Contacts of the helix formed by residues 161 - 172 (chain A) in PDB entry 2R8J
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 LEU 161 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A CYS* 3.1 25.9 + - - +
27A ALA* 4.1 8.5 - - + -
146A CYS* 4.8 4.0 - - + -
159A LEU* 3.5 39.3 - - + +
160A ASP* 1.3 69.0 - - - +
162A GLY* 1.3 65.5 + - - +
163A ARG 3.6 1.1 - - - -
164A ILE* 3.4 14.9 + - + -
165A CYS* 3.0 33.1 + - - -
241A GLY* 3.5 36.8 - - - +
244A VAL* 4.9 11.4 - - + -
245A CYS* 4.4 12.1 - - + +
248A ILE* 5.8 2.2 - - + -
264A LEU* 4.3 7.6 - - + -
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Residues in contact with GLY 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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12A LEU* 3.1 34.3 - - - +
18A ALA* 5.0 0.2 - - - -
25A CYS* 4.3 5.4 + - - -
160A ASP* 2.9 21.4 + - - -
161A LEU* 1.3 79.3 - - - +
163A ARG* 1.3 61.7 + - - -
165A CYS* 3.9 2.1 - - - +
166A PHE* 3.0 21.8 + - - +
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Residues in contact with ARG 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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12A LEU 3.0 29.1 + - - -
13A GLY* 3.1 26.7 - - - +
14A SER 3.3 5.3 + - - -
15A PRO* 3.7 15.6 - - + +
18A ALA* 3.2 26.1 - - - +
147A ASP* 3.1 34.9 + - - +
148A LEU* 3.4 37.2 - - - +
160A ASP* 3.3 23.8 + - - +
161A LEU 3.6 0.2 - - - -
162A GLY* 1.3 72.5 - - - +
164A ILE* 1.3 62.8 + - + +
166A PHE* 3.8 2.8 - - - +
167A ASN* 3.0 41.2 + - - +
147B ASP* 6.2 3.8 - - + -
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Residues in contact with ILE 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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145A ALA 3.2 27.6 - - - +
146A CYS* 4.6 9.2 - - + -
147A ASP* 5.1 6.7 - - - +
160A ASP 5.5 0.7 - - - +
161A LEU* 3.4 20.2 + - + +
162A GLY 3.2 1.0 - - - -
163A ARG* 1.3 79.3 - - + +
165A CYS* 1.3 58.3 + - - +
167A ASN* 4.0 3.1 - - - +
168A MET* 2.8 38.6 + - + +
244A VAL* 3.7 45.1 - - + -
248A ILE* 5.2 2.0 - - + -
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Residues in contact with CYS 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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12A LEU* 5.1 0.4 - - + -
25A CYS* 4.2 3.6 - - - -
161A LEU* 3.0 30.7 + - - +
162A GLY* 3.9 2.5 - - - +
164A ILE* 1.3 77.5 - - - +
166A PHE* 1.3 57.5 + - - +
168A MET* 3.7 6.4 - - - +
169A LEU* 2.8 32.1 + - - +
237A ILE* 3.5 37.9 - - + +
240A LEU* 4.0 8.8 - - + +
241A GLY* 3.5 34.1 - - - -
244A VAL* 5.4 2.0 - - - -
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Residues in contact with PHE 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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6A TRP* 6.4 0.2 - + - -
9A LEU* 3.6 50.3 - - + -
10A ILE* 4.2 14.8 - - + -
12A LEU* 4.1 11.0 - - + +
13A GLY* 4.9 11.0 - - - -
162A GLY 3.0 17.6 + - - +
163A ARG* 3.8 5.2 - - - +
165A CYS* 1.3 76.4 - - - +
167A ASN* 1.3 78.5 + - - +
169A LEU* 2.9 9.6 + - + +
170A MET* 2.9 41.8 + - + +
171A PHE* 5.0 2.9 - + - -
194A PHE* 3.5 37.5 - + - -
237A ILE* 4.8 4.2 - - - +
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Residues in contact with ASN 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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163A ARG* 3.0 32.4 + - - +
164A ILE* 4.0 3.1 - - - +
166A PHE* 1.3 90.8 - - - +
168A MET* 1.3 58.2 + - - +
170A MET 4.4 0.2 - - - +
171A PHE* 2.6 41.3 + - + +
172A ASP 3.4 3.2 + - - -
143B LYS 4.8 3.6 + - - -
144B SER* 3.1 47.7 + - - +
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Residues in contact with MET 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 ILE* 2.8 27.8 + - + +
165A CYS* 3.7 4.5 - - - +
167A ASN* 1.3 72.3 - - - +
169A LEU* 1.3 61.7 + - - +
172A ASP* 3.1 48.1 - - + +
175A TYR* 5.4 12.6 - - + -
183A LEU* 3.9 7.3 - - + +
191A ARG* 3.2 8.3 + - - -
240A LEU* 3.8 35.2 - - + +
243A GLN* 5.5 3.8 - - + -
244A VAL* 3.5 33.7 - - + +
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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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9A LEU* 4.0 22.4 - - + -
165A CYS 2.8 18.9 + - - +
166A PHE* 2.9 8.9 + - - +
168A MET* 1.3 77.6 - - - +
170A MET* 1.3 76.9 + - + +
183A LEU* 5.2 0.2 - - - -
187A LEU* 3.4 33.3 - - + +
190A ILE* 5.6 0.2 - - + -
191A ARG* 2.9 19.8 + - - +
233A TRP* 4.3 17.3 - - + -
236A VAL* 3.9 21.3 - - + -
237A ILE* 3.5 23.6 - - + -
240A LEU* 4.0 10.5 - - + -
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Residues in contact with MET 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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6A TRP* 5.2 0.4 - - - -
9A LEU* 5.1 1.3 - - - -
166A PHE* 2.9 43.8 + - + +
169A LEU* 1.3 115.6 - - + +
171A PHE* 1.3 84.5 + - + +
190A ILE* 3.5 47.6 - - + +
191A ARG* 3.1 35.3 + - + +
194A PHE* 3.7 26.5 - - + -
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Residues in contact with PHE 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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166A PHE* 5.0 3.4 - + - -
167A ASN* 2.6 27.0 + - + +
170A MET* 1.3 96.0 - - + +
172A ASP* 1.3 63.8 + - - +
173A ASN* 2.9 21.2 + - - +
191A ARG* 3.9 2.9 - - - +
194A PHE* 3.9 20.6 - + - -
195A ILE* 4.3 13.5 - - + -
140B LYS 3.9 10.8 - - - -
141B ILE* 4.0 23.8 - - + -
144B SER* 3.4 40.2 - - - +
255B ILE* 4.9 11.0 - - + -
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Residues in contact with ASP 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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167A ASN 3.4 3.2 + - - -
168A MET* 3.1 46.4 + - + +
171A PHE* 1.3 74.8 - - - +
173A ASN* 1.3 59.3 + - - +
174A GLU* 2.9 9.0 + - - +
175A TYR* 2.7 44.4 + - - +
183A LEU* 4.3 8.1 - - + +
184A LYS 4.4 0.3 + - - -
191A ARG* 2.7 26.3 + - - -
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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