Contacts of the helix formed by residues 172 - 180 (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 TYR 172 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98D PHE* 3.8 25.8 - + + -
148D ASP* 4.2 2.8 + - - -
149D PHE* 4.1 18.6 - + + -
150D LYS* 4.0 29.3 - - + +
164D VAL* 5.5 0.4 - - + -
166D VAL* 3.9 18.2 - - + +
168D GLU* 3.6 22.9 - - + -
169D PRO* 3.0 14.6 + - + +
171D HIS* 1.3 93.7 - + + +
173D LEU* 1.3 65.1 + - - +
174D GLU 3.3 2.7 - - - -
175D LYS* 3.3 8.9 + - + +
176D VAL* 3.0 26.2 + - + +
603D SAM 2.7 34.2 + - - -
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Residues in contact with LEU 173 (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 3.3 19.7 - - - +
170D TRP* 3.8 21.7 + - - +
171D HIS 3.7 0.8 - - - -
172D TYR* 1.3 77.1 - - - +
174D GLU* 1.3 57.8 + - - +
176D VAL* 3.9 4.5 - - + +
177D HIS* 2.9 31.7 + - - +
188D PHE* 3.7 32.5 - - + -
199D LEU* 3.9 10.1 - - + -
202D SER* 3.7 35.4 - - - +
203D ILE* 4.0 9.2 - - + -
206D TYR* 3.9 21.8 - - + -
207D PHE* 4.2 12.1 - - + -
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Residues in contact with GLU 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172D TYR 3.3 0.8 - - - -
173D LEU* 1.3 76.3 - - - +
175D LYS* 1.3 58.8 + - - +
177D HIS* 3.3 4.6 + - - +
178D LYS* 2.9 57.0 + - + +
206D TYR* 3.7 32.1 + - + +
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Residues in contact with LYS 175 (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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149D PHE* 2.8 43.3 + - + +
150D LYS* 3.1 23.6 + - - +
151D ASP 4.1 0.2 - - - -
152D ALA 2.6 29.8 + - - -
154D VAL* 4.1 19.1 - - - +
172D TYR* 3.3 7.8 + - + +
174D GLU* 1.3 75.1 - - - +
176D VAL* 1.3 60.7 + - - +
178D LYS* 3.3 9.6 + - + +
179D SER* 2.6 35.8 + - - +
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Residues in contact with VAL 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D LEU* 5.1 2.9 - - + -
98D PHE* 3.8 32.8 - - + -
149D PHE* 3.8 7.6 - - + -
162D ALA* 4.0 14.6 - - + -
164D VAL* 4.1 12.3 - - + -
172D TYR* 3.0 23.5 + - + +
173D LEU* 3.9 7.2 - - + +
175D LYS* 1.3 75.0 - - - +
177D HIS* 1.3 62.5 + - - +
179D SER* 3.1 16.8 + - - -
180D LEU* 3.3 14.6 + - - +
186D VAL* 3.8 29.4 - - + -
188D PHE* 5.5 1.8 - - + -
207D PHE* 4.0 6.1 - - + -
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Residues in contact with HIS 177 (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 2.9 19.7 + - - +
174D GLU* 3.3 6.8 + - - +
176D VAL* 1.3 78.1 - - - +
178D LYS* 1.3 61.2 + - - +
180D LEU* 3.4 5.5 + - - +
206D TYR* 3.2 45.1 + + + -
207D PHE* 3.9 13.4 - + + -
245D LYS* 2.8 59.2 + - + +
246D LEU 2.8 21.3 + - - -
248D THR* 3.2 33.8 - - + +
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Residues in contact with LYS 178 (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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156D GLU* 3.3 36.0 - - + +
157D GLY* 2.6 31.5 + - - -
174D GLU* 2.9 53.5 + - + +
175D LYS* 3.3 9.3 + - + +
177D HIS* 1.3 80.7 - - - +
179D SER* 1.3 51.8 + - - +
180D LEU 3.2 1.1 + - - +
245D LYS* 4.4 4.9 + - - +
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Residues in contact with SER 179 (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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96D LEU* 3.5 28.8 - - - +
149D PHE* 4.2 2.1 - - - -
154D VAL* 3.5 26.5 + - - +
155D PRO 3.7 5.5 - - - +
156D GLU* 4.2 1.6 - - - +
157D GLY 3.4 4.9 + - - +
158D ILE 3.1 7.1 + - - -
159D PHE* 3.0 28.4 + - - -
175D LYS* 2.6 25.0 + - - +
176D VAL* 3.1 4.8 + - - -
178D LYS* 1.3 77.0 - - - +
180D LEU* 1.3 58.9 + - - +
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Residues in contact with LEU 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D LEU* 5.5 0.9 - - + -
157D GLY* 3.3 12.0 - - - -
159D PHE* 3.5 17.9 - - + +
161D ALA* 3.4 37.7 - - - +
162D ALA* 3.6 7.4 - - + +
176D VAL* 3.3 17.7 - - + +
177D HIS* 3.8 6.7 - - - +
178D LYS 3.2 1.0 - - - -
179D SER* 1.3 80.2 - - - +
181D MET* 1.3 67.3 + - - +
182D GLU* 4.2 0.7 - - - +
184D ALA* 4.0 13.7 - - + +
186D VAL* 3.4 29.4 - - + -
207D PHE* 3.7 15.7 - - + -
245D LYS* 2.9 26.5 + - + -
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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