Contacts of the helix formed by residues 147 - 159 (chain D) in PDB entry 4RZR
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 ASN 147 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1D MET* 4.7 2.7 - - - -
3D VAL* 3.6 13.3 - - - +
145D SER* 3.4 1.5 + - - -
146D LYS* 1.3 90.3 - - - +
148D LYS* 1.3 63.4 + - - +
149D VAL* 3.2 5.1 + - - +
150D PHE* 3.0 40.3 + - - -
151D ALA* 3.0 24.4 + - - +
228D LEU* 4.3 2.0 - - - +
231D ASP* 5.0 5.9 + - - +
233D TYR* 3.4 51.2 + - + +
234D ASN* 4.7 4.5 - - - -
235D GLU 6.0 0.2 - - - +
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Residues in contact with LYS 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D VAL* 4.0 2.9 - - + -
100D GLU* 2.8 27.1 + - - +
108D TYR* 3.3 45.0 - - + -
147D ASN* 1.3 73.8 - - - +
149D VAL* 1.3 66.4 + - - +
151D ALA* 3.2 1.2 + - - +
152D LYS* 3.0 19.2 + - - +
233D TYR* 3.9 7.7 - - + +
235D GLU* 3.6 35.9 + - - +
236D PRO 3.5 6.9 + - - -
237D ILE* 3.8 24.0 - - + +
240D ARG* 4.3 5.3 - - - +
406D GOL 2.7 38.8 + - - +
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Residues in contact with VAL 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D TYR* 5.6 0.4 - - - -
147D ASN* 3.2 6.2 + - - +
148D LYS* 1.3 76.3 - - - +
150D PHE* 1.3 58.7 + - + +
152D LYS* 3.1 10.3 + - - +
153D ILE* 3.0 33.5 + - + +
183D VAL* 4.4 2.2 - - + -
184D PRO* 3.8 22.2 - - + +
224D TYR* 3.3 31.6 - - + +
228D LEU* 3.8 24.2 - - + -
233D TYR* 3.7 28.9 - - + -
406D GOL 3.8 9.2 - - - +
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Residues in contact with PHE 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145D SER* 3.5 23.7 - - - +
146D LYS* 5.4 0.2 - - + -
147D ASN* 3.0 28.7 + - - +
149D VAL* 1.3 78.4 - - + +
151D ALA* 1.3 58.2 + - - +
153D ILE* 3.9 22.9 - - + -
154D ALA* 3.1 26.2 + - - +
166D ILE* 3.7 8.5 - - + +
171D VAL* 3.8 35.2 - - + -
174D LEU* 4.1 33.9 - - + -
175D ILE* 4.2 11.4 - - + -
178D LEU* 5.2 2.2 - - + -
202D LEU* 4.1 22.2 - - + -
228D LEU* 4.0 24.2 - - + -
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Residues in contact with ALA 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D VAL* 3.9 22.0 - - + +
5D PHE* 3.7 15.4 - - + -
143D GLY* 3.3 33.0 - - - +
145D SER* 3.8 8.2 - - - +
147D ASN 3.0 18.4 + - - +
148D LYS 3.5 4.9 - - - +
149D VAL 3.2 0.2 - - - -
150D PHE* 1.3 77.2 - - - +
152D LYS* 1.3 61.2 + - - +
154D ALA 3.5 0.3 + - - -
155D ALA 3.2 16.1 + - - -
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Residues in contact with LYS 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D PHE* 3.7 20.8 - - + +
7D ASP* 4.8 4.0 + - - -
106D GLU* 2.8 28.6 + - - +
108D TYR* 3.5 22.2 - - + +
148D LYS 3.0 11.6 + - - +
149D VAL* 3.5 8.1 - - - +
151D ALA* 1.3 75.4 - - - +
153D ILE* 1.3 59.7 + - - +
155D ALA* 3.2 3.6 + - - +
156D ASP* 2.8 48.8 + - - +
184D PRO* 3.8 28.3 - - + -
13F C 2.8 37.5 + - - -
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Residues in contact with ILE 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149D VAL* 3.0 26.9 + - + +
150D PHE* 3.9 25.4 - - + +
152D LYS* 1.3 76.1 - - - +
154D ALA* 1.3 62.5 + - - +
156D ASP* 3.0 11.0 + - - +
157D MET* 2.9 47.0 + - + +
166D ILE* 3.9 9.2 - - + -
174D LEU* 4.6 2.9 - - + -
178D LEU* 3.8 25.8 - - + -
182D ASP* 3.7 10.8 - - + +
183D VAL* 4.5 6.1 - - + -
184D PRO* 3.6 25.1 - - + -
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Residues in contact with ALA 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143D GLY* 3.8 4.0 - - - -
144D ILE 4.0 4.7 - - - +
150D PHE 3.1 18.6 + - - +
151D ALA 3.7 5.8 - - - +
152D LYS 3.2 0.2 - - - -
153D ILE* 1.3 75.3 - - - +
155D ALA* 1.3 63.3 + - - +
157D MET* 3.2 8.7 + - - +
158D ALA* 3.1 22.3 + - - +
164D LYS* 3.7 30.8 - - + +
166D ILE* 3.6 24.5 - - + -
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Residues in contact with ALA 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D PHE* 3.6 35.4 - - + -
7D ASP* 4.8 3.8 - - + -
141D THR* 3.3 23.0 - - + +
142D VAL 4.1 1.1 - - - -
143D GLY* 3.7 16.7 - - - +
151D ALA 3.2 2.2 + - - -
152D LYS 3.2 3.6 + - - +
154D ALA* 1.3 78.4 - - - +
156D ASP* 1.3 63.8 + - - +
158D ALA 3.2 0.9 + - - -
159D LYS* 3.1 29.3 + - - +
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Residues in contact with ASP 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D PHE* 5.5 0.5 - - - -
7D ASP* 4.7 1.7 - - - +
152D LYS* 2.8 42.5 + - - +
153D ILE* 3.0 12.2 + - + +
155D ALA* 1.3 78.0 - - - +
157D MET* 1.3 61.4 + - + +
158D ALA 3.3 1.0 + - - -
159D LYS* 3.7 35.1 + - - +
182D ASP 4.9 5.2 - - - +
184D PRO* 4.7 5.5 - - - +
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Residues in contact with MET 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153D ILE* 2.9 31.1 + - + +
154D ALA 3.2 7.8 + - - +
156D ASP* 1.3 76.9 - - + +
158D ALA* 1.3 57.2 + - - +
159D LYS 4.8 2.1 - - - +
164D LYS* 3.6 31.6 - - + -
166D ILE* 4.1 13.0 - - - -
170D GLU* 5.1 2.9 - - - +
173D ARG* 5.8 0.7 - - - +
174D LEU* 3.9 20.2 - - + -
178D LEU* 3.9 23.3 - - + -
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Residues in contact with ALA 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D THR* 3.8 15.3 - - + -
154D ALA 3.1 15.1 + - - +
155D ALA 3.2 0.6 + - - -
157D MET* 1.3 76.0 - - - +
159D LYS* 1.3 67.4 + - - +
160D PRO 3.4 3.1 - - - +
162D GLY* 3.3 17.1 - - - -
163D ILE 3.9 18.8 - - - +
164D LYS* 3.9 16.6 - - + +
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Residues in contact with LYS 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D ASP* 2.8 31.3 + - - -
9D ASP* 5.0 2.0 - - - +
48D TYR* 3.9 9.3 - - - +
141D THR* 3.5 13.0 - - - +
155D ALA* 3.1 16.9 + - - +
156D ASP* 3.7 31.7 + - - +
157D MET 3.6 3.3 - - - +
158D ALA* 1.3 80.5 - - - +
160D PRO* 1.3 68.5 - - + +
401D DCP 2.7 49.0 + - - +
403D CA 4.5 0.2 - - - -
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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