A ILE* 1.3 60.7 + - - +
186A ALA 3.6 2.4 + - - -
187A ALA* 3.1 29.7 + - + +
188A LYS* 3.2 19.4 + - - +
217A ARG* 2.8 43.4 + - - -
222A LEU* 4.8 0.7 - - - +
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Residues in contact with ILE 185 (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 LEU* 3.2 30.7 - - + +
67A VAL* 3.5 20.6 - - - -
68A MET* 3.6 15.5 - - + -
74A LEU* 3.7 16.4 - - + -
172A ILE* 3.4 24.0 - - + -
173A LYS 4.1 2.5 - - - +
175A PRO* 3.7 25.4 - - + +
178A HIS* 3.6 24.2 - - + +
179A HIS* 5.5 1.6 - - - +
183A LYS 3.7 4.4 + - - -
184A ASP* 1.3 71.5 + - - +
186A ALA* 1.3 61.1 + - - +
188A LYS* 3.3 1.5 + - - +
189A THR* 2.8 39.3 + - - +
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Residues in contact with ALA 186 (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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172A ILE* 3.8 15.7 - - + +
184A ASP* 3.3 2.5 + - - +
185A ILE* 1.3 82.9 - - - +
187A ALA* 1.3 63.1 + - - +
189A THR* 3.3 1.9 + - - -
190A LEU* 3.0 28.2 + - - +
214A GLU* 3.6 27.1 + - + +
218A ILE* 3.9 21.3 - - + -
222A LEU* 3.8 16.6 - - + -
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Residues in contact with ALA 187 (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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184A ASP* 3.1 32.9 + - + +
186A ALA* 1.3 76.0 - - - +
188A LYS* 1.3 64.3 + - - +
190A LEU* 3.3 6.4 + - - +
191A GLU* 2.9 40.2 + - + +
222A LEU* 4.0 18.8 - - + +
226A MET* 4.5 4.4 - - - +
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Residues in contact with LYS 188 (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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68A MET* 4.2 16.6 - - + -
72A ASP* 3.5 21.6 + - + +
73A ASN* 4.9 2.6 + - - +
74A LEU* 3.5 28.3 - - + +
149A GLU* 4.6 11.4 + - - -
184A ASP 3.2 14.7 + - - +
185A ILE* 3.7 5.6 - - - +
187A ALA* 1.3 80.2 - - - +
189A THR* 1.3 61.2 + - - +
191A GLU* 3.3 22.4 + - + +
192A VAL* 3.1 38.0 + - + +
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Residues in contact with THR 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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66A LEU* 3.8 24.4 - - + +
74A LEU* 3.7 17.4 - - - +
148A PHE* 4.2 4.2 - - + -
170A PRO* 5.1 0.2 - - + -
172A ILE* 3.8 25.7 - - + +
185A ILE* 2.8 29.0 + - - +
186A ALA 3.6 4.0 - - - -
188A LYS* 1.3 76.1 - - - +
190A LEU* 1.3 62.2 + - - +
192A VAL* 3.2 4.3 + - - +
193A LEU* 3.0 31.2 + - + +
207A LEU* 4.1 17.9 - - + -
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Residues in contact with LEU 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 ALA 3.0 22.4 + - - +
187A ALA 3.8 1.1 - - - +
189A THR* 1.3 76.1 - - - +
191A GLU* 1.3 58.0 + - - +
193A LEU* 3.4 3.5 + - + -
194A LYS* 2.9 31.2 + - - +
207A LEU* 3.9 27.4 - - + -
218A ILE* 4.2 17.5 - - + -
222A LEU* 3.6 34.8 - - + -
223A GLU* 4.5 10.5 - - + +
226A MET* 3.6 23.3 - - + -
228A MET* 3.5 25.0 - - + +
230A LEU* 4.0 8.7 - - + -
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Residues in contact with GLU 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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187A ALA* 2.9 37.2 + - - +
188A LYS* 3.5 24.0 + - - +
189A THR 3.2 0.2 - - - -
190A LEU* 1.3 77.0 - - - +
192A VAL* 1.3 59.5 + - + +
194A LYS* 3.4 3.3 + - - +
195A LYS* 2.9 29.9 + - - +
226A MET* 3.7 18.2 - - + -
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Residues in contact with VAL 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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74A LEU* 4.0 13.5 - - + -
148A PHE* 3.5 27.1 - - + -
149A GLU* 3.7 40.8 - - + +
152A ILE* 5.0 2.9 - - + -
188A LYS* 3.1 25.7 + - + +
189A THR 3.7 6.1 - - - +
191A GLU* 1.3 73.6 - - + +
193A LEU* 1.3 66.2 - - - +
195A LYS* 3.2 8.2 + - + +
196A TYR* 3.1 34.0 + - + -
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Residues in contact with LEU 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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148A PHE* 3.8 17.5 - - + -
152A ILE* 5.4 1.3 - - + -
168A ILE* 3.6 31.4 - - + -
170A PRO* 4.3 4.3 - - + -
189A THR* 3.0 33.1 + - + +
190A LEU* 3.7 9.9 - - + +
192A VAL* 1.3 77.4 - - - +
194A LYS* 1.3 60.1 + - - +
196A TYR* 3.1 8.7 + - - -
197A GLY 3.2 0.3 + - - -
198A TYR* 2.9 47.9 + - + +
205A VAL* 4.1 8.3 - - + -
207A LEU* 4.4 11.4 - - + -
228A MET* 4.1 1.8 - - + -
230A LEU* 3.6 26.5 - - + -
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Residues in contact with LYS 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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190A LEU 2.9 17.9 + - - +
191A GLU* 3.7 5.6 - - - +
193A LEU* 1.3 77.6 - - - +
195A LYS* 1.3 63.5 + - - +
197A GLY* 3.1 13.3 + - - -
198A TYR 3.8 8.7 + - - -
199A THR* 3.9 17.7 - - + +
226A MET* 2.7 43.2 + - + +
227A GLY* 5.0 1.5 - - - -
228A MET* 4.0 13.0 - - + +
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Residues in contact with LYS 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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149A GLU* 4.9 10.2 + - + +
191A GLU 2.9 18.6 + - - +
192A VAL* 3.2 9.6 + - + +
194A LYS* 1.3 75.7 - - - +
196A TYR* 1.3 93.9 + - + +
197A GLY 3.6 0.7 + - - -
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Residues in contact with TYR 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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149A GLU* 3.8 31.8 - - + +
152A ILE* 3.7 31.6 - - + -
153A GLU* 2.6 43.4 + - + -
156A GLN* 3.0 32.1 + - - +
192A VAL* 3.1 32.2 + - + +
193A LEU* 3.1 0.4 + - - -
194A LYS 3.1 0.6 - - - -
195A LYS* 1.3 111.0 + - + +
197A GLY* 1.3 58.0 + - - +
198A TYR* 3.5 12.1 - - + -
140B LYS* 5.9 2.5 - - - -
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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