Contacts of the helix formed by residues 154 - 160 (chain B) in PDB entry 2R8P
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 GLY 154 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64B ASN* 4.0 12.6 - - - +
153B MET* 1.3 75.2 - - - +
155B ASP* 1.3 65.5 + - - -
156B GLY 3.2 3.1 + - - -
157B CYS* 3.4 6.4 + - - +
158B MET* 3.1 24.6 + - - +
182B TYR* 3.7 7.0 - - - -
183B ASP* 4.1 16.2 - - - -
671B T6F 4.1 11.9 - - - -
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Residues in contact with ASP 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B GLY* 1.3 71.8 - - - -
156B GLY* 1.3 58.5 + - - +
158B MET* 3.2 2.5 + - - +
159B MET* 2.9 49.1 + - + +
182B TYR* 2.5 34.5 + - - -
183B ASP 4.2 3.5 + - - +
184B ASP* 4.8 3.3 - - - +
185B ASN* 3.2 8.5 - - - +
186B GLY 4.0 5.0 + - - -
187B ILE 3.3 8.0 + - - +
188B SER* 5.0 0.2 - - - -
193B VAL* 4.3 14.3 - - + +
197B PHE* 3.6 13.0 - - + -
670B CA 2.3 26.7 - - - -
671B T6F 3.3 11.3 + - - +
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Residues in contact with GLY 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409A VAL* 3.9 24.1 - - - +
116B LEU* 4.0 15.7 - - - -
155B ASP* 1.3 77.8 - - - +
157B CYS* 1.3 60.5 + - - +
159B MET* 3.3 3.5 + - - +
160B GLU* 3.2 27.2 + - - +
671B T6F 3.2 19.5 + - - -
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Residues in contact with CYS 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B SER* 3.1 46.0 - - - +
64B ASN* 4.1 2.0 - - - -
116B LEU* 3.9 9.8 - - - +
117B GLY* 3.3 27.7 - - - +
120B ILE* 4.8 0.2 - - + -
153B MET* 4.0 22.7 - - + -
154B GLY 3.4 11.9 + - - +
156B GLY* 1.3 75.0 - - - +
158B MET* 1.3 61.5 + - - +
160B GLU* 3.4 10.7 + - - +
163B SER* 3.1 21.5 + - - -
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Residues in contact with MET 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A HIS* 2.8 23.4 + - - -
153B MET* 3.8 17.7 - - + -
154B GLY 3.1 15.5 + - - +
155B ASP 3.5 9.2 - - - +
156B GLY 3.2 0.2 - - - -
157B CYS* 1.3 76.7 - - - +
159B MET* 1.3 56.5 + - - +
163B SER* 3.1 6.5 + - - -
182B TYR* 3.7 39.9 - - + -
197B PHE* 3.7 18.2 - - + -
201B THR* 3.9 12.3 - - + +
204B ARG* 2.9 14.3 + - - +
205B PHE* 3.5 41.3 - - + -
240B LEU* 3.8 18.2 - - + -
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Residues in contact with MET 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A HIS* 3.5 13.9 + - - -
165A GLU* 3.7 9.9 - - - +
408A GLY* 3.8 10.8 - - - -
409A VAL* 3.5 46.8 - - + +
410A ARG* 3.9 19.3 + - + +
155B ASP* 2.9 43.7 + - + +
156B GLY 3.3 3.1 + - - +
158B MET* 1.3 75.5 - - - +
160B GLU* 1.3 66.5 + - - +
161B GLY 3.5 1.6 + - - -
188B SER* 4.5 7.9 - - - -
193B VAL* 4.8 0.7 - - + -
196B TRP* 3.9 15.3 - - + +
197B PHE* 3.6 42.4 - - + -
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Residues in contact with GLU 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A HIS* 3.6 2.1 - - - -
165A GLU* 3.3 15.0 - - - +
409A VAL* 3.3 18.2 - - + +
411A GLU* 2.5 32.5 - - - +
440A TYR* 3.4 19.4 - - - -
116B LEU* 3.8 17.0 - - + +
117B GLY* 4.5 0.7 - - - -
156B GLY 3.2 15.4 + - - +
157B CYS 3.7 9.4 - - - +
158B MET 3.3 0.6 - - - -
159B MET* 1.3 77.8 - - - +
161B GLY* 1.3 62.2 + - - +
162B ILE* 4.2 16.3 + - + -
163B SER* 2.8 28.8 + - - -
412B PHE* 5.5 0.3 - - - -
671B T6F 3.2 15.4 - - - +
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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