Contacts of the helix formed by residues 172 - 180 (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 TYR 172 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A PHE* 3.8 26.0 - + + -
148A ASP* 4.0 11.8 + - - -
149A PHE* 4.0 18.4 - + + -
150A LYS* 4.1 20.0 - - + +
164A VAL* 5.7 0.4 - - + -
166A VAL* 4.1 13.2 - - + -
168A GLU* 3.6 18.8 - - + -
169A PRO* 3.0 18.8 + - + +
171A HIS* 1.3 92.5 - + + +
173A LEU* 1.3 64.9 - - - +
174A GLU 3.4 2.9 - - - -
175A LYS* 3.4 8.3 + - + +
176A VAL* 3.0 25.2 + - + +
601A SAM 3.0 33.8 + - - -
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Residues in contact with LEU 173 (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 4.0 7.9 - - - +
170A TRP* 3.6 26.7 - - - +
171A HIS 3.5 2.0 - - - -
172A TYR* 1.3 77.3 - - - +
174A GLU* 1.3 57.2 + - - +
176A VAL* 3.9 4.9 - - + +
177A HIS* 2.9 32.2 + - - +
188A PHE* 3.7 36.3 - - + -
199A LEU* 4.0 8.1 - - + -
202A SER* 3.8 35.2 - - - +
203A ILE* 4.1 9.0 - - + -
206A TYR* 3.9 26.1 - - + -
207A PHE* 4.3 11.7 - - + -
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Residues in contact with GLU 174 (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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171A HIS 5.1 2.1 + - - +
172A TYR 3.4 0.6 - - - -
173A LEU* 1.3 78.8 - - - +
175A LYS* 1.3 58.7 + - - +
177A HIS* 3.3 3.6 - - + +
178A LYS* 3.0 61.4 + - + +
206A TYR* 3.5 29.4 + - + +
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Residues in contact with LYS 175 (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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149A PHE* 2.7 46.7 + - + +
150A LYS* 3.2 22.9 + - - +
151A ASP 4.1 0.2 - - - -
152A ALA 2.6 29.5 + - - -
154A VAL* 4.1 19.1 - - - +
172A TYR* 3.4 8.2 + - + +
174A GLU* 1.3 76.2 - - - +
176A VAL* 1.3 60.5 + - - +
178A LYS* 3.4 8.5 + - + +
179A SER* 2.6 36.0 + - - +
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Residues in contact with VAL 176 (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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96A LEU* 4.6 2.2 - - + -
98A PHE* 3.7 21.3 - - + -
149A PHE* 3.7 22.4 - - + -
162A ALA* 3.7 29.6 - - + -
164A VAL* 4.2 9.0 - - + -
172A TYR* 3.0 23.4 + - + +
173A LEU* 3.9 7.4 - - + +
175A LYS* 1.3 74.1 - - - +
177A HIS* 1.3 64.0 + - - +
179A SER* 3.2 14.1 + - - -
180A LEU* 3.3 22.2 + - + +
186A VAL* 4.1 13.2 - - + -
188A PHE* 5.7 0.7 - - + -
207A PHE* 4.3 4.9 - - + -
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Residues in contact with HIS 177 (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 2.9 19.3 + - - +
174A GLU 3.3 6.7 - - - +
176A VAL* 1.3 76.8 - - - +
178A LYS* 1.3 72.8 + - + +
180A LEU* 3.3 6.9 + - - -
206A TYR* 3.3 42.5 + + + +
207A PHE* 4.0 13.9 - - + -
245A LYS* 2.8 48.1 + - + +
246A LEU 2.9 28.5 + - - -
248A THR* 3.5 32.4 + - + +
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Residues in contact with LYS 178 (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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156A GLU* 3.4 39.2 - - + +
157A GLY* 2.8 28.8 + - - -
174A GLU* 3.0 48.5 + - + +
175A LYS* 3.8 8.5 - - + +
176A VAL 3.4 0.2 - - - -
177A HIS* 1.3 86.7 - - + +
179A SER* 1.3 52.3 + - - +
180A LEU 3.3 2.3 + - - +
245A LYS* 4.4 5.1 + - - +
248A THR* 5.6 3.2 + - - -
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Residues in contact with SER 179 (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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96A LEU* 4.1 11.4 - - - -
149A PHE* 4.3 4.5 - - - -
154A VAL* 3.6 23.6 + - - +
155A PRO 4.0 5.1 + - - -
156A GLU* 4.2 1.6 - - - +
157A GLY 3.5 4.5 - - - +
158A ILE 3.2 8.5 + - - -
159A PHE* 3.0 43.0 + - - -
175A LYS* 2.6 26.9 + - - +
176A VAL* 3.2 6.3 + - - -
178A LYS* 1.3 76.6 - - - +
180A LEU* 1.3 58.4 + - - +
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Residues in contact with LEU 180 (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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96A LEU* 5.9 0.4 - - + -
157A GLY* 3.7 9.7 - - - -
159A PHE* 3.5 17.5 - - + +
161A ALA* 3.5 37.2 - - - +
162A ALA* 3.7 5.8 - - + +
176A VAL* 3.4 21.3 - - + +
177A HIS* 3.7 7.6 - - - +
178A LYS 3.2 1.2 - - - -
179A SER* 1.3 80.0 - - - +
181A MET* 1.3 62.3 + - - +
182A GLU* 4.3 0.5 - - - +
184A ALA* 3.7 16.6 - - + +
185A PRO 4.3 5.2 - - - +
186A VAL* 4.3 3.1 - - + -
207A PHE* 3.6 32.5 - - + -
245A LYS* 2.6 33.1 + - + -
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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