Contacts of the helix formed by residues 192 - 204 (chain B) in PDB entry 2YVL
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 192 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190B LEU 4.2 0.5 - - - +
191B PRO* 1.3 84.8 - - + +
193B ALA* 1.3 62.8 + - - +
194B ASN* 3.8 12.0 + - - +
195B GLN* 2.7 39.4 + - - +
196B VAL* 3.3 22.3 + - - +
239B TYR* 3.8 4.7 - - - -
225D GLU 4.8 1.0 + - - -
226D ARG* 3.9 34.4 - - + +
227D PHE 3.6 9.4 - - - -
228D ARG* 4.0 12.3 - - + +
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Residues in contact with ALA 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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227A PHE* 3.8 24.2 - - + -
192B THR* 1.3 68.5 - - - +
194B ASN* 1.3 59.9 - - - +
196B VAL* 3.3 3.5 + - - +
197B ILE* 2.8 35.8 + - - +
239B TYR* 3.6 17.2 - - - +
193C ALA* 4.1 18.2 - - + -
197C ILE* 4.4 3.1 - - + -
227D PHE* 3.0 25.2 + - + +
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Residues in contact with ASN 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B TRP* 5.6 0.2 - - - -
192B THR* 3.9 5.1 - - - +
193B ALA* 1.3 77.2 - - - +
195B GLN* 1.3 60.6 + - + +
197B ILE* 3.7 5.5 - - - +
198B LYS* 3.1 23.9 + - - +
197C ILE* 3.7 24.5 - - - +
224D SER 2.9 22.6 + - - -
225D GLU* 3.1 23.8 + - - +
226D ARG* 3.6 1.0 - - - -
227D PHE* 2.8 32.9 + - - +
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Residues in contact with GLN 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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166B VAL 4.3 0.2 + - - -
167B ARG* 2.9 41.8 + - - +
170B TRP* 3.4 21.4 - - + -
190B LEU* 3.7 24.1 - - + +
191B PRO* 3.5 19.1 - - - +
192B THR* 2.7 43.2 + - - +
193B ALA 3.2 0.6 - - - -
194B ASN* 1.3 78.6 - - + +
196B VAL* 1.3 60.2 + - - +
198B LYS 3.3 0.9 + - - -
199B LEU* 2.9 27.7 + - - +
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Residues in contact with VAL 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A PHE* 3.5 31.9 - - + -
190B LEU* 3.8 19.5 - - + -
192B THR 3.3 14.3 + - - +
193B ALA* 3.3 7.5 + - - +
195B GLN* 1.3 73.9 - - - +
197B ILE* 1.3 64.4 + - - +
199B LEU* 3.3 3.1 + - - +
200B LEU* 2.9 35.0 + - + +
212B VAL* 4.2 13.5 - - + -
239B TYR* 3.6 33.0 - - + -
241B VAL* 4.3 7.4 - - + -
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Residues in contact with ILE 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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224A SER* 2.7 42.3 + - - +
227A PHE* 3.7 28.3 - - + -
193B ALA 2.8 25.3 + - - +
194B ASN* 3.7 6.3 - - - +
196B VAL* 1.3 73.1 - - - +
198B LYS* 1.3 56.5 + - - +
200B LEU* 3.3 5.2 + - - +
201B GLU* 3.1 27.2 + - - +
193C ALA* 4.6 0.9 - - + -
194C ASN* 3.6 28.5 - - - +
197C ILE* 3.6 27.6 - - + -
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Residues in contact with LYS 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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170B TRP* 3.5 42.0 - - + +
194B ASN 3.1 17.3 + - - +
195B GLN 3.7 4.7 - - - +
197B ILE* 1.3 75.3 - - - +
199B LEU* 1.3 62.2 + - - +
201B GLU* 3.0 31.7 + - + +
202B SER* 2.8 33.5 + - - +
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Residues in contact with LEU 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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169B PRO* 4.3 2.0 - - + -
170B TRP* 3.8 23.4 - - + +
173B LEU* 4.0 33.4 - - + -
188B PHE* 3.6 39.3 - - + -
190B LEU* 3.8 20.6 - - + -
195B GLN 2.9 16.4 + - - +
196B VAL 3.7 3.8 - - - +
198B LYS* 1.3 75.4 - - - +
200B LEU* 1.3 59.3 + - + +
202B SER* 3.0 3.9 + - - -
203B ILE* 2.9 42.3 + - + +
241B VAL* 4.0 16.6 - - + -
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Residues in contact with LEU 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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222A THR* 3.8 45.1 - - + +
224A SER* 3.9 23.1 - - - +
227A PHE* 4.0 15.3 - - + -
196B VAL* 2.9 38.5 + - + +
197B ILE* 3.6 4.7 - - - +
199B LEU* 1.3 76.9 - - + +
201B GLU* 1.3 61.9 + - - +
202B SER 3.4 0.5 + - - -
203B ILE* 3.8 16.6 + - + +
204B GLU* 4.4 6.6 + - - +
210B LEU* 3.9 22.1 - - + +
212B VAL* 4.5 7.9 - - + -
241B VAL* 4.9 10.3 - - + -
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Residues in contact with GLU 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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224A SER* 2.8 29.0 + - - +
225A GLU* 5.5 5.3 - - + +
197B ILE* 3.1 22.1 + - - +
198B LYS* 3.0 44.8 + - + +
200B LEU* 1.3 76.9 - - - +
202B SER* 1.3 60.0 + - - +
203B ILE 3.6 0.2 - - - -
204B GLU* 4.2 17.0 - - - +
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Residues in contact with SER 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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170B TRP* 3.5 31.1 - - - +
173B LEU* 3.6 13.8 - - - +
198B LYS* 2.8 26.2 + - - +
199B LEU 3.0 5.2 + - - -
201B GLU* 1.3 79.2 - - - +
203B ILE* 1.3 60.8 + - - +
204B GLU* 3.4 4.3 + - - +
205B ASN* 4.6 1.9 + - - +
206B TYR* 3.9 13.0 - - - -
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Residues in contact with ILE 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B LEU* 4.0 11.9 - - + -
186B VAL* 5.3 0.7 - - + -
188B PHE* 3.7 33.0 - - + -
199B LEU* 2.9 26.9 + - + +
200B LEU* 3.8 13.5 - - + +
202B SER* 1.3 76.3 - - - +
204B GLU* 1.3 62.3 + - - +
205B ASN 3.2 2.5 - - - -
206B TYR* 2.9 22.1 + - - -
207B PHE* 3.1 43.0 + - + +
210B LEU* 3.7 39.3 - - + -
241B VAL* 5.1 4.3 - - + -
242B PHE 6.4 0.2 - - - -
243B GLY* 5.9 0.2 - - - -
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Residues in contact with GLU 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B LEU 4.4 6.1 + - - +
201B GLU 4.2 15.3 - - - +
202B SER 3.4 2.2 - - - +
203B ILE* 1.3 82.7 - - - +
205B ASN* 1.3 80.8 + - - +
207B PHE 4.3 2.8 - - - +
210B LEU* 6.0 1.1 - - - -
246B LEU* 3.4 18.2 - - - +
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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