Contacts of the helix formed by residues 170 - 179 (chain C) in PDB entry 1YAA
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 LEU 170 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168C LEU* 3.0 15.4 + - + +
169C ASP* 1.3 73.2 - - - +
171C ASN* 1.3 65.0 + - - +
173C PHE* 3.0 10.3 + - + +
174C LEU* 2.9 56.1 + - + +
204C GLN* 3.6 36.3 - - + +
207C GLN* 4.0 19.5 - - + +
208C ILE* 4.0 30.7 - - + -
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Residues in contact with ASN 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* 3.4 4.4 - - - +
170C LEU* 1.3 82.7 - - + +
172C GLY* 1.3 59.9 + - - +
174C LEU* 3.4 7.8 + - - +
175C ASN* 3.0 29.8 + - - +
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Residues in contact with GLY 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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159C PRO* 3.4 24.2 - - - +
169C ASP* 3.1 23.6 + - - -
171C ASN* 1.3 76.5 + - - +
173C PHE* 1.3 63.6 + - - +
175C ASN* 3.6 9.0 + - - +
176C ALA 3.2 17.0 + - - -
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Residues in contact with PHE 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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158C TYR* 3.4 37.0 - + - -
159C PRO* 3.6 13.6 + - - +
160C TYR* 4.0 30.5 - + - -
168C LEU* 5.1 5.6 - - + -
169C ASP 2.8 13.8 + - - +
170C LEU* 3.2 14.8 - - + +
172C GLY* 1.3 76.9 - - - +
174C LEU* 1.3 60.8 + - - +
176C ALA* 3.3 11.1 + - - +
177C ILE* 3.3 31.3 + - + +
186C PHE* 4.8 1.3 - + - -
188C LEU* 4.0 17.3 - - + -
200C PRO* 5.4 1.8 - - + -
205C TRP* 5.7 2.9 - + - -
208C ILE* 3.7 41.3 - - + -
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Residues in contact with LEU 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 LEU* 2.9 45.8 + - + +
171C ASN* 3.8 6.7 - - - +
173C PHE* 1.3 75.0 - - - +
175C ASN* 1.3 63.1 - - - +
177C ILE* 3.3 16.5 + - + +
178C GLN* 3.2 27.9 + - + +
207C GLN* 3.6 41.7 - - + +
208C ILE* 3.8 20.4 - - + +
211C ALA* 4.1 6.9 - - + +
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Residues in contact with ASN 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 ASN* 3.0 20.0 + - - +
172C GLY* 3.6 10.6 + - - +
173C PHE 3.3 0.2 - - - -
174C LEU* 1.3 76.8 - - - +
176C ALA* 1.3 59.6 + - - +
178C GLN* 3.2 6.9 + - - +
179C LYS* 3.0 51.3 + - - +
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Residues in contact with ALA 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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134C TYR* 5.0 4.5 - - + -
156C THR 4.8 3.6 - - - +
158C TYR* 3.5 33.0 - - + -
159C PRO* 3.8 7.2 - - + -
172C GLY 3.2 12.1 + - - +
173C PHE 3.5 6.3 - - - +
174C LEU 3.2 0.2 - - - -
175C ASN* 1.3 76.9 - - - +
177C ILE* 1.3 63.1 + - - +
179C LYS* 3.3 4.3 + - - +
180C ALA* 3.0 28.1 + - - +
186C PHE* 4.1 4.2 - - + -
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Residues in contact with ILE 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 PHE* 3.3 34.3 - - + +
174C LEU* 3.6 16.4 - - + +
175C ASN 3.3 0.6 - - - -
176C ALA* 1.3 76.2 - - - +
178C GLN* 1.3 60.9 + - - +
180C ALA 3.8 2.3 + - - -
186C PHE* 3.8 24.2 - - + -
208C ILE* 4.0 23.8 - - + +
211C ALA* 3.8 32.3 - - + +
212C ILE* 3.9 9.2 - - + +
215C LYS* 3.5 4.7 - - - +
217C HIS* 2.9 46.0 + - + -
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Residues in contact with GLN 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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174C LEU* 3.2 15.0 + - + +
175C ASN* 3.7 9.9 - - - +
176C ALA 3.2 0.4 - - - -
177C ILE* 1.3 78.5 + - - +
179C LYS* 1.3 67.0 + - + +
180C ALA 3.4 0.2 - - - -
211C ALA* 3.8 16.9 + - + +
214C SER* 3.5 17.3 + - - -
215C LYS* 2.9 51.8 + - - +
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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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134C TYR* 5.1 0.2 + - - -
175C ASN* 3.0 35.8 + - - +
176C ALA* 3.3 4.9 + - - +
178C GLN* 1.3 85.4 - - + +
180C ALA* 1.3 64.0 + - - +
181C PRO* 3.8 3.5 - - - +
215C LYS* 5.1 0.7 - - - -
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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