Contacts of the helix formed by residues 167 - 179 (chain C) in PDB entry 5H1C
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 ARG 167 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138C HIS* 3.3 17.9 - - + +
164C GLY 4.6 9.5 + - - -
165C THR* 3.2 24.2 + - - +
166C PHE* 1.3 84.2 + - - +
168C PRO* 1.3 72.2 - - + +
169C GLU* 4.4 12.1 - - + +
170C ARG* 3.2 24.2 + - + +
171C LEU* 3.6 11.3 + - - +
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Residues in contact with PRO 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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166C PHE* 3.8 22.8 - - + +
167C ARG* 1.3 86.7 - - + +
169C GLU* 1.3 66.3 + - + +
171C LEU* 2.9 33.2 + - + +
172C LEU* 2.9 18.3 + - + +
186C LEU* 4.6 14.9 - - + +
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Residues in contact with GLU 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 ARG* 3.1 11.0 - - + +
168C PRO* 1.3 87.8 - - + +
170C ARG* 1.3 58.1 + - - +
172C LEU* 3.1 16.7 + - + +
173C ALA* 3.0 24.5 + - - +
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Residues in contact with ARG 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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135C GLN* 2.6 53.9 + - - +
138C HIS* 4.2 22.9 - - + -
167C ARG* 3.2 18.1 + - + +
168C PRO 3.2 0.4 - - - -
169C GLU* 1.3 78.8 - - - +
171C LEU* 1.3 58.2 + - - +
173C ALA* 3.0 16.5 + - - +
174C VAL* 2.9 35.7 + - + +
330C ASN 4.4 9.3 + - - -
331C ALA* 4.1 16.8 + - - -
332C ASP 5.4 1.8 - - - -
333C GLY* 4.6 1.8 - - - -
401C ANP 3.1 42.0 + - - -
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Residues in contact with LEU 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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138C HIS* 3.8 34.1 - - + +
141C ALA* 4.6 6.5 - - + -
142C VAL* 3.5 30.1 - - + +
166C PHE* 3.3 33.4 - - + -
167C ARG 3.8 8.5 - - - +
168C PRO* 2.9 9.2 + - + +
170C ARG* 1.3 77.3 - - - +
172C LEU* 1.3 59.1 + - - +
174C VAL* 3.5 2.7 + - + +
175C ALA* 2.9 26.9 + - - +
182C GLY* 6.1 0.2 - - - -
185C VAL* 4.9 3.4 - - + +
186C LEU* 3.7 27.1 - - + -
189C VAL* 3.9 15.7 - - + -
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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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168C PRO* 2.9 18.8 + - + +
169C GLU* 3.1 15.2 + - + +
171C LEU* 1.3 78.1 - - - +
173C ALA* 1.3 56.5 + - - +
175C ALA* 3.1 5.0 + - - +
176C GLU* 2.9 32.3 + - - +
182C GLY* 3.7 28.3 - - - +
186C LEU* 3.7 24.9 - - + -
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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 GLU 3.0 12.2 + - - +
170C ARG* 3.0 25.3 + - - +
172C LEU* 1.3 74.1 - - - +
174C VAL* 1.3 67.0 + - + +
176C GLU* 3.0 19.4 + - - +
177C ARG* 2.9 18.7 + - - +
331C ALA 3.9 14.6 - - - +
332C ASP* 3.8 8.6 - - - +
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Residues in contact with VAL 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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138C HIS 5.2 0.9 - - - -
139C THR* 4.0 35.0 - - + +
142C VAL* 3.6 27.8 - - + -
170C ARG* 2.9 30.2 + - + +
171C LEU* 3.9 3.8 - - - +
173C ALA* 1.3 75.9 - - + +
175C ALA* 1.3 58.1 + - - +
177C ARG* 2.8 23.0 + - + +
178C TYR* 2.9 42.2 + - + +
332C ASP 4.5 10.1 - - - +
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Residues in contact with ALA 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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142C VAL* 4.7 6.3 - - - +
171C LEU 2.9 16.7 + - - +
172C LEU* 3.2 10.8 - - + +
173C ALA 3.1 0.4 - - - -
174C VAL* 1.3 77.6 - - - +
176C GLU* 1.3 60.1 + - - +
178C TYR* 4.6 1.3 - - - +
179C GLY* 3.1 15.2 + - - -
180C LEU* 3.0 31.0 + - - +
182C GLY* 3.7 24.9 - - - +
185C VAL* 4.4 9.4 - - + -
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Residues in contact with GLU 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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172C LEU* 2.9 20.8 + - - +
173C ALA* 3.0 15.1 + - - +
175C ALA* 1.3 75.9 - - - +
177C ARG* 1.3 62.5 + - - +
178C TYR 3.3 0.9 + - - -
179C GLY* 3.6 8.0 + - - -
332C ASP* 5.0 5.8 - - - +
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Residues in contact with ARG 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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105C GLY 3.3 13.1 + - - -
106C SER* 5.3 0.2 - - - +
139C THR* 5.5 3.8 - - - +
173C ALA 2.9 6.7 + - - +
174C VAL* 2.8 23.7 + - - +
176C GLU* 1.3 79.3 - - - +
178C TYR* 1.3 113.7 + - - +
179C GLY 3.6 0.2 - - - -
330C ASN* 6.1 0.4 - - - +
332C ASP* 3.2 46.8 + - + +
334C VAL* 3.0 29.5 + - - +
335C GLY* 3.9 10.1 - - - -
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Residues in contact with TYR 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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105C GLY* 3.1 31.1 + - - -
139C THR* 6.0 1.3 - - - -
142C VAL* 4.9 6.7 - - + -
143C THR* 3.4 29.2 - - + -
146C LEU* 4.3 28.4 - - + +
150C ARG* 4.3 16.6 + - - +
174C VAL* 2.9 33.7 + - + +
175C ALA* 3.9 1.3 - - - +
177C ARG* 1.3 119.2 + - - +
179C GLY* 1.3 58.3 + - - +
180C LEU* 3.0 20.2 + - + +
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Residues in contact with GLY 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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175C ALA 3.1 8.7 + - - -
176C GLU* 3.6 6.3 + - - -
177C ARG 3.6 2.2 - - - -
178C TYR* 1.3 75.9 - - - +
180C LEU* 1.3 64.3 + - - +
181C SER 3.8 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