Contacts of the helix formed by residues 172 - 180 (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 TYR 172 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98C PHE* 3.8 26.9 - + + -
148C ASP* 4.1 10.8 + - - -
149C PHE* 4.2 12.1 - + + -
150C LYS* 4.1 20.2 - - + +
164C VAL* 5.4 0.9 - - + -
166C VAL* 4.0 22.2 - - + -
168C GLU* 3.6 23.3 - - + -
169C PRO* 2.9 10.1 + - + +
171C HIS* 1.3 92.5 - + + +
173C LEU* 1.3 65.3 + - - +
174C GLU 3.3 3.2 + - - -
175C LYS* 3.4 8.6 + - + +
176C VAL* 3.1 26.2 + - + +
604C SAM 3.0 35.1 + - - -
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Residues in contact with LEU 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169C PRO 3.6 2.2 + - - +
170C TRP* 3.7 23.7 + - - +
171C HIS 3.6 2.0 - - - -
172C TYR* 1.3 78.2 - - - +
174C GLU* 1.3 57.1 + - - +
176C VAL* 4.0 3.8 - - + +
177C HIS* 3.0 31.6 + - - +
188C PHE* 3.6 35.7 - - + -
199C LEU* 4.0 11.0 - - + -
202C SER* 3.5 27.1 - - - +
203C ILE* 3.9 19.7 - - + -
206C TYR* 3.7 24.9 - - + -
207C PHE* 3.9 18.8 - - + -
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Residues in contact with GLU 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171C HIS 5.4 1.0 + - - +
172C TYR 3.3 0.6 - - - -
173C LEU* 1.3 79.0 - - - +
175C LYS* 1.3 59.0 + - - +
177C HIS* 3.6 3.2 - - + +
178C LYS* 3.0 50.4 + - - +
206C TYR* 3.8 32.9 + - + +
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Residues in contact with LYS 175 (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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149C PHE* 2.8 50.6 + - + +
150C LYS* 3.0 24.9 + - + +
152C ALA 2.8 28.6 + - - -
154C VAL* 4.3 13.9 - - - +
172C TYR* 3.4 8.9 + - + +
174C GLU* 1.3 76.0 - - - +
176C VAL* 1.3 56.9 + - - +
178C LYS* 3.3 11.6 + - + +
179C SER* 2.6 39.9 + - - +
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Residues in contact with VAL 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C LEU* 4.6 2.2 - - + -
98C PHE* 3.9 31.6 - - + -
149C PHE* 3.9 9.2 - - + -
162C ALA* 3.8 28.0 - - + -
164C VAL* 4.2 9.0 - - + -
172C TYR* 3.1 20.0 + - + +
173C LEU* 4.0 5.2 - - + +
175C LYS* 1.3 75.9 - - - +
177C HIS* 1.3 61.6 + - - +
179C SER* 3.1 7.8 + - - -
180C LEU* 3.0 31.7 + - + +
186C VAL* 4.2 12.6 - - + -
188C PHE* 5.7 1.8 - - + -
207C PHE* 4.2 5.8 - - + -
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Residues in contact with HIS 177 (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 3.0 19.8 + - - +
174C GLU* 3.6 5.6 - - + +
176C VAL* 1.3 78.6 - - - +
178C LYS* 1.3 64.4 + - + +
180C LEU* 3.4 4.3 + - - -
206C TYR* 3.1 42.2 + + + +
207C PHE* 3.9 14.9 - - + -
245C LYS* 2.8 54.2 + - + +
246C LEU 2.9 27.8 + - - -
248C THR* 3.2 33.4 + - + +
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Residues in contact with LYS 178 (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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156C GLU* 3.2 51.1 + - + +
157C GLY* 2.9 20.4 + - - -
174C GLU* 3.0 41.5 + - - +
175C LYS* 3.4 16.3 - - + +
177C HIS* 1.3 85.1 - - + +
179C SER* 1.3 58.6 + - - +
180C LEU 3.5 3.6 + - - +
245C LYS* 4.3 4.4 + - - +
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Residues in contact with SER 179 (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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96C LEU* 4.4 6.3 - - - -
149C PHE* 4.0 6.8 - - - -
154C VAL* 3.7 21.8 + - - +
155C PRO 4.2 4.3 - - - -
156C GLU* 4.4 0.9 - - - +
157C GLY 3.7 5.2 - - - +
158C ILE* 3.0 22.7 + - - +
159C PHE* 3.1 30.6 + - - -
175C LYS* 2.6 27.5 + - - +
176C VAL* 3.1 7.1 + - - -
178C LYS* 1.3 76.0 - - - +
180C LEU* 1.3 58.0 + - - +
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Residues in contact with LEU 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157C GLY* 3.4 11.3 - - - -
159C PHE* 3.5 18.2 - - + +
161C ALA* 3.5 35.9 - - - +
162C ALA* 3.7 7.4 - - + +
176C VAL* 3.0 24.2 + - + +
177C HIS* 3.6 6.2 - - - +
178C LYS 3.3 1.1 - - - +
179C SER* 1.3 79.7 - - - +
181C MET* 1.3 65.5 + - - +
182C GLU* 4.8 0.3 - - - +
184C ALA* 3.7 17.5 - - + +
185C PRO 4.0 0.7 - - - +
186C VAL* 4.2 7.9 - - + -
207C PHE* 3.5 34.3 - - + -
245C LYS* 2.9 25.6 + - + -
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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