Contacts of the helix formed by residues 159 - 171 (chain C) in PDB entry 3HB8
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 159 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139C TRP 3.7 0.2 - - - +
140C ARG* 2.9 58.2 + - - +
141C HIS* 5.7 1.0 - - - -
157C GLY 4.0 2.0 + - - -
158C VAL* 1.3 72.4 - - - +
160C GLN* 1.3 58.2 + - - +
161C LEU 3.5 1.7 + - - -
162C GLN* 2.9 35.5 + - + +
163C LYS* 2.9 26.0 + - - +
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Residues in contact with GLN 160 (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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138C GLN 2.6 30.1 + - - -
139C TRP* 3.0 9.2 + - - +
142C PHE* 3.5 16.1 - - + +
158C VAL* 3.0 19.3 + - + +
159C ASP* 1.3 72.7 - - - +
161C LEU* 1.3 53.3 + - - +
163C LYS* 3.3 10.1 - - + +
164C VAL* 2.7 38.3 + - - +
178C ILE 4.3 6.8 - - - +
179C MET* 3.6 19.8 - - + +
180C CYS* 2.6 50.8 + - - +
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Residues in contact with LEU 161 (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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92C ILE* 3.8 14.8 - - + -
139C TRP* 3.2 18.3 + - + +
140C ARG* 3.5 31.6 - - - +
159C ASP* 3.8 6.1 - - - +
160C GLN* 1.3 77.7 - - - +
162C GLN* 1.3 60.9 + - - +
164C VAL* 3.4 5.1 + - + +
165C ILE* 3.1 27.4 + - + +
179C MET* 3.8 31.2 - - + -
233C LEU* 4.2 12.6 - - + -
237C ILE* 4.6 9.4 - - + -
288C ILE* 3.3 40.2 - - + -
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Residues in contact with GLN 162 (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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140C ARG* 4.3 7.8 + - - +
159C ASP* 2.9 29.5 + - + +
161C LEU* 1.3 74.6 - - - +
163C LYS* 1.3 60.7 + - - +
165C ILE* 3.3 25.1 + - - +
166C ASP* 2.8 64.0 + - - +
287C LYS* 6.0 1.6 - - - +
288C ILE* 4.4 11.4 + - - +
289C ASP* 4.5 4.2 - - - +
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Residues in contact with LYS 163 (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 VAL* 4.5 19.5 - - + +
159C ASP 2.9 20.0 + - - +
160C GLN* 3.3 9.2 - - + +
162C GLN* 1.3 73.8 - - - +
164C VAL* 1.3 69.9 + - + +
166C ASP* 3.1 9.5 + - - +
167C THR* 2.9 33.8 + - - +
178C ILE 5.9 3.6 - - - +
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Residues in contact with VAL 164 (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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160C GLN 2.7 23.0 + - - +
161C LEU* 3.5 7.6 - - + +
163C LYS* 1.3 74.7 - - + +
165C ILE* 1.3 64.1 + - - +
167C THR* 3.2 4.4 + - - -
168C ILE* 2.9 36.7 + - + +
177C ILE* 3.7 21.7 - - + +
178C ILE 3.9 24.7 - - - +
179C MET* 4.2 10.5 - - + -
201C PHE* 3.3 36.6 - - + -
237C ILE* 4.3 9.4 - - + -
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Residues in contact with ILE 165 (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 LEU* 3.1 18.2 + - + +
162C GLN* 3.6 23.6 - - - +
164C VAL* 1.3 77.2 - - + +
166C ASP* 1.3 65.5 + - - +
168C ILE* 3.1 10.4 + - - +
169C LYS* 3.1 28.6 + - + +
237C ILE* 4.4 22.4 - - + -
240C ILE* 4.0 27.6 - - + -
241C THR* 4.1 8.3 - - + -
288C ILE* 3.9 42.8 - - + +
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Residues in contact with ASP 166 (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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162C GLN* 2.8 55.7 + - - +
163C LYS* 3.5 7.4 - - + +
165C ILE* 1.3 70.5 - - - +
167C THR* 1.3 59.1 + - - +
169C LYS* 3.0 11.7 + - - +
170C THR* 2.8 36.6 + - + +
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Residues in contact with THR 167 (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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163C LYS* 2.9 27.6 + - - +
164C VAL* 3.5 7.7 - - - -
166C ASP* 1.3 71.5 - - - +
168C ILE* 1.3 61.7 + - - +
169C LYS 3.0 0.3 + - - -
170C THR* 3.6 7.0 - - - +
171C ASN* 2.6 50.9 + - + +
174C ASP* 3.4 31.4 - - + +
177C ILE* 3.8 13.4 - - + -
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Residues in contact with ILE 168 (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 VAL* 2.9 32.2 + - + +
165C ILE 3.1 6.9 + - - +
167C THR* 1.3 75.8 - - - +
169C LYS* 1.3 63.0 + - - +
172C PRO* 3.6 22.0 - - - +
177C ILE* 4.1 21.3 - - + -
201C PHE* 4.4 5.2 - - + -
203C VAL* 4.0 5.4 - - + -
208C LEU* 3.7 17.9 - - + -
237C ILE* 3.4 30.3 - - + -
241C THR* 3.5 20.2 - - + -
243C LEU* 3.6 28.2 - - + +
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Residues in contact with LYS 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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165C ILE* 3.1 19.5 + - + +
166C ASP* 3.0 11.8 + - - +
167C THR 3.0 0.4 - - - -
168C ILE* 1.3 81.3 - - - +
170C THR* 1.3 66.6 + - + +
172C PRO* 3.9 5.7 - - - +
240C ILE* 5.2 4.7 - - + +
241C THR* 4.0 27.6 - - + +
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Residues in contact with THR 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166C ASP* 2.8 29.5 + - + +
167C THR* 3.6 7.1 + - - -
169C LYS* 1.3 80.9 - - + +
171C ASN* 1.3 83.7 + - - +
172C PRO* 3.7 4.4 - - - +
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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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167C THR* 2.6 25.3 + - + +
170C THR* 1.3 100.4 + - - +
172C PRO* 1.3 66.5 - - - +
173C ASP* 3.1 3.4 - - + +
174C ASP* 3.1 32.4 - - + +
177C ILE* 4.4 1.0 - - - +
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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