Contacts of the helix formed by residues 160 - 173 (chain A) in PDB entry 2R8O
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 GLU 160 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116A LEU 3.7 17.5 - - - +
117A GLY* 4.5 0.4 - - - -
156A GLY 3.1 20.2 + - - +
157A CYS 3.7 7.2 - - - +
158A MET 3.4 0.6 - - - -
159A MET* 1.3 76.5 - - - +
161A GLY* 1.3 63.2 + - - +
162A ILE* 4.1 16.4 + - + -
163A SER* 2.8 29.5 + - - -
412A PHE* 5.5 0.2 - - - -
671A T5X 3.2 15.1 - - - +
164B HIS* 3.6 2.3 - - - -
165B GLU* 3.3 14.8 - - - +
409B VAL* 3.3 23.5 - - + +
411B GLU* 2.6 27.6 - - - +
440B TYR* 3.4 19.9 - - - -
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Residues in contact with GLY 161 (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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160A GLU* 1.3 72.2 + - - +
162A ILE* 1.3 62.6 + - - +
164A HIS* 2.9 17.0 + - - +
165A GLU* 3.2 8.5 + - - -
161B GLY* 3.3 38.1 - - - -
164B HIS* 4.1 4.7 - - - -
165B GLU* 2.8 24.2 + - - +
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Residues in contact with ILE 162 (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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116A LEU 4.4 2.5 - - - +
117A GLY* 3.5 32.5 - - - +
118A GLN* 3.9 7.4 - - + +
121A ALA* 3.9 7.9 - - + -
160A GLU* 4.1 8.9 + - + +
161A GLY* 1.3 75.7 - - - +
163A SER* 1.3 64.9 + - - +
165A GLU* 3.2 9.2 + - - +
166A VAL* 3.0 28.0 + - + +
412A PHE* 3.7 51.9 - - + +
413A GLY* 3.9 19.1 - - - +
416A ALA* 3.8 23.3 - - + -
440B TYR* 5.2 0.2 - - + -
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Residues in contact with SER 163 (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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120A ILE* 4.5 12.6 - - - -
153A MET* 4.6 5.8 - - - -
157A CYS 3.1 21.3 - - - -
158A MET* 3.1 13.1 + - - -
160A GLU 2.8 16.2 + - - -
162A ILE* 1.3 83.7 - - - +
164A HIS* 1.3 54.9 + - - +
166A VAL* 4.2 7.4 - - - -
167A CYS* 3.0 38.9 + - - +
204A ARG* 2.8 26.8 + - - -
205A PHE* 5.4 0.2 - - - -
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Residues in contact with HIS 164 (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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161A GLY 2.9 9.7 + - - +
163A SER* 1.3 79.5 + - - +
165A GLU* 1.3 65.5 + - - +
168A SER* 3.0 32.2 + - - -
204A ARG* 3.4 0.7 - - - +
208A TYR* 2.7 33.7 + + - +
158B MET 2.8 20.8 + - - -
159B MET* 3.4 22.4 + - - -
160B GLU 3.6 15.5 - - - -
161B GLY* 4.1 0.9 - - - -
164B HIS* 3.4 23.6 - - + -
197B PHE* 5.5 0.2 - + - -
199B ASP* 3.5 19.7 - - - -
204B ARG* 3.2 33.9 + - - -
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Residues in contact with GLU 165 (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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161A GLY 3.2 2.9 + - - +
162A ILE* 3.2 9.9 + - - +
164A HIS* 1.3 79.3 - - - +
166A VAL* 1.3 62.3 + - - +
169A LEU* 3.3 16.3 + - - +
410A ARG* 3.2 51.1 + - + +
412A PHE* 3.5 11.9 + - - +
413A GLY* 2.7 36.3 + - - -
417A ILE* 5.8 0.4 - - - -
440A TYR* 5.6 0.7 - - - -
159B MET 3.7 9.6 - - - +
160B GLU* 3.3 12.5 - - - +
161B GLY* 2.8 37.8 + - - +
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Residues in contact with VAL 166 (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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120A ILE* 4.3 3.1 - - + -
121A ALA* 3.6 39.0 - - + +
124A VAL* 3.8 21.5 - - + +
162A ILE* 3.0 17.9 + - + +
163A SER* 3.9 8.1 - - - +
165A GLU* 1.3 74.4 - - - +
167A CYS* 1.3 71.3 + - - +
169A LEU* 3.5 1.3 + - - +
170A ALA* 2.9 28.4 + - - +
413A GLY* 3.5 29.6 - - - -
417A ILE* 3.8 18.8 - - + -
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Residues in contact with CYS 167 (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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120A ILE* 4.0 25.8 - - - -
124A VAL* 5.1 0.7 - - - -
153A MET* 5.1 1.1 - - - -
163A SER* 3.0 26.0 + - - +
166A VAL* 1.3 76.5 - - - +
168A SER* 1.3 65.5 + - - +
170A ALA* 3.4 0.6 + - - -
171A GLY 3.1 7.8 + - - -
205A PHE* 3.6 37.2 - - + -
208A TYR* 3.8 12.2 - - + +
210A TRP* 2.9 41.3 + - + -
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Residues in contact with SER 168 (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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164A HIS* 3.0 25.8 + - - -
165A GLU 3.7 3.4 - - - -
167A CYS* 1.3 76.8 - - - +
169A LEU* 1.3 63.1 + - - +
171A GLY* 3.2 10.6 + - - -
172A THR* 3.2 15.9 + - - -
208A TYR* 3.9 22.0 - - - +
410A ARG* 3.0 22.5 + - - -
197B PHE* 4.3 0.7 - - - -
198B THR* 4.9 0.7 + - - -
199B ASP* 2.6 31.1 + - - +
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Residues in contact with LEU 169 (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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124A VAL* 5.7 0.2 - - + -
128A ILE* 5.0 2.2 - - + -
165A GLU 3.3 14.9 + - - +
166A VAL* 3.9 5.2 - - - +
167A CYS 3.3 0.2 - - - -
168A SER* 1.3 79.0 + - - +
170A ALA* 1.3 62.9 + - - +
172A THR* 3.1 11.4 + - + -
173A LEU* 3.0 48.2 + - + +
405A ILE* 4.6 3.8 - - + -
406A HIS 4.1 13.9 - - - +
407A TYR* 3.9 39.3 - - + +
410A ARG* 4.0 22.6 - - - +
417A ILE* 4.0 17.7 - - + -
195B GLY 5.5 0.4 - - - +
196B TRP* 4.2 9.9 - - - +
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Residues in contact with ALA 170 (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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124A VAL* 4.1 12.3 - - + +
166A VAL 2.9 17.9 + - - +
167A CYS 3.7 5.6 - - - +
168A SER 3.3 0.2 - - - -
169A LEU* 1.3 75.9 - - - +
171A GLY* 1.3 61.7 + - - +
173A LEU* 3.4 1.1 + - - -
174A LYS 3.1 17.2 + - - -
175A LEU* 3.4 36.9 + - + +
178A LEU* 4.2 4.0 - - + -
210A TRP* 3.9 20.4 - - + -
238A PRO* 3.8 5.3 - - + +
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Residues in contact with GLY 171 (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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167A CYS 3.1 11.4 + - - -
168A SER 3.7 0.4 - - - -
169A LEU 3.2 0.4 - - - -
170A ALA* 1.3 74.4 - - - +
172A THR* 1.3 65.5 + - - +
174A LYS* 3.1 19.2 + - - +
208A TYR 3.1 27.1 - - - -
209A GLY* 4.6 5.9 - - - +
210A TRP* 3.8 8.4 - - - +
238A PRO* 4.2 6.7 - - - +
198B THR* 4.7 1.1 - - - -
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Residues in contact with THR 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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168A SER 3.2 11.5 + - - -
169A LEU* 3.1 18.0 + - + -
171A GLY* 1.3 75.9 - - - +
173A LEU* 1.3 65.0 + - + +
174A LYS* 3.4 11.6 + - - +
208A TYR 4.4 0.2 + - - -
397A ASN* 5.4 3.4 - - + +
194B GLU 4.1 4.3 - - - +
195B GLY 3.9 21.1 - - - +
196B TRP* 4.1 12.7 + - - -
197B PHE* 4.4 0.3 - - - -
198B THR* 2.6 48.1 + - + +
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Residues in contact with LEU 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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128A ILE* 3.8 32.3 - - + -
131A LYS* 2.7 33.6 + - + +
169A LEU* 3.0 40.2 + - + +
171A GLY 3.2 0.2 - - - -
172A THR* 1.3 78.1 - - + +
174A LYS* 1.3 65.0 + - - +
175A LEU* 3.3 19.0 + - + +
396A ILE* 4.1 26.0 - - + +
397A ASN* 4.2 31.4 - - + -
405A ILE* 4.9 4.9 - - + -
195B GLY 5.4 0.9 - - - +
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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