Contacts of the helix formed by residues 173 - 181 (chain C) in PDB entry 6UZA
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 TYR 173 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141C VAL 3.3 27.6 - - - -
142C ALA 4.1 7.0 + - - -
143C ASN 4.8 0.9 - - - -
144C GLU* 3.8 27.2 + - + +
168C ALA* 3.1 14.1 + - + +
171C LYS* 3.7 45.2 + - + +
172C GLY* 1.3 77.9 - - - +
174C VAL* 1.3 65.2 + - - +
175C ARG 3.4 1.3 - - - -
176C ILE* 3.9 25.4 - - + +
177C VAL* 3.1 26.7 + - - +
234C ILE* 4.9 0.4 - - - -
882C GLY 5.1 4.3 + - - -
885C LYS* 4.9 3.3 + - - -
886C GLU* 3.7 32.9 - - - +
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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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172C GLY 3.4 13.2 + - - +
173C TYR* 1.3 70.3 - - - +
175C ARG* 1.3 61.4 + - + +
177C VAL* 3.4 6.7 + - + +
178C GLU* 2.9 29.6 + - + +
231C GLU* 5.6 1.8 - - - +
233C GLU* 3.6 45.8 - - + +
234C ILE* 4.4 20.4 - - + -
237C THR* 5.6 2.7 - - - +
108D TYR* 5.1 8.7 - - - +
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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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144C GLU* 5.2 9.9 + - - +
146C LEU* 3.5 36.6 - - + +
173C TYR 3.4 0.4 - - - -
174C VAL* 1.3 74.3 - - + +
176C ILE* 1.3 62.3 + - + +
178C GLU* 3.4 5.8 + - - +
179C ALA* 2.9 29.1 + - - +
104D ASP* 5.6 4.2 + - - +
108D TYR* 3.7 62.5 - - + +
892D SER* 4.9 6.3 + - - -
896D TYR* 3.4 24.7 + - - -
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Residues in contact with ILE 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 ALA 4.4 0.4 - - - +
141C VAL* 3.9 21.8 - - + +
144C GLU* 3.7 37.0 - - + +
145C HIS 4.1 8.7 - - - +
146C LEU* 4.3 22.0 - - + +
149C THR* 4.4 11.0 - - + +
168C ALA* 3.8 13.2 - - + -
173C TYR* 3.6 27.2 + - + +
174C VAL 3.3 0.2 - - - -
175C ARG* 1.3 75.1 - - + +
177C VAL* 1.3 60.0 + - - +
179C ALA* 3.3 2.3 + - - +
180C ILE* 2.9 48.5 + - + +
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Residues in contact with VAL 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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165C LEU* 4.5 8.7 - - + +
168C ALA* 3.7 20.4 - - + +
169C ILE* 3.7 26.7 - - + -
173C TYR 3.1 19.3 + - - +
174C VAL* 3.7 7.6 - - + +
175C ARG 3.3 0.2 - - - -
176C ILE* 1.3 76.0 - - - +
178C GLU* 1.3 57.4 + - - +
180C ILE* 3.3 4.2 + - - +
181C LEU* 2.9 51.0 + - + +
234C ILE* 4.2 25.1 - - + -
237C THR* 5.5 4.7 - - + -
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Residues in contact with GLU 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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174C VAL* 2.9 19.9 + - + +
175C ARG* 3.9 6.7 - - - +
176C ILE 3.4 0.2 - - - -
177C VAL* 1.3 77.2 - - - +
179C ALA* 1.3 57.0 + - - +
181C LEU* 4.2 8.8 - - - +
182C SER* 4.1 15.4 + - - -
237C THR* 5.9 5.8 - - + -
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Residues in contact with ALA 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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146C LEU* 4.1 8.7 - - + -
149C THR* 5.2 2.2 - - + -
150C GLU* 4.0 32.3 - - + +
153C LEU* 3.5 17.4 - - + +
175C ARG 2.9 17.9 + - - +
176C ILE* 3.8 4.5 - - - +
177C VAL 3.2 0.2 - - - -
178C GLU* 1.3 77.4 - - - +
180C ILE* 1.3 62.3 + - - +
181C LEU 3.4 0.2 - - - -
182C SER* 3.3 18.7 + - - -
183C HIS 4.1 1.4 + - - -
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Residues in contact with ILE 180 (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 LEU* 5.5 1.1 - - + -
141C VAL* 4.0 11.0 - - + -
149C THR* 4.3 4.5 - - + -
153C LEU* 3.9 23.1 - - + -
161C VAL* 4.1 16.4 - - + +
164C ALA* 3.9 29.6 - - + +
165C LEU* 3.8 29.6 - - + -
168C ALA* 4.6 1.3 - - + -
176C ILE* 2.9 38.4 + - + +
177C VAL 4.0 2.7 - - - +
179C ALA* 1.3 71.9 - - - +
181C LEU* 1.3 57.4 + - - +
182C SER 3.1 4.3 - - - -
183C HIS* 3.1 26.0 + - - +
186C PHE* 3.6 13.5 - - + -
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Residues in contact with LEU 181 (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 LEU* 3.8 19.1 - - + -
177C VAL* 2.9 36.8 + - + +
178C GLU* 4.6 7.0 - - - +
179C ALA 3.4 0.6 - - - -
180C ILE* 1.3 75.1 - - - +
182C SER* 1.3 56.8 + - - +
183C HIS 3.4 2.3 - - - +
186C PHE* 3.9 34.7 - - + +
192C LEU* 3.8 31.9 - - + -
237C THR* 4.1 10.5 - - + -
238C LEU* 4.1 16.2 - - + -
241C LYS* 3.8 31.6 + - + +
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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