Contacts of the helix formed by residues 198 - 220 (chain E) in PDB entry 1VYH
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 THR 198 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56E TYR* 3.5 10.3 - - - -
188E CYS 4.1 3.4 - - - +
189E HIS* 3.3 22.3 + - - +
190E ASP 3.2 25.1 + - - -
191E MET 3.7 1.8 - - - +
192E PHE* 3.8 12.8 - - + +
197E LEU* 1.3 77.1 - - - +
199E GLY* 1.3 65.2 + - - +
200E GLY* 3.0 6.5 + - - -
201E GLY 3.0 15.8 + - - -
202E TYR* 3.1 21.5 + - - -
55F GLN* 3.7 18.6 - - - +
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Residues in contact with GLY 199 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56E TYR* 3.4 33.5 + - - -
58E ILE* 4.8 4.9 - - - +
198E THR* 1.3 75.0 - - - +
200E GLY* 1.3 64.5 + - - +
202E TYR* 3.3 4.0 + - - +
203E ALA* 3.3 18.4 + - - +
55F GLN* 4.5 2.4 + - - +
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Residues in contact with GLY 200 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189E HIS 5.1 3.1 - - - -
190E ASP* 5.1 3.6 - - - -
198E THR* 3.0 6.7 + - - -
199E GLY* 1.3 74.2 - - - +
201E GLY* 1.3 62.9 + - - +
203E ALA* 3.0 17.6 + - - +
204E LYS* 3.4 14.9 + - - +
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Residues in contact with GLY 201 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179E PHE* 3.8 15.1 - - - -
190E ASP* 4.0 11.3 + - - -
197E LEU* 3.8 22.9 - - - -
198E THR* 3.0 16.7 + - - -
200E GLY* 1.3 74.9 - - - +
202E TYR* 1.3 62.2 + - - +
204E LYS* 2.9 18.4 + - - +
205E ILE* 3.3 7.4 + - - +
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Residues in contact with TYR 202 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E MET* 2.7 38.3 + - - +
52E LEU* 3.3 17.5 - - + +
53E MET* 3.6 38.4 - - + -
56E TYR* 3.5 31.6 - + + -
58E ILE* 4.4 11.4 - - + -
101E TRP* 4.5 4.5 - + - -
196E HIS* 5.8 0.7 - - - +
197E LEU* 3.5 41.9 + - + +
198E THR 3.1 22.4 + - - -
199E GLY 3.3 7.4 + - - +
201E GLY* 1.3 75.2 - - - +
203E ALA* 1.3 52.9 + - - +
205E ILE* 3.0 3.2 + - + +
206E CYS* 2.6 48.9 + - - -
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Residues in contact with ALA 203 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58E ILE* 3.9 22.8 - - + +
199E GLY 3.3 8.5 + - - +
200E GLY* 3.0 13.8 + - - +
202E TYR* 1.3 80.0 - - - +
204E LYS* 1.3 59.0 + - - +
207E LYS* 3.4 26.5 + - - +
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Residues in contact with LYS 204 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175E THR* 3.7 8.5 - - - +
177E GLY* 4.1 20.7 + - - -
178E GLY 4.2 10.5 + - - +
179E PHE* 3.7 25.5 - - + -
181E HIS* 6.1 0.4 - - - -
190E ASP* 3.1 34.6 + - - -
200E GLY 3.4 8.9 + - - +
201E GLY 2.9 10.7 + - - +
203E ALA* 1.3 79.0 - - - +
205E ILE* 1.3 58.0 + - + +
207E LYS* 5.3 0.2 - - - -
208E PRO* 3.3 19.2 - - - +
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Residues in contact with ILE 205 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53E MET* 5.2 1.8 - - + -
101E TRP* 4.1 23.8 - - + -
137E LEU* 4.3 13.9 - - + -
140E LEU* 4.2 14.8 - - + -
175E THR* 3.6 34.8 + - + +
177E GLY 4.9 2.2 - - - +
179E PHE* 3.7 24.2 - - + -
197E LEU* 4.1 17.5 - - + -
201E GLY 3.3 8.2 + - - +
202E TYR* 3.0 10.3 + - + +
204E LYS* 1.3 83.0 - - + +
206E CYS* 1.3 70.3 + - - +
207E LYS 3.5 0.2 - - - -
208E PRO* 3.2 13.6 - - - +
209E LEU* 3.3 11.5 + - + +
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Residues in contact with CYS 206 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53E MET* 3.6 38.8 - - - -
58E ILE* 3.3 27.8 - - + -
62E LEU* 4.5 1.3 - - + -
63E PHE* 3.9 15.2 - - + -
202E TYR* 2.6 36.5 + - - +
205E ILE* 1.3 74.7 - - - +
207E LYS* 1.3 58.1 + - - +
209E LEU* 3.0 6.1 + - - +
210E HIS* 2.7 38.4 + - - +
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Residues in contact with LYS 207 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58E ILE* 4.9 1.2 - - - +
62E LEU* 4.7 6.8 - - - +
203E ALA 3.4 16.5 + - - +
204E LYS* 5.3 0.4 - - - -
206E CYS* 1.3 78.7 - - - +
208E PRO* 1.3 70.1 - - + +
210E HIS* 3.7 5.2 + - - +
211E GLU* 3.1 32.3 + - - +
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Residues in contact with PRO 208 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173E LEU* 4.4 13.3 - - + +
175E THR* 3.9 17.9 - - + +
204E LYS 3.3 20.2 - - - +
205E ILE 3.2 13.9 - - - +
207E LYS* 1.3 96.9 - - + +
209E LEU* 1.3 63.4 + - - +
211E GLU* 3.2 15.5 + - + +
212E LEU* 2.9 22.9 + - - +
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Residues in contact with LEU 209 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E PHE* 4.0 26.5 - - + -
53E MET* 4.9 6.5 - - + -
63E PHE* 4.6 5.8 - - + -
99E VAL* 4.2 6.5 - - + -
135E ILE* 4.0 20.9 - - + -
137E LEU* 3.5 35.7 - - + -
173E LEU* 3.8 24.8 - - + +
205E ILE* 3.3 15.9 + - + +
206E CYS* 3.0 6.3 + - - +
208E PRO* 1.3 80.3 - - - +
210E HIS* 1.3 63.9 + - - +
212E LEU* 3.1 4.7 + - - +
213E ILE* 2.9 35.1 + - + +
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Residues in contact with HIS 210 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62E LEU* 3.6 55.1 + - + +
63E PHE* 3.9 14.6 - + + -
66E LEU* 4.0 12.0 - - + +
206E CYS 2.7 20.3 + - - +
207E LYS* 3.7 4.8 + - - +
209E LEU* 1.3 71.5 - - - +
211E GLU* 1.3 68.8 + - - +
213E ILE* 3.1 4.6 + - - +
214E MET* 2.9 63.5 + - + +
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Residues in contact with GLU 211 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207E LYS* 3.1 24.4 + - - +
208E PRO* 3.7 13.2 - - - +
210E HIS* 1.3 88.0 - - - +
212E LEU* 1.3 61.7 + - - +
214E MET* 3.8 6.4 + - - +
215E GLN* 3.4 33.4 + - - +
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Residues in contact with LEU 212 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135E ILE* 3.7 23.6 - - + -
171E GLN* 3.4 31.6 - - - +
173E LEU* 3.6 26.5 - - + -
208E PRO 2.9 13.1 + - - +
209E LEU 3.4 8.3 - - - +
211E GLU* 1.3 75.0 - - - +
213E ILE* 1.3 69.8 + - - +
215E GLN* 2.9 33.2 + - + +
216E LEU* 3.0 34.6 + - + +
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Residues in contact with ILE 213 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42E VAL* 4.1 14.1 - - + -
44E PHE* 4.4 2.7 - - + -
63E PHE* 3.7 30.7 - - + -
66E LEU* 4.6 6.5 - - + -
97E VAL* 3.9 20.4 - - + -
99E VAL* 4.3 13.5 - - + -
135E ILE* 3.8 18.6 - - + -
209E LEU* 2.9 33.8 + - + +
210E HIS* 3.1 4.0 + - - +
212E LEU* 1.3 74.2 - - - +
214E MET* 1.3 65.1 + - - +
216E LEU* 2.8 13.1 + - - +
217E LEU* 2.8 42.6 + - + +
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Residues in contact with MET 214 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66E LEU* 3.7 29.6 - - + -
210E HIS* 2.9 58.0 + - + +
211E GLU* 3.9 7.9 - - - +
213E ILE* 1.3 76.3 - - - +
215E GLN* 1.3 60.4 + - - +
217E LEU* 3.5 12.9 + - + +
218E GLU* 3.0 24.8 + - - +
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Residues in contact with GLN 215 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211E GLU* 3.4 30.0 + - - +
212E LEU* 2.9 26.7 + - + +
214E MET* 1.3 77.0 - - - +
216E LEU* 1.3 64.1 + - + +
218E GLU* 2.9 18.8 + - - +
219E GLU* 3.2 10.4 + - - +
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Residues in contact with LEU 216 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96E LYS* 6.1 0.3 - - - +
97E VAL* 4.2 15.2 - - + +
133E LYS* 3.2 55.6 - - + +
135E ILE* 3.9 18.6 - - + -
171E GLN* 4.0 16.6 - - + +
212E LEU* 3.0 44.8 + - + +
213E ILE 2.8 12.0 + - - +
215E GLN* 1.3 78.0 - - + +
217E LEU* 1.3 60.8 + - - +
219E GLU* 3.3 18.5 - - - +
220E THR 4.2 2.3 + - - +
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Residues in contact with LEU 217 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E ASP* 4.2 18.4 - - + +
42E VAL* 4.3 4.0 - - + -
66E LEU* 4.2 21.8 - - + +
96E LYS* 3.9 38.0 - - + +
97E VAL* 4.0 11.0 - - + -
213E ILE* 2.8 41.7 + - + +
214E MET* 3.8 15.5 - - + +
216E LEU* 1.3 68.6 - - - +
218E GLU* 1.3 59.4 + - - +
219E GLU 3.0 9.9 + - - -
220E THR 3.4 21.6 + - - +
221E PRO* 4.6 3.6 - - - +
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Residues in contact with GLU 218 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214E MET 3.0 17.6 + - - +
215E GLN* 2.9 9.0 + - - +
217E LEU* 1.3 74.6 - - - +
219E GLU* 1.3 60.6 + - - +
220E THR* 3.7 0.8 - - - -
221E PRO* 5.5 5.0 - - - +
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Residues in contact with GLU 219 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133E LYS* 3.8 24.2 - - - +
215E GLN 3.2 6.5 + - - +
216E LEU* 3.3 17.7 - - - +
217E LEU 3.0 2.2 - - - -
218E GLU* 1.3 80.3 - - - +
220E THR* 1.3 66.9 + - - +
221E PRO* 4.5 2.2 - - - +
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Residues in contact with THR 220 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96E LYS* 4.2 18.0 - - - +
133E LYS* 5.5 4.8 - - - +
216E LEU 4.2 1.5 + - - +
217E LEU* 3.4 12.0 + - - +
219E GLU* 1.3 87.1 + - - +
221E PRO* 1.3 71.7 - - + +
222E GLU* 3.9 9.4 - - + +
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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
------------------------------------------------------------
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