Contacts of the helix formed by residues 219 - 232 (chain V) in PDB entry 1I84
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 GLU 219 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202V LYS* 3.3 38.8 + - - +
218V GLY* 1.3 77.0 - - - -
220V LEU* 1.3 62.4 + - - +
221V GLU* 3.2 0.8 + - - -
222V LYS* 3.1 23.5 - - + +
223V GLN* 3.8 11.8 + - - +
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Residues in contact with LEU 220 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219V GLU* 1.3 77.4 - - - +
221V GLU* 1.3 63.9 + - - +
222V LYS 2.8 5.4 - - - -
223V GLN* 2.9 25.6 + - + +
224V LEU* 2.8 29.7 + - + +
262V ILE* 4.8 9.6 - - + +
263V VAL* 3.2 37.7 - - - +
264V GLY* 4.4 5.8 - - - +
265V ALA* 6.3 0.4 - - + -
449V ALA 3.4 26.0 - - - +
450V LEU* 4.4 7.9 - - - +
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Residues in contact with GLU 221 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195V ALA* 3.7 22.3 - - + +
199V SER* 3.0 35.7 - - - -
200V SER* 3.4 14.4 + - - +
217V TYR* 4.2 6.3 - - + -
218V GLY* 2.8 34.3 - - - +
219V GLU 3.2 2.1 + - - -
220V LEU* 1.3 77.9 + - - +
222V LYS* 1.3 62.5 + - - +
224V LEU* 3.8 11.6 - - - +
225V LEU* 3.2 29.6 + - - +
262V ILE* 4.0 27.5 - - + +
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Residues in contact with LYS 222 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216V SER* 3.9 7.8 - - - +
217V TYR* 2.8 54.0 + - + +
218V GLY 3.3 12.8 + - - +
219V GLU* 3.1 18.6 + - + +
221V GLU* 1.3 79.6 - - - +
223V GLN* 1.3 61.9 + - + +
225V LEU* 3.3 19.5 - - - +
226V GLN* 3.4 11.6 + - - +
341V ILE* 4.2 15.7 - - + +
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Residues in contact with GLN 223 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219V GLU 4.4 8.6 - - - +
220V LEU* 2.9 27.7 + - - +
222V LYS* 1.3 77.8 - - + +
224V LEU* 1.3 53.6 + - - +
225V LEU 2.6 15.2 + - - -
226V GLN* 2.6 19.3 + - - +
227V ALA* 3.0 12.5 + - - +
341V ILE* 3.4 27.3 - - + +
342V MET* 3.6 30.1 - - - +
449V ALA* 3.6 22.3 - - - +
450V LEU* 4.2 6.1 - - + -
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Residues in contact with LEU 224 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191V ILE* 3.7 37.8 - - + +
195V ALA* 5.3 4.5 - - + -
220V LEU* 2.8 23.3 + - + +
221V GLU* 3.8 10.3 - - - +
223V GLN* 1.3 72.3 - - - +
225V LEU* 1.3 59.2 + - - +
227V ALA* 4.0 9.2 + - + +
228V ASN* 4.8 3.1 + - - +
252V ILE* 5.2 4.0 - - + -
254V ILE* 4.0 16.4 - - + -
262V ILE* 3.4 38.8 - - + -
264V GLY 5.3 0.7 - - - +
265V ALA* 4.2 22.2 - - + -
450V LEU* 4.4 18.5 - - + +
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Residues in contact with LEU 225 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188V LYS 5.8 0.4 - - - +
191V ILE* 4.5 8.3 - - + -
192V GLN* 4.3 17.9 - - + +
195V ALA* 3.9 24.2 - - + -
217V TYR* 4.2 37.9 - - + +
221V GLU 3.2 10.4 + - - +
222V LYS* 3.3 12.8 - - - +
223V GLN 2.6 1.0 + - - -
224V LEU* 1.3 81.5 - - - +
226V GLN* 1.3 63.9 + - - +
227V ALA 3.3 2.7 - - - -
228V ASN* 4.4 2.9 + - - +
229V PRO* 3.3 16.8 - - - +
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Residues in contact with GLN 226 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222V LYS 3.4 6.6 + - - +
223V GLN* 2.6 12.3 + - - +
225V LEU* 1.3 81.0 + - - +
227V ALA* 1.3 53.4 + - - -
229V PRO* 2.8 30.4 - - - +
230V ILE* 3.1 19.1 - - - +
334V GLU 4.9 2.3 - - - +
337V GLU* 5.9 0.5 - - - +
338V ALA* 3.4 34.7 + - + +
341V ILE* 3.5 36.0 - - + +
342V MET* 4.4 4.7 - - + +
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Residues in contact with ALA 227 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223V GLN 3.0 9.7 + - - +
224V LEU* 4.0 7.0 - - + +
225V LEU 3.3 1.2 - - - -
226V GLN* 1.3 73.3 - - - +
228V ASN* 1.3 56.1 + - - +
229V PRO* 3.0 3.8 - - - -
230V ILE* 2.7 35.6 + - - +
231V LEU* 3.3 8.5 + - + +
267V ILE* 5.1 2.9 - - + -
342V MET* 4.4 11.2 - - - -
446V VAL* 4.1 13.7 - - + -
450V LEU* 3.8 29.2 - - + -
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Residues in contact with ASN 228 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184V THR* 5.0 0.7 - - - +
187V THR* 5.1 2.6 - - - +
188V LYS* 4.5 25.4 - - + +
191V ILE* 4.2 22.3 - - + +
224V LEU 4.8 2.6 + - - +
225V LEU 4.4 3.3 + - - +
227V ALA* 1.3 77.6 - - - +
229V PRO* 1.3 66.4 - - + +
231V LEU* 4.1 9.9 - - - +
232V GLU* 3.1 39.5 + - - +
250V LYS* 3.3 40.4 + - - +
252V ILE* 4.6 6.7 - - - +
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Residues in contact with PRO 229 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188V LYS* 6.1 0.6 - - + -
225V LEU 3.3 11.4 - - - +
226V GLN* 2.8 45.3 - - + +
227V ALA 3.0 4.7 - - - -
228V ASN* 1.3 93.2 - - + +
230V ILE* 1.3 59.5 + - - +
232V GLU* 4.0 16.9 - - + +
233V ALA* 4.1 2.8 + - - +
335V THR* 4.6 16.9 - - - +
338V ALA* 4.4 8.1 - - + -
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Residues in contact with ILE 230 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226V GLN 3.1 21.3 - - - +
227V ALA 2.7 14.7 + - - +
229V PRO* 1.3 71.9 - - - +
231V LEU* 1.3 73.4 + - + +
232V GLU 2.7 4.2 + - - -
233V ALA* 2.6 37.1 + - - +
234V PHE* 3.8 10.6 + - + -
335V THR* 4.7 2.2 - - - +
338V ALA* 3.7 11.2 - - + -
339V MET* 3.6 36.6 - - + +
342V MET* 3.3 29.4 - - + -
344V PHE* 5.1 2.5 - - + -
442V ILE* 4.0 21.3 - - + -
446V VAL* 4.1 4.7 - - + -
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Residues in contact with LEU 231 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227V ALA* 3.3 11.4 + - + +
228V ASN* 4.4 8.5 - - - +
230V ILE* 1.3 95.5 - - + +
232V GLU* 1.3 62.4 + - + +
233V ALA 3.1 0.6 + - - -
234V PHE* 3.5 19.6 - - + +
235V GLY* 3.5 8.8 - - - -
236V ASN* 3.6 2.0 - - - +
248V PHE* 3.7 22.4 - - + -
250V LYS* 5.5 7.6 - - + +
267V ILE* 4.0 24.5 - - + -
439V PHE* 4.5 11.9 - - + -
442V ILE* 4.7 7.4 - - + -
443V LEU* 3.9 33.0 - - + -
446V VAL* 4.1 20.6 - - + -
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Residues in contact with GLU 232 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184V THR* 5.2 5.2 - - + -
188V LYS* 2.7 42.7 + - - +
228V ASN* 3.1 30.2 + - - +
229V PRO* 4.0 11.7 - - + +
230V ILE 2.7 0.8 + - - -
231V LEU* 1.3 76.6 - - + +
233V ALA* 1.3 66.6 + - - +
236V ASN* 2.7 40.6 - - - +
244V ASN* 3.2 32.5 + - - +
248V PHE* 6.3 0.2 - - + -
250V LYS* 5.4 4.9 - - - +
288V HIS* 4.3 7.0 + - - -
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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