Contacts of the helix formed by residues 168 - 176 (chain C) in PDB entry 3R9A
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 GLY 168 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136C LEU* 3.7 11.9 - - - +
166C LEU 3.3 1.0 + - - -
167C ASP* 1.3 71.5 - - - +
169C PHE* 1.3 58.0 + - - +
170C GLY 3.2 3.9 - - - +
171C GLU* 3.6 11.1 + - - +
172C LEU* 2.9 30.7 + - - +
175C ARG* 5.3 0.5 + - - -
198C GLN* 5.4 3.6 + - - +
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Residues in contact with PHE 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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134C TYR 3.2 23.1 - - - -
135C THR* 3.6 17.3 - - - -
136C LEU* 3.7 20.6 - - + -
139C VAL* 3.5 40.8 - - + -
151C LEU* 5.2 0.2 - - + -
153C LEU* 4.1 15.9 - - + -
164C GLN* 3.7 5.4 - - - -
165C PRO* 3.1 36.6 - - + -
166C LEU* 3.2 22.0 + - + +
167C ASP 3.2 6.2 - - - -
168C GLY* 1.3 77.7 - - - +
170C GLY* 1.3 57.5 + - - +
172C LEU* 3.7 3.3 - - + +
173C CYS* 2.9 34.9 + - - +
180C LEU* 3.8 16.2 - - + -
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Residues in contact with GLY 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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166C LEU 4.4 0.4 + - - -
168C GLY 3.2 0.6 - - - -
169C PHE* 1.3 74.3 - - - +
171C GLU* 1.3 65.9 + - - +
173C CYS* 3.1 6.2 + - - +
174C HIS* 3.0 32.5 + - - -
180C LEU* 3.6 11.2 - - - +
198C GLN 3.7 14.6 + - - -
199C GLY 3.6 21.5 - - - -
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Residues in contact with GLU 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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168C GLY* 3.6 13.4 + - - +
170C GLY* 1.3 72.2 - - - +
172C LEU* 1.3 62.5 + - - +
174C HIS* 3.4 11.0 + - - +
175C ARG* 3.3 40.1 + - - +
198C GLN 4.9 1.2 + - - -
199C GLY* 5.4 1.6 - - - -
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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
----------------------------------------------------------
136C LEU* 3.4 44.6 - - + +
139C VAL* 3.8 22.0 - - + -
140C GLU* 3.7 37.2 - - + +
143C LEU* 3.7 6.3 - - + -
168C GLY 2.9 19.5 + - - +
169C PHE* 3.7 4.9 - - + +
171C GLU* 1.3 77.4 - - - +
173C CYS* 1.3 63.3 + - - +
175C ARG* 3.2 41.1 + - - +
176C TYR* 3.5 16.8 - - + -
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Residues in contact with CYS 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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139C VAL* 5.0 0.9 - - - -
143C LEU* 4.0 14.4 - - - -
151C LEU* 3.5 42.0 - - - -
169C PHE 2.9 24.1 + - - +
170C GLY 3.1 3.8 + - - +
172C LEU* 1.3 75.0 - - - +
174C HIS* 1.3 58.6 + - + +
176C TYR* 3.0 13.0 + - - +
178C CYS* 3.0 46.4 + - - +
180C LEU* 4.1 19.1 - - + +
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Residues in contact with HIS 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 GLY* 3.0 22.6 + - - +
171C GLU* 3.8 8.4 + - - +
172C LEU 3.2 0.2 - - - -
173C CYS* 1.3 73.6 - - + +
175C ARG* 1.3 66.1 + - - +
177C LYS* 3.1 16.0 + - - +
178C CYS 3.6 11.9 - - - +
179C LEU* 5.7 1.1 - - + -
199C GLY* 3.2 30.0 + - - -
201C ASP* 2.8 36.1 + - - -
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Residues in contact with ARG 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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140C GLU* 5.0 8.5 + - - -
168C GLY 5.3 0.6 + - - -
171C GLU* 3.3 26.9 + - - +
172C LEU* 3.2 43.3 + - - +
174C HIS* 1.3 76.2 - - - +
176C TYR* 1.3 69.3 + - + +
177C LYS* 3.4 4.4 + - - +
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Residues in contact with TYR 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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140C GLU* 3.1 44.2 + - + +
143C LEU* 3.9 40.4 - - + +
144C ALA* 3.9 26.7 - - + +
147C LYS* 5.4 10.3 - - - -
148C PRO* 4.3 5.8 - - + +
172C LEU* 3.5 20.0 - - + -
173C CYS 3.0 7.7 + - - +
175C ARG* 1.3 87.5 - - + +
177C LYS* 1.3 67.2 + - - +
178C CYS* 3.0 8.7 + - - +
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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