Contacts of the helix formed by residues 168 - 177 (chain C) in PDB entry 1YKI
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 168 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63C SER* 2.8 25.6 + - - +
65C ALA* 5.3 2.5 - - + +
68C TYR* 3.6 14.2 - - + -
167C PHE* 1.3 71.7 - - - +
169C ALA* 1.3 57.8 + - - +
170C ALA* 3.0 23.2 + - - +
171C ILE* 3.1 35.2 + - + +
172C LEU 3.0 21.5 + - - -
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Residues in contact with ALA 169 (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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167C PHE* 3.4 16.5 + - + +
168C ASP* 1.3 70.6 + - - +
170C ALA* 1.3 60.3 + - - +
172C LEU* 4.3 0.4 - - - -
173C ASP* 2.8 40.6 + - - +
184C THR* 4.9 2.2 - - - +
185C SER* 3.6 33.4 - - - +
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Residues in contact with ALA 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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168C ASP* 3.0 10.4 + - - +
169C ALA* 1.3 78.8 - - - +
171C ILE* 1.3 62.1 + - + +
173C ASP* 3.9 4.9 - - - +
174C ALA* 3.0 25.8 + - - +
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Residues in contact with ILE 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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62C LYS* 3.5 44.6 - - + +
63C SER* 3.9 1.6 - - - +
65C ALA* 4.1 14.8 - - + -
168C ASP* 3.1 39.4 + - + +
170C ALA* 1.3 74.9 - - + +
172C LEU* 1.3 64.9 + - - +
174C ALA* 3.3 5.3 + - - +
175C GLU* 3.0 23.8 + - + +
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Residues in contact with LEU 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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59C ARG 4.4 3.1 - - - +
60C VAL* 3.8 26.7 - - + +
63C SER* 3.8 14.6 - - - +
83C VAL* 3.8 20.4 - - + -
167C PHE* 3.7 24.7 - - + -
168C ASP 3.0 9.6 + - - +
169C ALA* 3.4 0.9 + - - +
171C ILE* 1.3 76.3 - - - +
173C ASP* 1.3 63.9 + - - +
175C GLU* 3.2 13.3 + - + +
176C PHE* 3.3 40.2 + - + +
178C LEU* 4.5 2.5 - - + +
185C SER* 3.6 14.4 - - - +
188C VAL* 3.7 20.6 - - + -
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Residues in contact with ASP 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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169C ALA* 2.8 27.8 + - - +
170C ALA* 3.9 5.0 - - - +
172C LEU* 1.3 73.8 - - - +
174C ALA* 1.3 58.3 + - - +
176C PHE 3.3 1.2 + - - -
177C GLY* 2.8 25.3 + - - -
178C LEU* 2.9 27.1 + - + +
179C LYS* 4.7 12.4 + - + +
183C TYR 4.3 1.7 - - - +
184C THR* 2.7 30.3 + - - -
185C SER* 2.8 37.5 + - - -
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Residues in contact with ALA 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 ALA 3.0 19.4 + - - +
171C ILE* 3.7 5.8 - - - +
173C ASP* 1.3 77.2 - - - +
175C GLU* 1.3 63.0 + - - +
176C PHE 3.3 0.5 + - - -
177C GLY* 3.3 10.8 + - - -
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Residues in contact with GLU 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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59C ARG* 2.9 71.0 + - + +
62C LYS* 3.3 31.9 - - + +
171C ILE* 3.0 18.6 + - + +
172C LEU* 3.6 8.1 - - - +
173C ASP 3.2 0.2 - - - -
174C ALA* 1.3 77.4 - - - +
176C PHE* 1.3 72.5 + - + +
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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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49C ILE* 3.9 25.4 - - + -
56C GLY 4.4 2.9 - - - -
59C ARG* 3.5 48.2 - - + +
60C VAL* 3.9 21.5 - - + -
172C LEU* 3.3 40.9 + - + +
174C ALA 3.2 0.4 - - - -
175C GLU* 1.3 88.4 - - + +
177C GLY* 1.3 61.3 + - - +
178C LEU* 3.2 21.8 + - + +
181C LYS* 2.9 27.5 + - - +
215D THR* 6.4 0.4 - - + -
217D VAL* 4.2 21.3 - - + -
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Residues in contact with GLY 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 ASP 2.8 6.3 + - - -
174C ALA* 3.3 11.8 + - - -
175C GLU 3.6 0.4 - - - -
176C PHE* 1.3 76.7 - - - +
178C LEU* 1.3 64.1 + - - +
179C LYS 3.5 2.4 + - - -
180C GLU* 3.6 10.4 + - - +
181C LYS* 3.3 27.7 + - - +
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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