Contacts of the helix formed by residues 168 - 179 (chain C) in PDB entry 3ELP
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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137C CYS 5.1 1.0 + - - -
138C SER* 5.8 0.4 - - - +
140C ILE* 4.1 22.7 - - + +
166C VAL 4.0 0.2 + - - -
167C ILE* 1.3 73.9 - - - +
169C ILE* 1.3 65.2 + - - +
170C GLU* 3.1 13.7 + - - +
171C GLY* 2.8 26.9 + - - -
172C CYS* 3.1 22.7 + - - -
302C LEU* 3.6 21.3 - - + +
305C ARG* 2.9 31.5 + - - -
306C GLN* 3.6 5.4 - - - +
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Residues in contact with ILE 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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156C ILE* 4.5 6.3 - - + -
158C THR* 3.4 33.0 - - + -
167C ILE* 3.1 4.9 + - - +
168C ASP* 1.3 70.9 - - - +
170C GLU* 1.3 63.8 + - - +
172C CYS* 3.5 5.6 + - - +
173C ALA* 2.9 19.9 + - - +
184C LEU* 3.9 3.8 - - + +
186C VAL* 3.8 37.7 - - + -
196C GLN* 3.8 7.2 - - - +
198C PRO* 4.0 13.5 - - + +
201C LEU* 3.9 28.5 - - + +
203C ALA* 4.1 6.7 - - + +
306C GLN* 2.9 24.4 + - - +
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Residues in contact with GLU 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* 3.1 9.7 + - - +
169C ILE* 1.3 76.1 - - - +
171C GLY* 1.3 71.0 + - - +
173C ALA* 2.7 18.9 + - - +
174C HIS* 2.9 37.7 + - + +
200C ALA 4.9 1.9 - - - +
201C LEU* 3.2 51.3 + - + +
202C GLY* 4.2 4.0 + - - -
305C ARG* 6.3 0.4 - - - +
306C GLN* 4.6 0.8 + - - -
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Residues in contact with GLY 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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140C ILE* 4.1 17.0 - - - -
168C ASP* 2.8 21.2 + - - -
170C GLU* 1.3 76.0 - - - +
172C CYS* 1.3 62.9 + - - +
174C HIS* 2.8 17.8 + - - +
175C ILE* 2.9 21.5 + - - +
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Residues in contact with CYS 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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137C CYS* 4.1 12.8 - - - -
140C ILE* 4.8 9.0 - - - +
143C LEU* 3.6 25.8 - - + -
156C ILE* 4.5 5.6 - - + -
167C ILE* 3.6 30.5 - - + -
168C ASP 3.1 11.7 + - - +
169C ILE* 3.8 5.4 - - - +
171C GLY* 1.3 72.8 - - - +
173C ALA* 1.3 56.7 + - - +
175C ILE* 4.0 9.6 - - - +
176C VAL* 2.8 36.0 + - - +
184C LEU* 4.0 17.3 - - + -
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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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169C ILE 2.9 13.1 + - - +
170C GLU* 2.7 23.2 + - - +
172C CYS* 1.3 71.5 - - - +
174C HIS* 1.3 59.9 + - + +
176C VAL* 4.9 0.4 - - - -
177C HIS* 2.8 49.6 + - + -
184C LEU* 3.7 10.3 - - + +
202C GLY* 3.8 31.9 - - - -
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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 GLU* 2.9 46.5 + - + +
171C GLY* 2.8 14.8 + - - +
173C ALA* 1.3 76.2 - - + +
175C ILE* 1.3 67.7 + - + +
177C HIS* 4.3 3.8 - + - +
178C LYS* 3.0 28.5 + - - +
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Residues in contact with ILE 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 ILE* 3.4 29.4 - - + -
143C LEU* 4.8 9.9 - - + -
144C GLU* 3.5 54.8 - - + +
147C ILE* 4.9 6.5 - - + +
171C GLY* 2.9 20.1 + - - +
172C CYS* 3.8 6.1 - - - +
174C HIS* 1.3 80.2 - - + +
176C VAL* 1.3 66.1 + - + +
178C LYS* 3.1 24.5 - - + +
179C HIS* 4.1 2.1 + - - +
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Residues in contact with VAL 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C LEU* 4.2 14.4 - - + -
147C ILE* 4.4 14.7 - - + +
154C VAL* 3.8 28.5 - - + -
172C CYS 2.8 26.9 + - - +
173C ALA 4.1 0.9 - - - +
175C ILE* 1.3 75.6 - - - +
177C HIS* 1.3 64.8 + - - +
178C LYS 3.2 0.5 + - - -
179C HIS 3.3 8.7 + - - +
182C ILE* 3.2 59.8 - - + +
183C ILE 4.5 0.7 - - - +
184C LEU* 4.5 17.5 - - + -
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Residues in contact with HIS 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 ALA* 2.8 39.1 + - + +
174C HIS* 4.3 3.8 - + - +
176C VAL* 1.3 73.2 - - - +
178C LYS* 1.3 65.8 + - - +
179C HIS* 3.2 0.9 + - - -
180C GLY 3.8 12.1 - - - +
182C ILE* 4.0 11.3 + - - -
184C LEU* 4.6 8.6 - - + +
202C GLY* 3.0 25.1 + - - -
204C ASP* 3.1 39.2 + - - -
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Residues in contact with LYS 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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144C GLU* 5.1 13.0 + - - +
174C HIS 3.0 22.5 + - - +
175C ILE* 3.1 15.7 - - + +
176C VAL 3.2 0.2 - - - -
177C HIS* 1.3 75.9 - - - +
179C HIS* 1.3 86.5 + - + +
180C GLY 4.3 0.3 + - - -
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Residues in contact with HIS 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C GLU* 5.6 3.8 + - - -
147C ILE* 5.4 13.8 - - + +
175C ILE 4.1 2.4 + - - +
176C VAL 3.3 14.3 + - - +
177C HIS 3.3 0.4 - - - -
178C LYS* 1.3 108.7 - - + +
180C GLY* 1.3 69.2 + - - +
182C ILE* 3.8 5.5 - - - +
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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