Contacts of the helix formed by residues 192 - 204 (chain B) in PDB entry 1YVP
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 ASN 192 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157B ASN 5.7 1.0 - - - +
159B LYS 5.4 1.0 - - - +
161B ALA* 5.0 2.5 + - - +
190B PRO 3.4 1.2 - - - -
191B ALA* 1.3 86.1 - - - +
193B GLU* 1.3 68.0 + - - +
194B GLY* 3.6 4.9 - - - +
195B LEU* 2.9 36.4 - - - +
196B THR* 2.9 23.7 + - - -
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Residues in contact with GLU 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192B ASN* 1.3 74.5 - - + +
194B GLY* 1.3 65.7 + - - +
196B THR* 3.0 16.6 + - - +
197B MET* 2.9 19.9 + - - +
213B TYR* 3.7 23.4 + - + -
217B GLU 5.9 3.1 - - - +
218B LEU* 6.0 2.0 - - + -
219B SER* 5.7 2.2 - - - +
222B THR* 4.7 19.1 - - + +
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Residues in contact with GLY 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B ALA* 3.7 23.6 - - - -
192B ASN* 3.3 4.6 - - - +
193B GLU* 1.3 77.4 - - - +
195B LEU* 1.3 57.4 + - - +
197B MET* 2.8 34.7 + - - +
198B VAL* 2.9 15.2 + - - +
222B THR* 4.7 7.6 + - - -
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Residues in contact with LEU 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B TYR* 3.6 26.5 - - + +
157B ASN* 3.8 24.7 - - - +
159B LYS 3.5 25.1 - - - +
161B ALA* 4.3 13.0 - - - +
164B LEU* 3.7 20.4 - - + -
188B ILE* 4.9 3.8 - - + -
190B PRO* 3.8 13.0 - - + -
191B ALA 4.4 1.3 - - - +
192B ASN* 2.9 32.3 - - - +
194B GLY* 1.3 74.8 - - - +
196B THR* 1.3 57.7 + - - +
198B VAL* 3.2 4.7 + - + +
199B ALA* 2.8 33.3 + - + +
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Residues in contact with THR 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189B LYS* 4.4 9.7 + - - -
190B PRO* 3.3 24.8 + - - +
192B ASN 2.9 13.4 + - - -
193B GLU* 3.0 19.0 + - - +
195B LEU* 1.3 75.7 - - - +
197B MET* 1.3 57.2 + - - +
199B ALA* 3.7 1.4 - - - +
200B LYS* 2.8 37.7 + - - +
213B TYR* 3.2 15.5 - - - +
1F IU 4.0 15.1 - - - +
2F IU 5.5 2.6 + - - +
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Residues in contact with MET 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193B GLU 2.9 6.7 + - - +
194B GLY* 2.8 10.4 + - - +
196B THR* 1.3 76.7 - - - +
198B VAL* 1.3 58.3 + - - +
200B LYS* 3.2 4.2 + - - +
201B TYR* 2.8 26.7 + - - +
209B VAL* 3.6 16.2 - - + +
213B TYR* 3.3 27.5 + - + +
218B LEU* 6.3 0.2 - - - -
222B THR* 2.8 48.7 - - - +
225B VAL* 3.4 23.1 - - + -
226B LEU* 3.8 33.9 - - - -
229B LEU* 4.0 10.1 - - + -
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Residues in contact with VAL 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B TYR* 6.1 0.2 - - + -
161B ALA 3.8 22.7 - - - +
164B LEU* 3.5 31.4 - - + +
165B ALA* 4.4 7.9 - - + +
168B VAL* 4.3 13.2 - - + -
194B GLY 2.9 17.8 + - - +
195B LEU* 3.7 6.3 - - - +
197B MET* 1.3 77.5 - - - +
199B ALA* 1.3 58.0 + - - +
201B TYR* 3.1 8.6 + - + +
202B VAL* 2.8 48.6 + - + +
225B VAL* 4.1 16.4 - - + -
229B LEU* 5.0 3.8 - - + -
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Residues in contact with ALA 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B LEU* 3.7 20.0 - - + -
188B ILE* 5.4 3.4 - - + -
190B PRO* 4.0 8.1 - - + -
195B LEU* 2.8 21.9 + - + +
196B THR 3.7 4.0 - - - +
198B VAL* 1.3 74.9 - - - +
200B LYS* 1.3 56.2 + - - +
202B VAL* 3.3 1.5 + - - +
203B SER* 2.7 38.1 + - - -
1F IU 3.7 28.7 - - + +
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Residues in contact with LYS 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196B THR* 2.8 24.6 + - - +
197B MET* 3.3 6.1 - - - +
199B ALA* 1.3 76.7 - - - +
201B TYR* 1.3 58.5 + - - +
203B SER 3.2 0.2 + - - -
204B LYS* 2.9 32.2 + - - +
205B GLY 3.6 3.6 + - - -
208B GLU* 3.0 30.7 - - - +
209B VAL* 4.2 5.8 - - + -
212B ALA* 3.8 21.8 - - + -
213B TYR* 3.9 24.0 - - + +
1F IU 2.7 39.4 + - + +
2F IU 3.6 14.1 + - - -
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Residues in contact with TYR 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B VAL* 4.2 14.1 - - + -
169B THR* 3.8 18.1 - - + +
172B LYS* 3.1 40.7 + - - -
197B MET 2.8 13.9 + - - +
198B VAL* 3.5 7.4 - - + +
200B LYS* 1.3 74.9 - - - +
202B VAL* 1.3 72.3 + - + +
205B GLY* 3.4 19.6 + - - -
206B TRP* 4.1 20.0 - + + -
209B VAL* 3.3 20.8 - - + +
229B LEU* 4.0 34.8 - - + -
232B THR* 4.1 3.0 + - - -
233B GLU* 3.0 37.7 + - + -
236B LYS* 4.8 2.8 + - - -
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Residues in contact with VAL 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B TYR* 6.2 0.9 - - + -
168B VAL* 3.3 36.3 - - + -
172B LYS* 5.6 2.5 - - - +
179B HIS* 3.4 29.8 - - + +
180B LYS* 3.5 30.8 - - - +
183B LEU* 4.2 12.8 - - + -
198B VAL* 2.8 32.0 + - + +
199B ALA* 3.7 4.0 - - - +
201B TYR* 1.3 77.8 - - + +
203B SER* 1.3 63.3 + - - +
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Residues in contact with SER 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180B LYS* 3.8 27.4 + - - +
183B LEU* 3.7 10.0 - - - +
184B ARG* 5.5 0.5 + - - -
199B ALA 2.7 21.0 + - - -
200B LYS 3.9 1.3 - - - -
202B VAL* 1.3 79.9 - - - +
204B LYS* 1.3 84.8 + - - +
1F IU 3.3 34.5 + - - -
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Residues in contact with LYS 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200B LYS 2.9 9.1 + - - -
201B TYR 4.2 0.2 - - - -
202B VAL 5.3 0.2 - - - -
203B SER* 1.3 82.3 + - - +
205B GLY* 1.3 58.0 + - - +
208B GLU* 3.3 43.7 - - + +
1F IU 3.1 55.5 + - + +
2F IU 4.7 6.0 - - - +
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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