Contacts of the helix formed by residues 159 - 166 (chain A) in PDB entry 7RDB
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 ASP 159 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A CYS 3.1 12.5 - - - +
156A GLY* 3.5 1.2 - - - -
157A GLY 3.3 0.8 - - - -
158A GLU* 1.3 86.7 - - - +
160A TYR* 1.3 67.3 + - + +
161A ARG* 3.0 13.9 + - - +
162A ASP* 3.1 27.3 + - - +
207A ARG* 3.8 25.7 + - - +
216A VAL 3.3 15.9 - - - +
217A ARG* 5.0 0.7 - - - -
218A GLY 3.8 1.3 - - - +
209D SER* 3.1 35.8 + - - +
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Residues in contact with TYR 160 (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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155A CYS* 3.1 38.0 + - + -
159A ASP* 1.3 79.5 - - + +
161A ARG* 1.3 96.8 + - + +
162A ASP 3.0 2.0 + - - -
163A TRP* 3.1 25.1 + - - +
181A VAL* 3.8 5.7 - - + +
202A THR* 2.8 45.2 + - - -
203A ILE* 3.6 14.5 - - + +
205A LYS 3.1 18.2 + - - -
206A GLU 4.4 0.2 + - - -
207A ARG* 4.8 4.7 - - - -
210A VAL* 3.9 11.3 - - + +
214A ILE* 3.7 14.8 - - + -
215A TYR 3.9 7.0 - - - +
216A VAL* 3.1 34.5 + - + +
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Residues in contact with ARG 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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159A ASP* 3.0 5.9 + - - +
160A TYR* 1.3 98.3 + - + +
162A ASP* 1.3 65.1 + - - +
163A TRP 3.0 3.4 - - - -
164A SER* 2.9 27.3 + - - -
203A ILE* 2.9 44.8 + - + +
205A LYS 3.0 21.4 + - - -
206A GLU* 4.1 1.0 + - - +
207A ARG* 3.3 41.4 - - - +
206D GLU* 3.8 19.7 - - + +
208D PHE* 3.3 21.8 - - - +
209D SER* 2.9 37.9 + - - +
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Residues in contact with ASP 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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125A ASN* 5.9 0.3 - - - +
128A ILE* 6.2 0.2 - - + -
129A ARG* 6.3 1.8 - - + -
132A ILE* 3.9 18.6 - - + +
156A GLY* 4.1 0.9 - - - -
157A GLY* 2.8 31.2 + - - +
158A GLU* 2.8 19.7 + - - +
159A ASP* 3.1 18.1 + - - +
160A TYR 3.0 0.8 + - - -
161A ARG* 1.3 77.9 - - - +
163A TRP* 1.3 58.1 + - - +
164A SER* 2.9 7.4 + - - -
165A LYS* 3.1 25.0 + - + +
205D LYS* 4.4 21.4 - - - +
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Residues in contact with TRP 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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132A ILE* 4.0 30.3 - - + -
135A TYR* 3.4 49.8 - + + -
145A MET* 3.9 11.4 - - + -
149A GLN* 3.0 34.1 + - - -
155A CYS* 3.6 7.9 - - - -
156A GLY* 3.8 9.0 - - - +
160A TYR 3.1 24.5 + - - +
161A ARG 3.0 1.0 - - - -
162A ASP* 1.3 76.7 - - - +
164A SER* 1.3 60.9 + - - +
165A LYS 3.1 0.7 - - - -
166A ASN* 3.0 16.7 + - + +
169A HIS* 3.1 28.7 - + + +
180A GLY 4.2 4.9 - - - +
181A VAL* 3.2 24.2 - - + -
182A PRO* 3.6 28.4 - - + +
203A ILE* 4.1 8.7 - - + -
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Residues in contact with SER 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 ARG 2.9 16.7 + - - -
162A ASP* 2.9 1.4 + - - -
163A TRP* 1.3 76.0 - - - +
165A LYS* 1.3 65.4 + - - +
166A ASN 3.2 8.9 - - - +
169A HIS 4.1 13.5 - - - -
170A ASP* 3.6 20.1 - - - +
171A CYS 4.7 3.6 - - - -
203A ILE* 4.1 11.0 - - - +
204D ASP 5.2 4.9 + - - -
205D LYS* 5.9 0.2 - - - -
206D GLU* 3.4 32.2 + - - +
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Residues in contact with LYS 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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129A ARG* 5.3 9.9 - - + +
132A ILE* 4.2 9.6 - - + -
133A GLU* 3.3 31.2 - - + +
162A ASP* 3.1 17.5 + - + +
164A SER* 1.3 80.6 - - - +
166A ASN* 1.3 62.4 + - - +
167A GLN* 3.6 2.4 + - - -
204D ASP* 3.2 55.0 + - - +
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Residues in contact with ASN 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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132A ILE* 2.8 35.7 + - + +
133A GLU* 3.7 14.7 + - - +
135A TYR* 4.1 5.8 - - - +
136A TYR* 3.6 19.3 - - - +
163A TRP* 3.0 16.3 + - + +
164A SER 3.4 4.0 - - - +
165A LYS* 1.3 76.5 - - - +
167A GLN* 1.3 67.1 + - - +
168A TYR* 3.0 38.5 + - - -
169A HIS* 3.1 22.7 + - + -
170A ASP* 3.0 18.9 + - - -
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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