Contacts of the helix formed by residues 180 - 190 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152D CYS* 3.8 0.2 - - - -
153D CYS 4.0 4.9 - - - -
154D GLY 3.6 7.4 - - - -
155D LEU 3.8 4.3 - - - -
156D ALA* 3.7 31.0 + - - +
178D VAL 3.6 3.0 + - - -
179D LYS* 1.3 75.8 - - - +
181D CYS* 1.3 57.9 + - - +
182D PRO* 3.7 5.6 - - - +
183D ASP* 3.3 34.9 + - - +
184D ALA* 3.0 23.0 + - - +
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Residues in contact with CYS 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A TYR* 3.6 31.2 - - + -
146D ILE* 4.6 1.1 - - + -
147D HIS* 3.5 26.5 - - - -
152D CYS* 2.1 48.2 - - - -
153D CYS 3.5 5.2 - - - -
154D GLY 2.9 9.4 + - - -
180D SER* 1.3 69.0 - - - +
182D PRO* 1.3 62.8 - - + +
185D ILE* 2.7 45.3 + - + +
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Residues in contact with PRO 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A GLN* 2.8 42.0 + - + +
125A TYR* 4.2 9.9 - - + -
126A LYS* 3.8 30.3 - - + +
154D GLY 3.4 10.1 - - - +
155D LEU* 4.0 14.8 - - + -
156D ALA* 5.1 3.6 - - + +
180D SER* 3.7 9.0 - - - +
181D CYS* 1.3 94.7 - - + +
183D ASP* 1.3 62.6 + - - +
185D ILE* 3.5 2.2 + - + +
186D LYS* 3.2 11.6 + - - +
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Residues in contact with ASP 183 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156D ALA* 5.8 2.8 - - - +
179D LYS* 5.4 5.4 - - + -
180D SER* 3.3 27.1 + - - +
181D CYS 3.2 0.6 - - - -
182D PRO* 1.3 76.6 - - - +
184D ALA* 1.3 65.7 + - - +
186D LYS* 3.1 12.5 + - - +
187D GLU* 3.1 38.4 + - - +
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Residues in contact with ALA 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150D LEU* 3.9 23.3 - - + +
152D CYS* 3.7 29.8 - - + -
179D LYS* 4.8 10.5 - - + +
180D SER 3.0 7.9 + - - +
181D CYS 3.1 3.6 + - - +
183D ASP* 1.3 74.3 - - - +
185D ILE* 1.3 61.7 + - - +
187D GLU* 3.2 11.9 + - - +
188D VAL* 3.1 26.7 + - - +
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Residues in contact with ILE 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A ILE* 3.9 5.8 - - + +
121A VAL* 3.5 40.6 - - + +
122A GLN* 3.7 22.4 - - + -
125A TYR* 3.9 27.6 - - + -
146D ILE* 5.0 3.6 - - + -
150D LEU* 3.8 20.0 - - + -
181D CYS* 2.7 34.4 + - + +
182D PRO 3.7 5.4 - - - +
184D ALA* 1.3 71.9 - - - +
186D LYS* 1.3 62.6 + - - +
188D VAL* 3.3 17.2 + - - +
189D PHE* 3.3 21.6 - - + -
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Residues in contact with LYS 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A ILE* 4.3 22.2 - - + +
122A GLN* 4.1 8.9 - - - +
182D PRO 3.2 12.6 + - - +
183D ASP* 3.1 15.7 + - - +
185D ILE* 1.3 76.9 - - - +
187D GLU* 1.3 62.0 + - + +
189D PHE* 3.1 18.9 + - - +
190D ASP* 3.2 43.0 + - + +
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Residues in contact with GLU 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179D LYS* 4.0 28.9 + - - +
183D ASP* 3.1 28.4 + - - +
184D ALA* 3.2 8.0 + - - +
186D LYS* 1.3 80.0 - - + +
188D VAL* 1.3 63.6 + - - +
189D PHE 3.2 0.4 - - - -
190D ASP 3.6 23.6 + - - +
191D ASN* 5.9 0.3 - - - +
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Residues in contact with VAL 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150D LEU* 3.7 29.8 - - + -
184D ALA 3.1 19.6 + - - +
185D ILE* 3.4 14.1 - - - +
186D LYS 3.2 0.4 - - - -
187D GLU* 1.3 78.3 - - - +
189D PHE* 1.3 82.7 + - + +
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Residues in contact with PHE 189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A LYS* 2.6 41.8 + - + +
117A VAL* 3.8 30.1 - - + -
118A ILE* 3.6 40.6 - - + -
121A VAL* 4.7 10.5 - - + -
185D ILE* 3.3 26.9 - - + -
186D LYS 3.1 3.4 + - - +
188D VAL* 1.3 96.1 - - + +
190D ASP* 1.3 53.0 + - - +
191D ASN 4.4 0.2 - - - -
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Residues in contact with ASP 190 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A LYS* 4.1 17.9 + - - +
118A ILE* 5.1 4.5 - - + +
186D LYS* 3.2 43.3 + - + +
187D GLU* 3.6 26.7 + - - +
188D VAL 3.6 2.4 - - - -
189D PHE* 1.3 81.1 - - + +
191D ASN* 1.3 73.3 + - - +
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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