Contacts of the helix formed by residues 171 - 185 (chain C) in PDB entry 3LL8
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 SER 171 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58C GLU* 2.6 37.5 + - - -
166C CYS* 2.9 16.3 + - - +
167C LYS* 4.2 5.6 - - - +
170C TYR* 1.3 78.8 - - - +
172C GLU* 1.3 64.5 + - - +
173C ARG* 3.3 15.1 + - - +
174C VAL* 3.1 13.9 + - - +
175C TYR 3.3 8.0 + - - -
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Residues in contact with GLU 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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163C LYS* 4.0 20.6 + - - -
167C LYS* 3.5 42.9 + - + +
171C SER* 1.3 70.5 - - - +
173C ARG* 1.3 55.4 + - - +
175C TYR* 3.2 10.8 + - + +
176C ASP* 2.8 47.8 + - - +
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Residues in contact with ARG 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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58C GLU* 3.5 19.0 + - - +
62C LEU* 3.7 26.6 - - + +
171C SER* 3.2 9.4 - - - +
172C GLU* 1.3 74.5 - - + +
174C VAL* 1.3 60.8 + - - +
176C ASP* 3.4 9.5 + - - +
177C ALA* 3.0 28.9 + - - +
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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
----------------------------------------------------------
58C GLU* 3.6 31.0 - - + +
61C ALA* 4.3 10.3 - - + -
62C LEU* 3.9 16.6 - - + -
65C ILE* 3.8 18.8 - - + +
127C ILE* 4.0 21.5 - - + -
166C CYS* 4.4 4.7 - - - -
170C TYR* 3.7 26.5 - - + -
171C SER 3.1 10.1 + - - +
173C ARG* 1.3 77.0 - - - +
175C TYR* 1.3 65.6 + - - +
177C ALA* 3.3 2.9 + - - +
178C CYS* 3.0 22.0 + - - -
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Residues in contact with TYR 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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154C ARG* 3.5 17.4 + - + +
157C THR* 2.7 32.8 + - - -
158C GLU* 3.8 5.0 + - - +
162C PHE* 4.1 9.0 - + - -
163C LYS* 3.6 61.8 - - + +
166C CYS* 3.8 21.2 - - + +
171C SER 3.3 3.2 + - - -
172C GLU* 3.2 17.0 + - + +
174C VAL* 1.3 79.4 - - - +
176C ASP* 1.3 73.1 + - - +
178C CYS* 3.0 6.7 + - - +
179C MET* 2.9 57.0 + - + +
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Residues in contact with ASP 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 GLU* 2.8 33.8 + - - +
173C ARG* 3.8 7.5 - - - +
175C TYR* 1.3 89.2 - - - +
177C ALA* 1.3 57.5 + - - +
179C MET* 3.2 9.3 + - - +
180C ASP* 3.0 33.9 + - - +
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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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62C LEU* 3.7 20.2 - - + -
65C ILE* 3.4 21.7 - - + +
66C THR* 4.6 13.1 - - + +
69C ALA* 5.8 0.2 - - - +
173C ARG 3.0 16.9 + - - +
174C VAL 3.7 4.3 - - - +
176C ASP* 1.3 72.5 - - - +
178C CYS* 1.3 61.2 + - - +
180C ASP* 3.3 11.2 + - - +
181C ALA* 2.9 22.7 + - - +
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Residues in contact with CYS 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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65C ILE* 3.7 30.3 - - - -
127C ILE* 4.0 10.5 - - - -
130C VAL* 4.2 11.4 - - - -
162C PHE* 3.8 36.8 - - + -
174C VAL 3.0 17.9 + - - -
175C TYR 3.0 8.5 + - - +
177C ALA* 1.3 77.5 - - - +
179C MET* 1.3 55.1 + - + +
181C ALA* 3.0 2.4 + - - -
182C PHE* 2.7 46.4 + - + -
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Residues in contact with MET 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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153C CYS* 3.7 3.6 - - - -
154C ARG* 3.6 57.3 + - + +
157C THR* 3.7 13.0 - - + +
162C PHE* 4.0 8.5 - - + -
175C TYR* 2.9 55.3 + - + +
176C ASP* 3.2 11.2 + - - +
178C CYS* 1.3 76.5 - - - +
180C ASP* 1.3 63.1 + - - +
182C PHE* 3.3 33.3 + - + +
183C ASP* 3.1 27.9 + - - +
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Residues in contact with ASP 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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69C ALA* 5.1 1.6 - - + -
73C ARG* 5.3 5.6 + - - +
154C ARG* 4.0 11.6 + - - -
176C ASP* 3.0 18.1 + - - +
177C ALA* 3.6 11.3 - - - +
179C MET* 1.3 76.4 - - - +
181C ALA* 1.3 63.7 + - - +
183C ASP* 3.3 22.1 + - - +
184C CYS* 3.6 12.6 - - - -
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Residues in contact with ALA 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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65C ILE* 3.8 13.2 - - + -
69C ALA* 3.8 21.3 - - + -
72C LEU* 4.0 7.8 - - - +
134C TRP* 3.6 29.6 - - + +
177C ALA 2.9 14.5 + - - +
178C CYS* 3.5 8.1 - - - +
180C ASP* 1.3 78.1 - - - +
182C PHE* 1.3 62.1 + - + +
184C CYS* 3.1 19.1 + - - +
185C LEU* 3.7 3.6 + - - +
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Residues in contact with PHE 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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119C TYR* 5.2 0.9 - + - -
120C VAL* 3.9 28.5 - - + -
130C VAL* 4.2 11.0 - - + -
134C TRP* 3.7 26.9 - + - -
148C ARG* 3.2 19.6 + - - +
152C GLU* 3.5 53.8 - - + +
153C CYS* 5.2 0.9 - - - -
157C THR* 4.7 0.7 - - + -
162C PHE* 4.0 13.7 - + - -
178C CYS* 2.7 23.9 + - + +
179C MET* 3.5 37.9 - - + +
181C ALA* 1.3 74.3 - - - +
183C ASP* 1.3 62.2 + - - +
184C CYS 3.2 0.9 + - - -
185C LEU* 3.2 24.5 + - + +
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Residues in contact with ASP 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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148C ARG* 3.0 27.5 + - - +
154C ARG* 2.9 36.6 + - - -
179C MET 3.1 10.8 + - - +
180C ASP* 3.5 12.7 - - - +
181C ALA 3.3 0.4 - - - -
182C PHE* 1.3 76.6 - - - +
184C CYS* 1.3 60.2 + - - +
185C LEU 3.7 0.7 + - - +
217C ARG* 3.2 22.3 - - - +
218C PHE* 3.6 14.3 - - + -
219C LYS* 3.4 26.0 - - - +
220C GLU 4.4 0.2 + - - -
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Residues in contact with CYS 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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69C ALA* 3.9 9.4 - - - +
72C LEU* 3.5 22.6 - - + +
73C ARG* 3.7 44.9 - - - +
180C ASP 3.6 14.6 - - - -
181C ALA 3.1 11.3 + - - +
183C ASP* 1.3 77.2 - - - +
185C LEU* 1.3 58.7 + - - +
186C PRO* 3.3 1.0 - - - +
217C ARG* 2.7 33.1 + - - -
218C PHE* 3.9 13.5 - - - -
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Residues in contact with LEU 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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72C LEU* 3.6 24.7 - - + -
119C TYR* 4.2 1.8 - - + -
134C TRP* 4.0 11.4 - - + -
146C LEU* 3.7 32.5 - - + +
147C LEU 4.1 5.6 - - - +
148C ARG* 3.9 27.8 + - + +
152C GLU* 3.8 29.8 - - + -
181C ALA 4.1 3.6 - - - +
182C PHE* 3.2 29.5 + - + +
183C ASP 4.3 1.4 - - - +
184C CYS* 1.3 76.9 - - - +
186C PRO* 1.3 70.1 - - - +
187C LEU* 4.3 2.6 - - - +
217C ARG* 3.2 14.0 + - - +
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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