Contacts of the helix formed by residues 167 - 179 (chain C) in PDB entry 8ATC
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
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C GLU* 2.9 27.0 + - - -
105C ARG* 3.2 21.6 - - - +
128C GLY* 3.5 25.6 + - - -
129C ASP 4.1 0.2 - - - +
130C GLY 2.9 26.4 + - - +
131C SER* 3.7 8.5 - - - -
132C ASN 3.2 31.4 - - - +
133C GLN 3.7 17.0 - - - -
134C HIS* 3.9 11.1 - - + +
165C TYR 3.0 7.0 + - - +
166C GLY* 1.3 72.3 - - - -
168C THR* 1.3 64.3 + - - +
170C HIS* 3.5 3.3 + - - +
171C SER* 3.5 23.2 + - - -
231C GLN* 5.4 2.6 - - - +
234C ARG* 3.7 11.6 - - - +
311C PAL 2.7 42.3 + - - +
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Residues in contact with THR 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134C HIS* 3.7 30.2 - - + +
137C GLN* 3.9 7.5 - - + +
138C THR* 4.1 1.6 + - - -
141C ASP* 5.0 0.9 - - - +
166C GLY* 3.0 5.9 - - - -
167C ARG* 1.3 79.4 - - - +
169C VAL* 1.3 61.1 + - - +
171C SER* 3.8 2.9 + - - -
172C LEU* 3.1 27.4 + - - +
226C TYR* 3.5 23.2 + - - -
228C THR* 4.2 4.5 - - - +
266C PRO* 3.6 34.8 - - + +
311C PAL 3.7 17.8 - - + +
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Residues in contact with VAL 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159C MET* 4.0 15.0 - - + -
162C ASP 4.4 0.9 - - - +
163C LEU* 3.6 50.3 - - + -
166C GLY* 3.1 21.1 - - - +
168C THR* 1.3 77.1 + - - +
170C HIS* 1.3 75.0 + - + +
172C LEU* 4.4 6.1 - - - +
173C THR* 3.0 26.1 + - - -
194C MET* 4.3 5.4 - - + -
226C TYR* 3.9 14.6 - - + -
228C THR* 3.8 24.5 - - + -
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Residues in contact with HIS 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C SER 3.0 28.9 + - - -
132C ASN 3.0 16.4 + - - +
133C GLN* 4.5 7.6 - - - +
163C LEU 2.9 26.5 + - - -
164C LYS 3.4 18.0 + - - -
165C TYR 4.4 0.2 - - - -
166C GLY 3.1 16.7 + - - -
167C ARG 3.7 1.3 - - - +
168C THR 3.4 0.4 - - - -
169C VAL* 1.3 83.0 - - + +
171C SER* 1.3 56.5 + - - +
173C THR* 3.8 3.1 - - - -
174C GLN* 3.1 33.6 + - - +
194C MET* 4.3 4.3 - - - -
195C PRO* 3.7 17.9 - - + +
197C TYR* 3.6 19.2 + + - +
198C ILE* 4.2 12.0 - - + +
143D LYS* 4.5 3.1 - - - -
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Residues in contact with SER 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C ILE* 3.3 17.6 - - - +
133C GLN* 2.6 28.9 + - - -
134C HIS 3.1 29.7 + - - -
135C PRO 3.8 0.3 - - - -
138C THR* 2.8 20.1 + - - -
167C ARG 3.5 9.4 + - - -
168C THR 3.8 2.2 - - - -
170C HIS* 1.3 76.7 - - - +
172C LEU* 1.3 57.3 + - - +
174C GLN* 3.5 3.6 + - - -
175C ALA* 3.0 20.8 + - - +
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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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138C THR* 3.0 14.4 + - + +
141C ASP* 4.1 21.1 - - + +
142C LEU* 4.1 17.5 - - + -
145C ILE* 4.5 8.7 - - + -
157C VAL* 5.6 1.1 - - + -
159C MET* 3.9 16.2 - - + -
168C THR 3.1 15.1 + - - +
169C VAL* 4.2 3.8 - - - +
170C HIS 3.4 0.2 - - - -
171C SER* 1.3 74.6 - - - +
173C THR* 1.3 60.4 + - - +
175C ALA* 3.2 1.5 + - - -
176C LEU* 3.1 50.6 + - + +
224C ILE* 6.2 0.2 - - + -
226C TYR* 3.6 42.0 - - + -
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Residues in contact with THR 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159C MET* 3.3 28.8 - - - +
169C VAL 3.0 18.8 + - - -
170C HIS 3.8 2.7 - - - -
172C LEU* 1.3 74.8 - - - +
174C GLN* 1.3 63.2 + - - +
176C LEU* 3.9 0.7 - - - -
177C ALA* 3.1 24.3 + - - +
184C PHE* 4.2 10.5 - - + -
186C PHE* 4.3 13.0 - - + -
194C MET* 3.9 6.2 - - - +
198C ILE* 3.4 31.2 - - + -
201C MET* 4.2 7.9 - - + -
202C LEU* 4.3 11.9 - - + -
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Residues in contact with GLN 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C ILE* 3.6 12.8 - - + +
13C ASN* 3.8 33.9 + - - +
133C GLN* 2.6 36.7 + - - +
170C HIS 3.1 15.6 + - - +
171C SER* 3.8 0.6 - - - +
172C LEU 3.3 0.2 - - - -
173C THR* 1.3 75.5 - - - +
175C ALA* 1.3 63.7 + - - +
177C ALA* 3.9 5.0 + - - +
178C LYS* 3.3 25.4 + - - +
197C TYR* 4.3 9.3 - - - -
198C ILE* 3.6 25.6 - - + +
201C MET* 4.4 20.4 - - + +
205C LYS* 5.8 0.3 + - - -
142D GLU* 5.2 1.2 + - - -
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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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12C ILE* 3.6 11.4 - - + -
20C LEU* 3.9 5.3 - - + +
138C THR* 3.2 35.4 - - + -
142C LEU* 3.8 16.8 - - + -
171C SER 3.0 8.6 + - - +
172C LEU* 3.6 5.2 - - - +
173C THR 3.1 1.0 - - - -
174C GLN* 1.3 78.1 - - - +
176C LEU* 1.3 56.6 + - - +
178C LYS* 3.1 26.2 - - - +
179C PHE* 3.4 13.3 - - - -
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Residues in contact with LEU 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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142C LEU* 4.0 17.0 - - + -
145C ILE* 4.8 7.4 - - + -
152C LEU* 4.1 12.3 - - + +
155C LEU* 4.6 13.7 - - + -
157C VAL* 4.3 14.1 - - + -
159C MET* 4.3 4.0 - - + -
172C LEU* 3.1 42.8 + - + +
175C ALA* 1.3 70.0 - - - +
177C ALA* 1.3 58.6 + - - +
178C LYS 3.0 5.6 - - - -
179C PHE* 3.2 15.2 + - + +
182C ASN* 2.9 43.6 + - - +
184C PHE* 3.7 31.0 - - + -
207C ILE* 5.0 0.2 - - - +
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Residues in contact with ALA 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 THR 3.1 18.5 + - - +
174C GLN 4.3 3.6 - - - +
175C ALA 3.3 0.4 - - - -
176C LEU* 1.3 75.4 - - - +
178C LYS* 1.3 57.2 + - - +
179C PHE 3.2 11.1 - - - +
184C PHE* 4.6 2.7 - - + -
201C MET* 4.0 27.1 - - + -
202C LEU* 4.2 4.5 - - + -
205C LYS* 4.2 14.2 - - + +
207C ILE* 3.2 37.5 - - + +
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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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12C ILE* 3.1 25.6 + - - -
13C ASN* 4.2 12.5 + - - +
15C LEU* 2.8 31.1 + - - +
16C SER* 4.6 1.8 - - - +
17C ARG* 4.0 40.5 + - + +
20C LEU* 4.3 11.2 - - + -
174C GLN* 3.3 21.0 + - - +
175C ALA 3.1 12.8 - - - +
176C LEU 3.0 0.2 - - - -
177C ALA* 1.3 77.6 - - - +
179C PHE* 1.3 62.0 + - + +
180C ASP* 5.0 2.6 - - - +
205C LYS* 4.8 17.8 - - - +
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Residues in contact with PHE 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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17C ARG* 3.5 50.3 - - + +
20C LEU* 3.9 22.9 - - + -
21C ASN* 3.8 22.7 - - - -
24C LEU* 5.8 0.2 - - + -
142C LEU* 4.5 4.5 - - + -
152C LEU* 3.5 52.3 - - + +
153C ASP* 3.7 7.9 - - - +
175C ALA 3.4 21.5 - - - -
176C LEU* 3.2 14.9 + - + +
177C ALA* 3.2 13.9 - - - +
178C LYS* 1.3 82.0 - - + +
180C ASP* 1.3 68.3 + - - +
182C ASN* 3.8 7.0 + - - +
207C ILE* 4.8 4.3 - - - +
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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