Contacts of the helix formed by residues 169 - 179 (chain A) in PDB entry 2Y96
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 169 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163A MET* 4.1 1.6 - - - -
167A ASP 4.0 1.3 + - - +
168A MET* 1.3 76.7 - - - +
170A LEU* 1.3 64.2 + - - +
171A VAL* 3.5 1.6 + - - +
172A ASP* 3.0 37.1 + - - +
173A ALA* 3.0 21.5 + - - +
197A ASP* 3.6 6.1 - - - -
201A VAL* 4.9 7.0 - - + -
33B TYR* 3.5 48.9 - - + -
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Residues in contact with LEU 170 (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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159A LEU* 4.9 4.3 - - + -
163A MET* 3.9 20.2 - - + +
169A THR* 1.3 69.8 - - - +
171A VAL* 1.3 56.9 + - - +
173A ALA* 3.2 2.8 + - - +
174A ILE* 2.9 56.0 + - + +
190A LEU* 4.7 1.6 - - + +
193A LEU* 3.9 53.4 - - + +
194A ARG* 3.9 20.6 - - + +
197A ASP* 2.9 29.0 + - + +
33B TYR* 3.7 1.5 + - - +
35B THR* 4.4 3.6 - - + -
41B LEU* 4.0 17.3 - - + -
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Residues in contact with VAL 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A THR* 3.2 7.0 + - - +
170A LEU* 1.3 76.7 - - - +
172A ASP* 1.3 62.4 + - - +
174A ILE* 3.3 9.2 + - - +
175A GLN* 2.9 52.2 + - + +
33B TYR* 3.6 20.5 + - + +
36B PRO* 3.5 32.8 - - + -
41B LEU* 4.7 1.3 - - + -
44B LEU* 4.0 17.9 - - + -
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Residues in contact with ASP 172 (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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167A ASP 4.9 1.6 - - - +
168A MET* 3.9 22.1 - - + +
169A THR* 3.0 42.3 + - - +
171A VAL* 1.3 80.2 - - - +
173A ALA* 1.3 57.8 + - - +
175A GLN* 3.4 8.2 + - - +
176A GLN* 3.0 28.8 + - - +
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Residues in contact with ALA 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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159A LEU* 3.3 39.9 - - + +
162A LEU* 4.1 12.1 - - + -
163A MET* 4.0 9.2 - - + -
168A MET* 3.8 12.5 - - + -
169A THR 3.0 16.0 + - - +
170A LEU* 3.5 5.4 - - - +
172A ASP* 1.3 75.7 - - - +
174A ILE* 1.3 64.2 + - - +
176A GLN* 3.3 1.6 + - - +
177A VAL* 3.1 21.5 + - - +
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Residues in contact with ILE 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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159A LEU* 3.8 9.9 - - + -
170A LEU* 2.9 36.9 + - + +
171A VAL* 3.6 4.5 - - - +
173A ALA* 1.3 74.1 - - - +
175A GLN* 1.3 62.3 + - - +
177A VAL* 3.2 0.7 + - - -
178A ALA* 2.8 35.9 + - + +
190A LEU* 5.2 0.7 - - + -
41B LEU* 3.8 29.6 - - + +
44B LEU* 4.1 29.6 - - + +
45B PHE* 3.5 50.3 - - + -
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Residues in contact with GLN 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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171A VAL* 2.9 38.2 + - + +
172A ASP* 3.4 8.0 + - - +
174A ILE* 1.3 79.0 - - + +
176A GLN* 1.3 62.9 + - - +
178A ALA* 4.9 0.2 - - - -
179A LYS* 3.4 30.8 + - + +
44B LEU* 4.6 18.4 - - + +
48B GLY* 3.2 28.9 + - - +
49B SER* 3.8 7.7 + - - -
51B GLN* 3.7 24.6 + - - +
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Residues in contact with GLN 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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58A VAL 3.0 26.7 + - - +
59A TRP* 3.6 36.3 - - + +
60A PRO* 5.4 1.0 - - - +
162A LEU* 3.9 15.3 - - + -
168A MET* 4.3 8.5 - - + +
172A ASP 3.0 17.2 + - - +
173A ALA 3.6 5.4 - - - +
174A ILE 3.2 0.2 - - - -
175A GLN* 1.3 78.1 - - - +
177A VAL* 1.3 59.1 + - - +
179A LYS* 3.5 25.3 + - - +
180A ASN* 2.9 35.1 + - - +
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Residues in contact with VAL 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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58A VAL* 4.4 15.9 - - + +
64A ILE* 4.2 16.6 - - + -
155A ALA* 5.2 3.1 - - + -
158A VAL* 4.1 15.0 - - + -
159A LEU* 3.8 18.6 - - + -
162A LEU* 3.9 18.6 - - + -
173A ALA 3.1 16.3 + - - +
174A ILE* 4.1 1.1 - - - +
176A GLN* 1.3 75.9 - - + +
178A ALA* 1.3 60.0 + - - +
179A LYS 3.1 1.3 - - - -
180A ASN* 2.9 21.1 + - - +
181A ARG 2.9 12.0 + - - -
183A VAL* 4.0 30.7 - - + -
45B PHE* 6.5 0.2 - - + -
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Residues in contact with ALA 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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50A PRO* 3.0 25.1 - - - +
174A ILE* 2.8 33.4 + - + +
175A GLN* 4.9 0.2 - - - -
177A VAL* 1.3 75.0 - - - +
179A LYS* 1.3 57.5 + - - +
181A ARG 3.3 16.8 - - - +
182A CYS* 5.0 0.2 - - - -
183A VAL* 4.6 4.0 - - + +
44B LEU 4.5 9.9 - - - +
45B PHE* 4.6 17.9 - - + +
49B SER* 3.7 13.9 - - - +
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Residues in contact with LYS 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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50A PRO* 3.9 14.6 - - - +
175A GLN* 3.4 20.0 + - + +
176A GLN* 3.5 34.8 + - - +
177A VAL 3.1 1.6 + - - -
178A ALA* 1.3 78.5 - - - +
180A ASN* 1.3 72.5 + - - +
49B SER* 3.4 18.8 + - - +
51B GLN* 5.6 4.5 - - - +
179B LYS* 3.5 48.9 - - + +
180B ASN* 2.8 33.3 + - - +
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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