Contacts of the helix formed by residues 192 - 203 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190A LEU 4.1 0.2 - - - +
191A PRO* 1.3 86.0 - - + +
193A ALA* 1.3 64.0 + - - +
194A ASN* 3.8 11.6 + - - +
195A GLN* 2.9 39.6 + - - +
196A VAL* 3.4 22.9 + - - +
239A TYR* 3.8 3.4 - - - -
225C GLU 4.7 1.6 + - - -
226C ARG* 4.0 29.4 - - + -
227C PHE 3.6 11.0 - - - -
228C ARG* 3.9 14.6 - - - +
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Residues in contact with ALA 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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192A THR* 1.3 68.5 - - - +
194A ASN* 1.3 64.8 + - - +
196A VAL* 3.1 3.8 + - - +
197A ILE* 3.0 28.5 + - - +
239A TYR* 3.5 19.8 - - - +
227B PHE* 4.0 21.9 - - + -
227C PHE* 2.8 37.5 + - + +
193D ALA* 4.2 10.8 - - + -
197D ILE* 4.6 1.8 - - + -
239D TYR* 6.0 0.2 - - - +
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Residues in contact with ASN 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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192A THR* 3.3 4.3 - - - +
193A ALA* 1.3 74.9 - - - +
195A GLN* 1.3 62.9 + - + +
197A ILE* 3.4 6.0 + - - +
198A LYS* 3.1 43.6 + - - +
224C SER 2.8 25.7 + - - -
225C GLU* 3.2 26.3 + - - +
226C ARG* 3.6 1.2 - - - -
227C PHE* 2.7 31.5 + - - +
197D ILE* 3.6 26.6 - - - +
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Residues in contact with GLN 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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166A VAL 4.3 0.4 + - - -
167A ARG* 2.8 48.6 + - + +
170A TRP* 3.4 22.1 - - + -
190A LEU* 3.7 24.5 - - + +
191A PRO* 3.4 20.5 - - - +
192A THR* 2.9 41.6 + - - +
193A ALA 3.3 0.4 - - - -
194A ASN* 1.3 80.0 - - + +
196A VAL* 1.3 56.8 + - - +
198A LYS* 3.3 1.6 + - - +
199A LEU* 3.0 27.2 + - - +
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Residues in contact with VAL 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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190A LEU* 3.9 20.4 - - + -
192A THR 3.5 15.5 - - - +
193A ALA 3.1 7.0 + - - +
195A GLN* 1.3 72.3 - - - +
197A ILE* 1.3 60.8 + - - +
199A LEU* 3.3 2.1 + - - +
200A LEU* 2.8 42.8 + - + +
212A VAL* 4.3 3.6 - - + -
239A TYR* 3.6 31.6 - - + -
241A VAL* 4.2 15.7 - - + -
227B PHE* 3.6 33.0 - - + -
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Residues in contact with ILE 197 (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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193A ALA 3.0 19.1 + - - +
194A ASN* 3.6 7.6 - - - +
196A VAL* 1.3 76.4 - - - +
198A LYS* 1.3 63.7 + - + +
200A LEU* 3.5 4.2 + - - -
201A GLU* 3.3 19.3 + - - +
224B SER* 2.6 41.9 + - - +
227B PHE* 3.7 23.3 - - + -
193D ALA* 4.6 1.1 - - + -
194D ASN* 3.5 33.2 - - - +
197D ILE* 3.7 26.9 - - + -
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Residues in contact with LYS 198 (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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170A TRP* 3.6 41.0 - - + -
194A ASN* 3.1 38.6 + - - +
195A GLN* 5.3 0.6 - - - +
196A VAL 3.2 0.2 - - - -
197A ILE* 1.3 76.4 - - + +
199A LEU* 1.3 66.5 + - - +
201A GLU* 3.3 28.4 - - - +
202A SER* 3.2 14.1 + - - -
225C GLU* 4.6 12.1 + - - -
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Residues in contact with LEU 199 (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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169A PRO* 4.1 14.6 - - + -
170A TRP* 3.7 10.7 - - + +
173A LEU* 4.0 33.7 - - + -
188A PHE* 3.5 38.1 - - + -
190A LEU* 3.6 20.4 - - + -
195A GLN 3.0 17.2 + - - +
196A VAL 3.7 3.4 - - - +
198A LYS* 1.3 75.4 - - - +
200A LEU* 1.3 59.2 + - + +
202A SER* 3.0 7.2 + - - +
203A ILE* 2.9 41.4 + - + +
241A VAL* 4.0 15.3 - - + -
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Residues in contact with LEU 200 (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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196A VAL* 2.8 37.4 + - + +
197A ILE* 3.8 5.2 - - - +
198A LYS 3.3 0.2 - - - -
199A LEU* 1.3 76.6 - - + +
201A GLU* 1.3 60.3 + - - +
203A ILE* 3.5 18.4 + - + +
204A GLU* 4.2 6.1 + - - +
210A LEU* 4.1 21.4 - - + +
212A VAL* 4.4 11.4 - - + -
241A VAL* 4.6 13.2 - - + -
222B THR* 3.9 41.3 - - + +
223B ILE 4.5 0.4 - - - +
224B SER* 4.0 21.4 - - - +
227B PHE* 4.0 16.8 - - + -
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Residues in contact with GLU 201 (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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197A ILE* 3.3 20.2 + - - +
198A LYS* 3.3 28.8 - - - +
200A LEU* 1.3 78.6 - - - +
202A SER* 1.3 57.9 + - - +
204A GLU* 4.4 13.7 - - - +
224B SER* 3.3 21.8 + - - +
225B GLU* 5.9 1.7 - - - +
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Residues in contact with SER 202 (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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170A TRP* 3.3 28.9 - - - +
173A LEU* 3.8 8.2 - - - +
198A LYS 3.2 12.6 + - - -
199A LEU* 3.0 12.0 + - - -
201A GLU* 1.3 75.9 - - - +
203A ILE* 1.3 59.5 + - - +
204A GLU* 3.3 6.9 + - - -
205A ASN* 4.6 1.2 + - - +
206A TYR* 3.7 19.2 - - - -
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Residues in contact with ILE 203 (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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173A LEU* 4.1 8.5 - - + -
186A VAL* 5.3 0.7 - - + -
188A PHE* 3.7 32.3 - - + -
199A LEU* 2.9 27.9 + - + +
200A LEU* 3.5 22.0 - - + +
202A SER* 1.3 75.7 - - - +
204A GLU* 1.3 65.8 + - - +
205A ASN 3.3 1.8 - - - -
206A TYR* 3.0 15.8 + - - -
207A PHE* 3.1 43.9 + - + +
210A LEU* 3.9 35.4 - - + -
241A VAL* 4.9 3.8 - - + -
243A GLY* 5.8 0.4 - - - -
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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
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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