Contacts of the helix formed by residues 169 - 184 (chain C) in PDB entry 2Y4T
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 ASP 169 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164C ALA* 2.9 20.6 + - - +
167C SER* 3.6 9.2 - - - +
168C GLY* 1.3 73.6 - - - +
170C TYR* 1.3 59.1 + - - +
171C THR* 3.7 9.4 + - - -
172C ALA* 3.3 33.2 + - + +
173C ALA* 3.1 23.0 + - - +
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Residues in contact with TYR 170 (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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165C PHE* 3.8 39.6 - + - -
168C GLY* 3.2 34.8 + - - -
169C ASP* 1.3 71.4 + - - +
171C THR* 1.3 60.7 + - - +
173C ALA* 3.3 5.6 + - - +
174C ILE* 2.8 34.0 + - + +
197C CYS* 4.1 19.6 - - + +
200C LYS* 3.7 44.3 - - + +
201C GLU* 3.2 23.1 - - - +
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Residues in contact with THR 171 (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 ASP* 3.7 8.3 + - - -
170C TYR* 1.3 72.7 - - - +
172C ALA* 1.3 65.3 + - - +
174C ILE* 3.5 12.1 + - + +
175C ALA* 3.1 23.0 + - - +
201C GLU* 3.5 33.4 + - + +
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Residues in contact with ALA 172 (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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164C ALA* 3.9 11.2 - - + -
169C ASP* 3.3 33.8 + - + +
170C TYR 3.3 0.2 - - - -
171C THR* 1.3 76.1 + - - +
173C ALA* 1.3 64.5 + - - +
175C ALA* 3.2 8.6 + - - +
176C PHE* 3.0 40.3 + - + -
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Residues in contact with ALA 173 (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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161C ALA 3.9 17.5 - - - +
164C ALA* 3.6 9.1 - - + +
165C PHE* 4.0 9.4 - - + +
169C ASP 3.1 16.2 + - - +
170C TYR* 3.3 5.4 + - - +
172C ALA* 1.3 77.4 - - - +
174C ILE* 1.3 53.5 + - - +
176C PHE* 3.2 5.7 + - - +
177C LEU* 2.8 45.1 + - + +
197C CYS* 3.8 19.1 - - - -
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Residues in contact with ILE 174 (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 TYR 2.8 24.8 + - - +
171C THR* 3.7 12.8 - - + +
172C ALA 3.3 0.2 - - - -
173C ALA* 1.3 74.8 - - - +
175C ALA* 1.3 54.9 + - - +
177C LEU* 4.5 4.7 - - - -
178C ASP* 2.8 58.7 + - - +
194C ARG* 4.5 10.1 - - + -
197C CYS* 3.6 26.2 - - + +
198C PHE* 4.1 37.9 - - + +
201C GLU* 4.7 11.4 - - + -
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Residues in contact with ALA 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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171C THR 3.1 14.9 + - - +
172C ALA* 3.4 11.2 - - - +
174C ILE* 1.3 76.6 - - - +
176C PHE* 1.3 71.1 + - + +
178C ASP* 3.8 6.9 - - - +
179C LYS* 3.3 25.6 + - - +
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Residues in contact with PHE 176 (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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157C LEU* 4.0 15.3 - - + +
160C GLN* 3.2 61.2 - - + -
161C ALA* 3.7 17.9 - - + +
163C ASN* 6.2 0.4 - - - -
164C ALA* 3.7 11.7 - - + -
172C ALA* 3.0 30.7 + - + -
173C ALA 3.2 3.6 + - - +
175C ALA* 1.3 78.9 - - + +
177C LEU* 1.3 56.4 + - - +
179C LYS* 2.7 27.9 + - + +
180C ILE* 3.0 16.4 + - - +
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Residues in contact with LEU 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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161C ALA* 4.0 12.1 - - + -
173C ALA* 2.8 31.4 + - + +
174C ILE 3.9 0.4 - - - +
176C PHE* 1.3 72.0 - - - +
178C ASP* 1.3 53.5 + - - +
180C ILE* 3.8 9.6 - - + +
181C LEU* 2.8 43.3 + - + +
190C LEU* 3.5 40.6 - - + +
193C LEU* 3.9 22.9 - - + -
194C ARG* 3.6 44.9 - - + +
197C CYS* 4.1 11.2 - - - -
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Residues in contact with ASP 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C ILE* 2.8 40.3 + - - +
175C ALA* 3.8 8.4 - - - +
177C LEU* 1.3 72.6 - - - +
179C LYS* 1.3 59.6 + - + +
181C LEU* 3.8 1.4 + - - +
182C GLU* 2.9 30.0 + - - +
194C ARG* 2.7 42.4 + - - +
198C PHE* 5.2 3.1 - - - -
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Residues in contact with LYS 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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153C GLU* 5.2 7.7 + - - +
154C MET* 4.2 9.9 - - - +
157C LEU* 3.8 29.6 - - + -
175C ALA 3.3 14.6 + - - +
176C PHE* 2.7 18.7 + - + +
178C ASP* 1.3 71.8 - - + +
180C ILE* 1.3 61.8 + - - +
182C GLU* 3.3 26.3 - - - +
183C VAL 4.1 1.4 + - - -
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Residues in contact with ILE 180 (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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121C LEU* 5.8 1.3 - - + -
154C MET* 3.8 26.0 - - - +
157C LEU* 3.5 38.8 - - + +
158C ARG* 3.9 6.7 - - + -
161C ALA* 3.7 18.6 - - + -
176C PHE 3.0 8.9 + - - +
177C LEU* 3.8 14.4 - - + +
179C LYS* 1.3 74.1 - - - +
181C LEU* 1.3 52.4 + - + +
182C GLU 3.2 0.2 - - - -
183C VAL* 3.1 5.9 + - - -
184C CYS* 2.7 55.8 + - + +
190C LEU* 3.9 27.8 - - + -
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Residues in contact with LEU 181 (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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177C LEU* 2.8 22.8 + - + +
178C ASP 4.1 1.3 - - - +
180C ILE* 1.3 70.2 - - + +
182C GLU* 1.3 61.8 + - - +
184C CYS* 3.6 22.4 - - + +
185C VAL* 3.3 20.4 - - - +
187C ASP* 4.0 5.6 - - + +
190C LEU* 3.8 30.5 - - + +
191C ARG* 3.8 45.1 + - + +
194C ARG* 3.4 46.0 - - + +
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Residues in contact with GLU 182 (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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178C ASP* 2.9 27.9 + - - +
179C LYS* 3.3 19.9 - - - +
181C LEU* 1.3 77.6 - - - +
183C VAL* 1.3 62.8 + - + +
185C VAL* 3.3 17.5 - - - +
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Residues in contact with VAL 183 (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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116C LEU* 4.0 31.2 - - + -
117C LYS* 3.9 15.6 + - - +
147C GLN* 5.3 0.7 - - - +
150C LYS* 3.9 31.0 - - + +
154C MET* 3.8 38.8 - - + -
179C LYS 4.1 0.2 + - - -
180C ILE 3.1 2.4 + - - -
182C GLU* 1.3 84.2 - - + +
184C CYS* 1.3 57.6 + - - +
185C VAL* 3.1 14.9 + - - +
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Residues in contact with CYS 184 (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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116C LEU* 3.3 19.1 - - - +
117C LYS 3.1 10.8 - - - +
119C GLY* 3.8 13.9 - - - -
121C LEU* 3.9 16.8 - - - -
154C MET* 4.2 9.4 - - - -
180C ILE* 2.7 43.2 + - + +
181C LEU* 3.6 11.2 - - + +
183C VAL* 1.3 69.9 - - - +
185C VAL* 1.3 62.2 + - - +
186C TRP 3.1 3.1 - - - -
187C ASP* 3.0 29.2 + - + +
190C LEU* 5.6 0.2 - - - -
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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