Contacts of the helix formed by residues 168 - 185 (chain C) in PDB entry 3C5C
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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39C LYS* 4.2 1.6 + - - -
167C LEU* 1.3 84.7 - - - +
169C PHE* 1.3 60.1 + - - +
170C GLU* 3.3 15.2 + - - +
171C HIS* 2.7 72.2 + - - +
172C VAL* 4.1 4.9 - - - +
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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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39C LYS* 3.5 37.8 - - + +
40C PHE* 3.4 32.5 - + - -
43C LYS* 3.8 48.7 - - + +
167C LEU 3.8 1.2 + - - -
168C ASP* 1.3 73.7 - - - +
170C GLU* 1.3 82.0 + - + +
172C VAL* 3.3 4.2 + - - +
173C GLN* 3.0 62.0 + - + -
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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* 3.3 14.2 + - - +
169C PHE* 1.3 97.4 + - + +
171C HIS* 1.3 57.5 + - - +
173C GLN* 3.4 18.7 + - - +
174C HIS* 2.9 27.7 + - - +
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Residues in contact with HIS 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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136C LEU* 5.7 3.1 - - + +
162C GLU 4.3 4.5 - - - -
163C VAL* 3.5 25.2 - - + -
164C SER* 2.9 44.8 + - - -
167C LEU* 4.1 10.2 - - + +
168C ASP* 2.7 63.0 + - - +
170C GLU* 1.3 72.8 - - - +
172C VAL* 1.3 64.9 + - + +
174C HIS* 3.4 9.8 - - - +
175C VAL* 3.3 26.2 + - - +
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Residues in contact with VAL 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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36C LEU* 3.9 29.2 - - + +
39C LYS* 4.2 12.8 - - + -
40C PHE* 4.0 14.6 - - + +
163C VAL* 5.0 1.3 - - + -
164C SER 3.4 25.6 - - - +
168C ASP 4.1 3.8 - - - +
169C PHE 3.3 7.8 + - - +
170C GLU 3.2 0.4 - - - -
171C HIS* 1.3 88.2 - - + +
173C GLN* 1.3 65.5 + - - +
175C VAL* 3.2 25.4 - - + +
176C PHE* 3.2 34.0 + - + -
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Residues in contact with GLN 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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40C PHE* 3.8 15.6 - - + -
61C GLU* 5.4 2.1 - - - +
169C PHE* 3.0 46.9 + - + +
170C GLU* 3.5 22.0 + - - +
172C VAL* 1.3 75.2 - - - +
174C HIS* 1.3 58.4 + - - +
176C PHE* 3.4 0.9 + - - -
177C HIS* 2.8 68.0 + - + +
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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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161C PHE* 3.7 34.1 - + - -
170C GLU 2.9 14.4 + - - +
171C HIS* 3.4 12.3 - - - +
172C VAL 3.2 0.2 - - - -
173C GLN* 1.3 78.7 - - - +
175C VAL* 1.3 57.5 + - + +
177C HIS* 3.5 5.5 + - - +
178C GLU* 2.7 52.0 + - - +
181C ARG* 3.9 11.0 + - - -
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Residues in contact with VAL 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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36C LEU* 5.9 1.1 - - + -
95C LEU* 4.2 3.0 - - + +
130C LEU* 3.4 12.6 - - + +
132C LEU* 4.1 27.4 - - + -
161C PHE* 3.7 35.0 - - + -
163C VAL* 3.7 21.3 - - + -
171C HIS 3.3 11.6 + - - +
172C VAL* 3.2 25.3 + - + +
174C HIS* 1.3 78.1 - - + +
176C PHE* 1.3 67.8 + - + +
178C GLU* 3.3 5.5 + - - -
179C ALA* 2.9 24.3 + - - +
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Residues in contact with PHE 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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23C LEU* 4.0 18.6 - - + +
25C ILE* 3.7 31.0 - - + -
36C LEU* 3.7 33.9 - - + -
37C THR* 4.1 4.5 - - - -
40C PHE* 3.4 50.7 - + + -
70C LEU* 4.8 0.4 - - + -
72C VAL* 4.2 16.6 - - + -
95C LEU* 3.9 15.3 - - + -
132C LEU* 5.7 0.9 - - + -
172C VAL* 3.2 31.0 + - + +
173C GLN 3.8 0.2 - - - +
175C VAL* 1.3 81.4 - - + +
177C HIS* 1.3 65.7 + - - +
179C ALA* 3.1 9.2 + - - +
180C VAL* 3.1 25.8 + - - +
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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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40C PHE* 4.1 16.7 - + - -
61C GLU* 4.2 11.2 + - + +
62C THR 3.2 23.5 + - - -
63C VAL* 3.4 27.6 - - + +
173C GLN* 2.8 58.6 + - + +
174C HIS* 3.7 5.5 - - - +
176C PHE* 1.3 72.7 - - - +
178C GLU* 1.3 57.3 + - - +
180C VAL* 3.2 5.5 + - + +
181C ARG* 2.9 51.0 + - - +
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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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130C LEU* 4.2 3.8 - - + -
159C LEU* 4.0 21.1 - - + +
161C PHE* 3.9 21.5 - - + -
174C HIS* 2.7 36.5 + - - +
175C VAL* 3.6 8.7 - - - +
176C PHE 3.3 0.2 - - - -
177C HIS* 1.3 73.1 - - - +
179C ALA* 1.3 56.9 + - - +
181C ARG* 3.0 37.8 + - - +
182C GLU* 3.0 33.1 + - - +
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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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23C LEU* 3.6 24.7 - - + -
93C ALA* 3.8 6.3 - - + +
94C PHE 5.7 0.4 - - - +
95C LEU* 3.8 22.2 - - + -
130C LEU* 3.8 14.5 - - + +
175C VAL 2.9 13.5 + - - +
176C PHE 3.1 10.9 + - - +
178C GLU* 1.3 72.8 - - - +
180C VAL* 1.3 59.5 + - - +
182C GLU* 3.2 3.8 + - - +
183C ALA* 2.9 28.4 + - - +
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Residues in contact with VAL 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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21C VAL* 3.9 20.2 - - + -
23C LEU* 4.3 1.5 - - + +
61C GLU* 6.3 0.4 - - + -
63C VAL* 4.0 20.0 - - + -
68C VAL* 3.9 33.9 - - + -
70C LEU* 3.8 31.0 - - + -
176C PHE 3.1 14.8 + - - +
177C HIS* 3.5 7.9 - - + +
179C ALA* 1.3 72.8 - - - +
181C ARG* 1.3 65.3 + - - +
183C ALA* 3.3 1.6 + - - +
184C ARG* 2.9 33.2 + - - +
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Residues in contact with ARG 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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63C VAL* 4.0 9.5 - - + +
64C ASP* 2.6 43.9 + - - +
174C HIS* 3.9 15.6 + - - -
177C HIS* 2.9 32.8 + - - +
178C GLU* 3.0 56.1 + - - +
179C ALA 3.3 0.2 - - - -
180C VAL* 1.3 75.5 - - - +
182C GLU* 1.3 58.3 + - - +
184C ARG* 3.0 7.9 + - - +
185C ARG* 3.0 27.6 + - - +
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Residues in contact with GLU 182 (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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93C ALA* 4.9 0.4 - - + -
128C PRO* 4.1 34.1 - - + +
129C ALA 4.8 3.6 - - - +
130C LEU* 4.0 10.1 - - + -
159C LEU* 3.5 38.2 - - + +
178C GLU* 3.0 23.2 + - - +
179C ALA* 3.4 10.3 - - - +
181C ARG* 1.3 73.4 - - - +
183C ALA* 1.3 66.8 + - - +
184C ARG 3.2 0.7 + - - -
185C ARG* 3.3 21.8 + - - +
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Residues in contact with ALA 183 (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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21C VAL* 3.9 18.4 - - + -
92C HIS* 3.8 42.6 - - + +
93C ALA* 4.1 4.8 - - + +
128C PRO* 4.6 2.2 - - - +
179C ALA 2.9 16.8 + - - +
180C VAL 3.3 7.8 + - - +
182C GLU* 1.3 73.1 - - - +
184C ARG* 1.3 64.1 + - + +
185C ARG 3.5 2.8 + - - -
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Residues in contact with ARG 184 (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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18C PRO 4.5 5.0 + - - -
19C LEU* 3.1 36.2 + - - +
21C VAL* 3.8 14.6 - - + +
63C VAL* 4.8 3.2 + - - +
66C GLN* 3.3 32.7 + - - +
67C PRO 2.9 28.5 + - - -
68C VAL* 3.4 23.9 - - - +
180C VAL* 2.9 24.8 + - + +
181C ARG* 3.0 7.4 + - - +
183C ALA* 1.3 76.0 - - - +
185C ARG* 1.3 62.7 + - - +
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Residues in contact with ARG 185 (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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181C ARG 3.0 10.7 + - - +
182C GLU* 3.3 22.6 + - - +
183C ALA 4.6 3.1 - - - -
184C ARG* 1.3 82.1 - - - +
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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