Contacts of the helix formed by residues 192 - 203 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225B GLU 4.5 2.0 - - - +
226B ARG* 3.6 29.0 + - + +
227B PHE 3.8 3.5 + - - -
228B ARG* 4.1 7.2 - - - +
190D LEU 3.2 0.6 - - - +
191D PRO* 1.3 82.4 - - - +
193D ALA* 1.3 60.0 + - - +
194D ASN* 3.2 35.7 - - + +
195D GLN* 3.1 31.5 + - + +
196D VAL* 3.4 22.9 + - - +
239D TYR* 3.7 4.0 - - - -
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Residues in contact with ALA 193 (chain D).
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* 4.2 10.1 - - + -
197A ILE* 4.6 2.2 - - + -
227B PHE* 2.8 38.5 + - + +
227C PHE* 4.1 17.0 - - + -
192D THR* 1.3 70.1 - - - +
194D ASN* 1.3 59.3 + - - +
196D VAL* 3.2 2.2 + - - +
197D ILE* 2.9 35.2 + - - +
239D TYR* 3.5 21.8 - - - +
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Residues in contact with ASN 194 (chain D).
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* 3.5 27.0 - - - +
224B SER 2.8 24.0 + - - -
225B GLU* 3.5 19.8 - - - +
227B PHE* 2.8 29.1 + - - +
192D THR* 3.2 10.2 - - + +
193D ALA* 1.3 73.1 - - - +
195D GLN* 1.3 59.1 + - + +
197D ILE* 3.5 5.4 + - - +
198D LYS* 2.9 30.2 + - - +
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Residues in contact with GLN 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166D VAL 4.3 0.4 + - - -
167D ARG* 2.8 41.4 + - - +
170D TRP* 3.4 19.9 - - + -
190D LEU* 3.5 25.5 - - + +
191D PRO* 3.3 18.3 - - - +
192D THR* 3.1 38.6 + - + +
193D ALA 3.3 0.6 - - - -
194D ASN* 1.3 76.4 - - + +
196D VAL* 1.3 60.4 + - - +
198D LYS 3.4 0.3 + - - -
199D LEU* 2.8 31.2 + - - +
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Residues in contact with VAL 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227C PHE* 3.5 33.0 - - + -
190D LEU* 3.8 20.2 - - + -
192D THR 3.4 14.7 + - - +
193D ALA 3.2 5.7 + - - +
195D GLN* 1.3 72.6 - - - +
197D ILE* 1.3 61.0 + - - +
199D LEU* 3.1 2.9 + - - +
200D LEU* 2.8 39.9 + - + +
212D VAL* 4.3 4.5 - - + -
239D TYR* 3.6 31.9 - - + -
241D VAL* 4.2 17.5 - - + -
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Residues in contact with ILE 197 (chain D).
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* 4.6 0.9 - - + -
194A ASN* 3.6 30.5 - - - +
197A ILE* 3.7 28.3 - - + -
224C SER* 2.9 39.9 + - - +
227C PHE* 3.7 27.6 - - + -
193D ALA 2.9 21.7 + - - +
194D ASN* 3.7 4.7 - - - +
196D VAL* 1.3 75.8 - - - +
198D LYS* 1.3 63.8 + - - +
200D LEU* 3.3 5.2 + - - -
201D GLU* 3.1 26.3 + - - +
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Residues in contact with LYS 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170D TRP* 3.5 52.3 - - + +
171D HIS* 6.0 0.2 - - - -
194D ASN 2.9 19.1 + - - +
195D GLN 3.6 4.3 - - - +
197D ILE* 1.3 75.4 - - - +
199D LEU* 1.3 61.5 + - - +
201D GLU* 3.4 28.2 + - - +
202D SER* 2.9 32.4 + - - -
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Residues in contact with LEU 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169D PRO* 4.1 14.6 - - + -
170D TRP* 3.9 11.8 - - + +
173D LEU* 3.9 35.0 - - + -
188D PHE* 3.6 38.6 - - + -
190D LEU* 3.7 20.6 - - + -
195D GLN 2.8 19.7 + - - +
196D VAL 3.6 3.6 - - - +
198D LYS* 1.3 73.1 - - - +
200D LEU* 1.3 59.0 + - + +
202D SER* 3.0 3.3 + - - -
203D ILE* 2.9 39.4 + - + +
241D VAL* 4.1 15.0 - - + -
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Residues in contact with LEU 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222C THR* 3.7 49.6 - - + +
224C SER* 3.8 26.3 - - - +
227C PHE* 4.0 23.6 - - + -
196D VAL* 2.8 27.3 + - + +
197D ILE* 3.3 6.0 + - - +
199D LEU* 1.3 76.1 - - + +
201D GLU* 1.3 59.7 + - - +
202D SER 3.5 0.2 + - - -
203D ILE* 3.9 16.2 + - + +
204D GLU* 4.5 8.1 + - - +
210D LEU* 4.1 16.8 - - + -
212D VAL* 4.7 7.0 - - + -
241D VAL* 5.1 9.4 - - + -
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Residues in contact with GLU 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224C SER* 2.8 26.6 + - - +
225C GLU* 4.8 13.9 - - + +
197D ILE* 3.1 23.3 + - - +
198D LYS* 3.5 32.8 - - - +
199D LEU 3.2 0.2 - - - -
200D LEU* 1.3 78.5 - - - +
202D SER* 1.3 59.2 + - - +
204D GLU* 4.5 14.5 - - - +
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Residues in contact with SER 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170D TRP* 3.7 27.9 - - - +
173D LEU* 3.7 12.5 - - - +
198D LYS* 2.9 29.8 + - - -
199D LEU 3.0 3.4 + - - -
201D GLU* 1.3 79.0 - - - +
203D ILE* 1.3 60.9 + - - +
204D GLU* 3.4 5.8 + - - +
205D ASN* 4.4 3.6 + - - +
206D TYR* 3.9 13.9 - - - -
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Residues in contact with ILE 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173D LEU* 4.0 12.8 - - + -
188D PHE* 3.8 30.7 - - + -
199D LEU* 2.9 27.5 + - + +
200D LEU* 3.9 16.2 - - + +
201D GLU 3.7 0.2 - - - -
202D SER* 1.3 74.5 - - - +
204D GLU* 1.3 61.4 + - + +
205D ASN 3.2 2.7 - - - -
206D TYR* 2.9 21.9 + - - -
207D PHE* 3.1 37.3 + - + +
210D LEU* 3.8 43.3 - - + -
241D VAL* 4.8 5.4 - - + -
243D GLY* 5.9 0.9 - - - +
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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