Contacts of the helix formed by residues 180 - 190 (chain A) in PDB entry 6RLR
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 180 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152A CYS* 3.8 0.2 - - - -
153A CYS 4.0 4.5 - - - -
154A GLY 3.6 4.7 - - - -
155A LEU 3.6 29.8 - - - -
156A ALA* 3.7 11.6 + - - +
157A GLY 5.2 0.2 - - - -
178A VAL 3.6 3.8 + - - -
179A LYS* 1.3 76.7 - - - +
181A CYS* 1.3 57.6 + - - +
182A PRO* 3.7 5.3 - - - +
183A ASP* 3.3 32.4 + - - +
184A ALA* 3.0 22.9 + - - +
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Residues in contact with CYS 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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146A ILE* 4.5 1.6 - - + -
147A HIS* 3.5 25.6 - - - -
152A CYS* 2.0 48.7 - - - -
153A CYS 3.5 5.6 - - - -
154A GLY 2.9 9.2 + - - -
180A SER* 1.3 67.8 - - - +
182A PRO* 1.4 64.2 - - + +
184A ALA* 3.6 0.2 - - - -
185A ILE* 2.7 44.9 + - + +
125D TYR* 3.6 30.5 - - + -
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Residues in contact with PRO 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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154A GLY 3.4 11.7 - - - +
155A LEU* 4.1 20.9 - - + -
156A ALA* 5.0 5.6 - - + +
180A SER* 3.7 8.7 - - - +
181A CYS* 1.4 92.6 - - + +
183A ASP* 1.3 61.9 + - - +
185A ILE* 3.5 1.5 + - + -
186A LYS 3.1 10.7 + - - -
122D GLN* 2.6 47.8 + - + +
125D TYR* 4.2 10.1 - - + -
126D LYS* 4.3 20.0 - - + +
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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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156A ALA* 5.1 7.9 - - - +
179A LYS* 4.1 24.5 + - + +
180A SER* 3.3 25.9 + - - +
181A CYS 3.2 0.4 - - - -
182A PRO* 1.3 76.8 - - - +
184A ALA* 1.3 66.1 + - - +
186A LYS* 3.1 10.4 + - - +
187A GLU* 3.1 30.2 + - - +
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Residues in contact with ALA 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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150A LEU* 3.9 24.0 - - + +
152A CYS* 3.7 21.3 - - + -
179A LYS* 4.2 13.8 - - + +
180A SER 3.0 15.6 + - - +
181A CYS 3.7 4.0 - - - +
183A ASP* 1.3 74.1 - - - +
185A ILE* 1.3 62.3 + - - +
187A GLU* 3.2 8.5 + - - +
188A VAL* 3.1 26.5 + - - +
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Residues in contact with ILE 185 (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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146A ILE* 5.1 3.8 - - + -
150A LEU* 3.8 18.4 - - + -
181A CYS* 2.7 33.3 + - + +
182A PRO 3.7 4.3 - - - +
184A ALA* 1.3 71.9 - - - +
186A LYS* 1.3 61.9 + - - +
188A VAL* 3.3 16.3 + - - +
189A PHE* 3.3 21.8 - - + -
118D ILE* 3.7 6.1 - - - +
121D VAL* 3.4 46.2 - - + +
122D GLN* 3.7 20.4 - - + -
125D TYR* 3.9 26.7 - - + -
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Residues in contact with LYS 186 (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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182A PRO 3.1 12.4 + - - +
183A ASP* 3.1 13.9 + - - +
185A ILE* 1.3 76.7 - - - +
187A GLU* 1.3 61.1 + - + +
189A PHE* 3.1 18.9 + - - +
190A ASP* 3.0 43.3 + - + +
118D ILE* 4.0 25.6 - - + +
122D GLN* 4.0 10.5 - - - +
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Residues in contact with GLU 187 (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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179A LYS* 2.7 44.2 + - - +
183A ASP* 3.1 17.3 + - - +
184A ALA* 3.2 6.7 + - - +
186A LYS* 1.3 76.4 - - + +
188A VAL* 1.3 63.4 + - - +
189A PHE 3.2 0.2 - - - -
190A ASP 3.6 24.2 + - - +
191A ASN* 4.7 8.4 - - + -
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Residues in contact with VAL 188 (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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150A LEU* 3.7 28.9 - - + -
184A ALA 3.1 19.7 + - - +
185A ILE* 3.4 14.4 - - - +
186A LYS 3.2 0.8 - - - -
187A GLU* 1.3 78.4 - - - +
189A PHE* 1.3 81.8 + - + +
190A ASP 4.0 0.2 + - - -
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Residues in contact with PHE 189 (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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185A ILE* 3.3 27.4 - - + -
186A LYS 3.1 2.6 + - - -
188A VAL* 1.3 94.9 - - + +
190A ASP* 1.3 58.3 + - - +
191A ASN 4.4 0.2 - - - -
114D LYS* 3.3 33.3 + - + +
117D VAL* 3.7 31.0 - - + -
118D ILE* 3.6 38.6 - - + -
121D VAL* 4.7 9.2 - - + -
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Residues in contact with ASP 190 (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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186A LYS* 3.0 42.5 + - + +
187A GLU* 3.6 20.5 + - - +
188A VAL 3.6 2.4 - - - -
189A PHE* 1.3 80.6 - - + +
191A ASN* 1.3 84.3 + - - +
114D LYS* 4.5 19.8 + - - +
115D ASP* 5.5 1.9 - - - +
118D ILE* 4.8 5.6 - - + +
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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