Contacts of the helix formed by residues 192 - 203 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225A GLU 4.8 0.7 + - - -
226A ARG* 4.0 33.0 - - + +
227A PHE 3.5 9.2 - - - -
228A ARG* 4.2 10.5 - - - +
190C LEU 4.2 0.5 - - - +
191C PRO* 1.3 86.7 - - + +
193C ALA* 1.3 63.7 + - - +
194C ASN* 3.6 12.2 + - - +
195C GLN* 2.9 39.9 + - - +
196C VAL* 3.3 22.0 + - - +
239C TYR* 3.8 2.9 - - - -
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Residues in contact with ALA 193 (chain C).
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* 2.8 35.2 + - + +
193B ALA* 4.1 11.9 - - + -
197B ILE* 4.6 1.3 - - + -
192C THR* 1.3 69.8 - - - +
194C ASN* 1.3 59.2 + - - +
196C VAL* 3.2 2.9 + - - +
197C ILE* 2.9 36.1 + - + +
239C TYR* 3.5 19.9 - - - +
227D PHE* 4.0 20.6 - - + -
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Residues in contact with ASN 194 (chain C).
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 25.3 + - - -
225A GLU* 3.3 23.5 + - - +
226A ARG* 3.6 1.0 - - - -
227A PHE* 2.7 32.2 + - - +
197B ILE* 3.6 24.9 - - - +
192C THR* 3.2 5.0 - - - +
193C ALA* 1.3 77.9 - - - +
195C GLN* 1.3 62.2 + - + +
197C ILE* 3.4 5.8 + - - +
198C LYS* 3.0 24.3 + - - +
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Residues in contact with GLN 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166C VAL 4.4 0.8 + - - -
167C ARG* 2.9 42.6 + - - +
170C TRP* 3.6 18.5 - - + -
190C LEU* 3.7 25.9 - - + +
191C PRO* 3.3 19.7 - - - +
192C THR* 2.9 41.2 + - - +
193C ALA 3.3 0.2 - - - -
194C ASN* 1.3 75.5 - - + +
196C VAL* 1.3 62.0 + - - +
198C LYS 3.3 0.7 + - - -
199C LEU* 2.9 30.1 + - - +
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Residues in contact with VAL 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190C LEU* 3.8 19.5 - - + -
192C THR 3.3 14.1 + - - +
193C ALA 3.2 7.0 + - - +
195C GLN* 1.3 75.8 - - - +
197C ILE* 1.3 57.6 + - - +
199C LEU* 3.2 2.8 + - - +
200C LEU* 2.9 42.0 + - + +
212C VAL* 4.3 11.4 - - + -
239C TYR* 3.6 33.7 - - + -
241C VAL* 4.9 8.3 - - + -
227D PHE* 3.5 32.1 - - + -
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Residues in contact with ILE 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193B ALA* 4.4 1.1 - - + -
194B ASN* 3.7 29.8 - - - +
197B ILE* 3.6 27.8 - - + -
193C ALA 2.9 22.2 + - - +
194C ASN* 3.7 5.8 - - - +
196C VAL* 1.3 74.4 - - - +
198C LYS* 1.3 63.2 + - - +
200C LEU* 3.3 10.6 + - - +
201C GLU* 3.2 13.3 - - - +
224D SER* 2.7 43.3 + - - +
227D PHE* 3.7 28.0 - - + -
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Residues in contact with LYS 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170C TRP* 3.5 58.0 - - + +
194C ASN 3.0 17.3 + - - +
195C GLN 3.7 3.4 - - - +
197C ILE* 1.3 74.2 - - - +
199C LEU* 1.3 64.8 + - - +
201C GLU* 3.2 43.8 + - - +
202C SER* 3.9 7.2 + - - -
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Residues in contact with LEU 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169C PRO* 4.4 4.3 - - + -
170C TRP* 3.8 23.9 - - + +
173C LEU* 4.0 34.8 - - + -
188C PHE* 3.6 37.2 - - + -
190C LEU* 3.7 20.9 - - + -
195C GLN 2.9 20.2 + - - +
196C VAL* 3.7 4.0 - - - +
198C LYS* 1.3 72.7 - - - +
200C LEU* 1.3 59.8 + - + +
201C GLU 3.2 0.7 + - - -
202C SER* 3.3 4.3 + - - -
203C ILE* 3.0 37.9 + - + +
241C VAL* 3.9 10.8 - - + -
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Residues in contact with LEU 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196C VAL* 2.9 37.4 + - + +
197C ILE* 3.7 5.6 - - - +
198C LYS 3.2 0.4 - - - -
199C LEU* 1.3 76.7 - - + +
201C GLU* 1.3 61.0 + - - +
202C SER 3.3 0.4 + - - -
203C ILE* 4.0 15.4 + - + +
204C GLU* 5.0 9.0 + - - +
210C LEU* 4.1 21.1 - - + -
212C VAL* 4.7 10.3 - - + -
241C VAL* 5.1 10.1 - - + -
221D LYS 4.4 0.2 - - - +
222D THR* 3.9 39.2 - - + +
223D ILE 4.3 0.2 - - - -
224D SER* 3.7 25.3 + - - +
227D PHE* 4.0 16.4 - - + -
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Residues in contact with GLU 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197C ILE* 3.2 19.2 - - - +
198C LYS* 3.4 34.0 + - + +
199C LEU 3.2 0.6 - - - -
200C LEU* 1.3 78.3 - - - +
202C SER* 1.3 58.2 + - - +
204C GLU* 5.4 0.9 + - - +
205C ASN* 5.2 1.2 + - - +
224D SER* 3.0 22.2 + - - +
225D GLU* 5.8 2.0 - - - +
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Residues in contact with SER 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C TRP* 3.8 16.1 - - - +
173C LEU* 3.5 18.5 - - - +
198C LYS* 3.9 5.3 + - - -
199C LEU 3.3 5.1 + - - -
201C GLU* 1.3 81.2 - - - +
203C ILE* 1.3 65.6 + - - +
204C GLU 3.2 4.2 + - - -
205C ASN* 3.2 34.9 + - - +
206C TYR* 4.0 6.4 - - - -
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Residues in contact with ILE 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173C LEU* 3.9 12.8 - - + -
186C VAL* 5.4 0.4 - - + -
188C PHE* 3.5 32.5 - - + -
199C LEU* 3.0 34.5 + - + +
200C LEU* 4.0 17.3 - - + +
201C GLU 3.8 0.4 - - - -
202C SER* 1.3 77.2 + - - +
204C GLU* 1.3 59.2 + - + +
205C ASN 3.1 0.2 - - - -
206C TYR* 2.8 8.0 + - - +
207C PHE* 2.8 47.4 + - + -
210C LEU* 3.7 38.6 - - + -
241C VAL* 4.2 7.6 - - + -
242C PHE 5.8 0.2 - - - +
243C GLY* 5.9 0.7 - - - -
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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