Contacts of the helix formed by residues 159 - 166 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155H CYS 3.1 14.2 - - - +
156H GLY* 4.1 0.2 - - - -
157H GLY 3.4 1.0 - - - -
158H GLU* 1.3 89.1 - - - +
160H TYR* 1.3 71.2 + - + +
161H ARG* 3.3 20.2 + - - +
162H ASP* 2.9 27.9 + - - +
207H ARG* 3.4 26.4 + - - +
216H VAL 3.4 16.2 - - - +
218H GLY 3.8 2.5 - - - +
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Residues in contact with TYR 160 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155H CYS* 3.1 35.7 + - + -
159H ASP* 1.3 80.5 - - + +
161H ARG* 1.3 69.4 + - + +
162H ASP 3.0 1.7 + - - -
163H TRP* 3.2 23.0 + - - +
181H VAL* 3.8 5.0 - - + +
202H THR* 3.2 25.7 + - - -
203H ILE* 3.8 22.1 + - + +
206H GLU* 3.5 33.8 + - - -
207H ARG* 3.7 17.8 + - + +
210H VAL* 4.3 8.5 - - + -
214H ILE* 4.1 20.2 - - + -
215H TYR 4.2 2.2 - - - +
216H VAL* 3.3 36.3 + - + -
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Residues in contact with ARG 161 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159H ASP* 2.9 16.4 + - - +
160H TYR* 1.3 89.9 - - + +
162H ASP* 1.3 65.5 + - - +
163H TRP 3.1 1.6 + - - -
164H SER* 3.0 23.4 + - - -
203H ILE* 4.6 21.2 - - + +
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Residues in contact with ASP 162 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129H ARG* 3.3 35.8 + - + +
132H ILE* 4.1 16.3 - - + +
156H GLY* 4.3 1.8 - - - -
157H GLY* 2.8 17.5 + - - +
158H GLU* 2.7 34.1 + - - +
159H ASP* 2.9 20.1 + - - +
161H ARG* 1.3 78.1 - - - +
163H TRP* 1.3 63.2 + - - +
164H SER* 3.0 0.8 + - - -
165H LYS* 2.9 27.3 + - - +
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Residues in contact with TRP 163 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132H ILE* 3.5 44.2 - - + -
135H TYR* 3.3 49.4 - + + -
145H MET* 4.5 8.1 - - + -
149H GLN* 2.9 35.2 + - - -
155H CYS* 3.6 9.4 - - - -
156H GLY* 3.7 10.5 - - - +
160H TYR 3.2 12.0 + - - +
161H ARG 3.1 2.0 - - - -
162H ASP* 1.3 75.5 - - - +
164H SER* 1.3 61.2 + - - +
165H LYS 3.0 0.9 - - - -
166H ASN* 3.0 16.5 + - + +
169H HIS* 3.2 26.1 - + + +
180H GLY 4.3 3.4 - - - +
181H VAL* 3.1 28.7 - - + -
182H PRO* 3.4 30.2 - - + +
203H ILE* 4.2 9.2 - - + -
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Residues in contact with SER 164 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161H ARG 3.0 17.2 + - - -
162H ASP 2.9 1.7 + - - -
163H TRP* 1.3 76.3 - - - +
165H LYS* 1.3 69.0 + - - +
166H ASN 3.2 8.3 + - - +
169H HIS 4.3 2.2 - - - -
170H ASP* 3.7 34.8 - - - +
171H CYS* 4.9 4.0 - - - -
203H ILE* 4.1 19.5 - - - +
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Residues in contact with LYS 165 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129H ARG* 3.9 42.2 - - + +
132H ILE* 4.2 3.8 - - + -
133H GLU* 3.8 36.6 - - + +
162H ASP* 2.9 18.3 + - - +
164H SER* 1.3 82.2 + - - +
166H ASN* 1.3 62.7 + - - +
167H GLN* 3.7 1.9 + - - -
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Residues in contact with ASN 166 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132H ILE* 3.0 35.3 + - + +
133H GLU* 4.0 11.8 + - - +
135H TYR* 3.8 4.8 - - - +
136H TYR* 3.5 24.0 - - - +
163H TRP* 3.0 14.6 + - + +
164H SER 3.4 3.1 - - - +
165H LYS* 1.3 80.0 - - - +
167H GLN* 1.3 67.7 + - - +
168H TYR* 2.8 33.7 + - - +
169H HIS* 3.4 23.5 - - + -
170H ASP* 3.1 20.4 + - - +
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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