Contacts of the helix formed by residues 171 - 184 (chain A) in PDB entry 6UUQ
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58A GLU* 2.5 29.8 + - - -
166A CYS 2.9 11.6 + - - +
167A LYS* 3.9 12.8 - - - -
170A TYR* 1.3 81.7 - - - +
172A GLU* 1.3 63.7 + - - +
173A ARG* 3.3 6.7 + - - +
174A VAL* 3.1 14.7 + - - +
175A TYR* 3.1 17.0 + - - +
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Residues in contact with GLU 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A LYS* 5.1 6.9 + - - -
167A LYS* 3.9 40.2 + - + +
171A SER* 1.3 72.0 - - - +
173A ARG* 1.3 60.6 + - - +
175A TYR* 3.2 11.1 + - + +
176A ASP* 2.8 45.7 + - - +
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Residues in contact with ARG 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A GLU* 4.1 7.6 - - - +
62A LEU* 4.0 12.7 - - + +
171A SER* 3.2 11.2 + - - +
172A GLU* 1.3 78.2 - - - +
174A VAL* 1.3 56.9 + - - +
176A ASP* 3.5 9.3 + - - +
177A ALA* 2.9 28.2 + - - +
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Residues in contact with VAL 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A GLU* 3.8 27.4 - - + +
61A ALA* 4.6 4.9 - - + -
62A LEU* 3.9 22.2 - - + +
65A ILE* 3.8 17.9 - - + +
127A ILE* 4.6 7.6 - - + -
166A CYS* 4.7 4.9 - - - -
170A TYR* 3.7 38.8 - - + -
171A SER* 3.1 10.5 + - - +
173A ARG* 1.3 76.2 - - - +
175A TYR* 1.3 65.2 + - - +
177A ALA* 3.3 2.4 + - - +
178A CYS* 3.0 26.6 + - - -
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Residues in contact with TYR 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A ARG* 3.5 17.2 + - + +
157A THR* 2.7 28.5 + - - -
158A GLU* 4.0 0.9 + - - +
162A PHE* 4.2 1.1 - + - -
163A LYS* 3.4 68.1 - - + +
166A CYS* 3.6 28.7 - - + +
167A LYS* 5.1 1.6 - - + +
171A SER 3.1 9.1 + - - +
172A GLU* 3.5 13.9 - - + +
174A VAL* 1.3 76.5 - - - +
176A ASP* 1.3 75.9 + - - +
178A CYS* 3.1 5.1 + - - +
179A MET* 2.9 52.3 + - + +
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Residues in contact with ASP 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A GLU* 2.8 39.2 + - - +
173A ARG* 3.8 8.6 - - - +
175A TYR* 1.3 87.1 - - - +
177A ALA* 1.3 58.9 + - - +
179A MET* 3.3 8.1 + - - +
180A ASP* 2.9 38.3 + - - +
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Residues in contact with ALA 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A LEU* 3.6 23.6 - - + -
65A ILE* 3.5 16.8 - - + +
66A THR* 4.6 11.8 - - + +
69A ALA* 5.4 0.3 - - - +
173A ARG 2.9 18.5 + - - +
174A VAL 3.6 4.3 - - - +
175A TYR 3.2 0.2 - - - -
176A ASP* 1.3 77.1 - - - +
178A CYS* 1.3 56.9 + - - +
180A ASP* 3.4 8.3 + - - +
181A ALA* 2.8 29.8 + - - +
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Residues in contact with CYS 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A ILE* 3.6 29.4 - - - -
127A ILE* 4.0 11.4 - - - -
130A VAL* 4.3 9.4 - - - -
162A PHE* 3.9 35.4 - - + -
166A CYS* 4.7 0.9 - - - -
174A VAL* 3.0 17.8 + - - -
175A TYR 3.4 8.5 - - - +
177A ALA* 1.3 76.8 - - - +
179A MET* 1.3 55.0 + - + +
181A ALA* 3.2 2.6 + - - -
182A PHE* 2.7 45.3 + - + -
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Residues in contact with MET 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A ARG* 4.9 0.2 + - - -
153A CYS* 3.7 14.6 - - - +
154A ARG* 3.7 34.4 + - + +
157A THR* 3.6 12.3 - - + +
162A PHE* 3.8 11.9 - - + -
175A TYR* 2.9 65.6 + - + +
176A ASP* 3.3 10.1 + - - +
178A CYS* 1.3 76.0 - - - +
180A ASP* 1.3 62.3 + - - +
182A PHE* 3.3 31.5 + - + +
183A ASP* 3.1 27.4 + - - +
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Residues in contact with ASP 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A ALA* 5.1 0.7 - - - -
73A ARG* 5.4 0.5 + - - -
154A ARG* 3.5 14.9 + - - -
176A ASP* 2.9 25.3 + - - +
177A ALA* 3.7 7.1 - - - +
179A MET* 1.3 75.0 - - - +
181A ALA* 1.3 62.5 + - - +
183A ASP* 3.3 22.2 + - - +
184A CYS* 3.4 14.0 - - - -
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Residues in contact with ALA 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A ILE* 4.0 8.5 - - + -
69A ALA* 3.6 29.3 - - + +
72A LEU* 4.3 3.8 - - - +
134A TRP* 3.7 26.2 - - + +
177A ALA 2.8 21.8 + - - +
178A CYS* 3.2 5.4 + - - +
180A ASP* 1.3 73.7 - - - +
182A PHE* 1.3 58.9 + - + +
184A CYS* 2.9 24.3 + - - +
185A LEU* 3.5 6.6 + - - +
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Residues in contact with PHE 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A TYR* 5.2 0.7 - + - -
120A VAL* 4.0 26.2 - - + -
130A VAL* 4.0 16.6 - - + -
134A TRP* 3.7 25.4 - + - -
148A ARG* 3.3 16.9 + - - +
152A GLU* 3.5 53.8 - - + +
153A CYS* 4.0 0.7 - - - -
157A THR* 4.6 0.7 - - + -
162A PHE* 4.0 11.2 - + - -
178A CYS* 2.7 27.2 + - + +
179A MET* 3.6 32.8 - - + +
180A ASP 3.3 0.2 - - - -
181A ALA* 1.3 72.9 - - + +
183A ASP* 1.3 61.2 + - - +
185A LEU* 3.0 32.7 + - + +
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Residues in contact with ASP 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A ARG* 5.7 2.0 - - - +
148A ARG* 3.0 22.3 + - - +
154A ARG* 2.8 38.9 + - - -
179A MET 3.1 15.8 + - - +
180A ASP* 3.4 13.2 - - - +
181A ALA 3.2 0.4 - - - -
182A PHE* 1.3 75.0 - - - +
184A CYS* 1.3 60.2 + - - +
185A LEU 3.6 0.9 + - - +
217A ARG* 3.2 20.8 - - - +
218A PHE* 3.5 16.5 - - + -
219A LYS* 3.3 25.9 - - - +
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Residues in contact with CYS 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A ALA* 3.8 31.6 - - - +
72A LEU* 3.4 13.0 - - + +
73A ARG* 3.8 41.1 - - - +
180A ASP 3.4 15.7 - - - -
181A ALA* 2.9 11.2 + - - +
183A ASP* 1.3 78.3 - - - +
185A LEU* 1.3 59.3 + - - +
186A PRO* 3.3 1.7 - - - +
217A ARG* 2.9 27.1 + - - -
218A PHE* 3.8 6.7 - - - -
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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