Contacts of the helix formed by residues 146 - 161 (chain D) in PDB entry 5XVO
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 146 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143D ASP* 3.2 16.1 + - - +
144D PRO 3.1 7.6 - - - +
145D ALA* 1.3 81.1 - - - +
147D ARG* 1.3 65.3 + - - +
148D GLU* 3.2 3.2 - - - +
149D GLY* 2.9 31.6 + - - -
150D HIS* 3.1 16.5 + - - +
153D ARG* 6.1 1.0 - - - +
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Residues in contact with ARG 147 (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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113D ILE* 4.6 2.7 - - + -
135D MET* 3.9 24.4 + - + +
138D GLU* 2.9 62.4 + - - +
139D LEU* 3.8 15.3 - - + +
140D ARG 5.1 0.9 - - - +
143D ASP* 2.9 14.1 + - - +
145D ALA* 3.1 30.0 - - + +
146D ASN* 1.3 71.6 - - - +
148D GLU* 1.3 61.7 + - - +
150D HIS* 3.9 6.0 - - + +
151D ALA* 2.8 34.1 + - - +
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Residues in contact with GLU 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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105D TRP* 4.0 14.4 - - - -
109D ILE* 3.2 38.7 - - + +
112D LYS* 3.0 33.9 + - + +
113D ILE* 4.1 13.7 - - + +
116D GLN* 4.8 1.9 - - - +
139D LEU* 4.7 0.2 - - - +
143D ASP* 2.9 15.4 + - + +
146D ASN* 4.5 3.2 - - - +
147D ARG* 1.3 77.7 - - - +
149D GLY* 1.3 58.6 + - - +
151D ALA* 3.4 2.9 + - - +
152D ALA* 2.9 28.8 + - + +
203D LYS* 5.4 1.9 + - - -
219D GLU* 3.4 5.7 - - - +
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Residues in contact with GLY 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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146D ASN* 2.9 29.5 + - - -
148D GLU* 1.3 76.7 - - - +
150D HIS* 1.3 60.1 + - - +
152D ALA* 3.8 6.0 - - - +
153D ARG* 3.1 34.0 + - - +
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Residues in contact with HIS 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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135D MET* 3.5 33.7 - - + +
146D ASN* 3.1 16.6 + - - +
147D ARG* 3.9 5.6 - - - +
149D GLY* 1.3 74.7 - - - +
151D ALA* 1.3 66.0 + - - +
153D ARG* 3.1 33.6 + - - +
154D SER* 3.1 27.6 + - - -
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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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113D ILE* 4.3 17.0 - - + -
116D GLN* 4.3 11.2 - - - +
132D LEU* 4.1 18.5 - - + +
135D MET* 3.6 21.4 - - + -
147D ARG 2.8 19.0 + - - +
148D GLU 3.5 5.4 - - - +
150D HIS* 1.3 76.8 - - - +
152D ALA* 1.3 55.9 + - - +
154D SER* 3.6 2.4 - - - -
155D TYR* 2.9 31.4 + - - +
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Residues in contact with ALA 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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112D LYS* 5.2 7.9 - - - +
116D GLN* 4.1 16.6 + - - +
148D GLU* 2.9 18.7 + - + +
149D GLY* 3.8 7.9 - - - +
151D ALA* 1.3 74.6 - - - +
153D ARG* 1.3 59.3 + - - +
155D TYR* 3.3 6.0 + - - +
156D PHE* 2.9 46.5 + - + -
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Residues in contact with ARG 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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146D ASN* 6.1 0.8 - - - +
149D GLY 3.1 21.7 + - - +
150D HIS* 3.1 35.3 + - - +
152D ALA* 1.3 76.9 - - - +
154D SER* 1.3 55.3 + - - +
156D PHE* 3.9 3.5 - - - +
157D ASN* 2.5 53.9 + - - +
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Residues in contact with SER 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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128D LYS* 4.4 15.8 + - - +
131D ALA* 5.6 1.2 - - - +
132D LEU* 4.0 15.4 - - - +
135D MET* 4.5 12.4 - - - +
150D HIS* 3.1 19.6 + - - -
151D ALA 3.6 4.7 - - - -
153D ARG* 1.3 77.4 - - - +
155D TYR* 1.3 61.6 + - - +
157D ASN* 3.2 7.9 + - - +
158D THR* 2.8 37.9 + - - -
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Residues in contact with TYR 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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116D GLN* 3.2 55.2 - - + +
119D HIS* 2.8 29.2 + - - +
120D LEU* 3.8 24.7 - - + +
132D LEU* 4.2 6.2 - - + +
151D ALA 2.9 19.3 + - - +
152D ALA* 3.4 4.9 - - - +
154D SER* 1.3 76.1 - - - +
156D PHE* 1.3 95.9 + + - +
158D THR* 3.4 3.0 + - - -
159D LEU* 3.1 44.0 + - + +
223D PRO* 4.3 3.8 - - - +
226D ASP* 2.8 33.7 + - - +
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Residues in contact with PHE 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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116D GLN* 4.4 7.9 - - - -
152D ALA* 2.9 38.7 + - + +
153D ARG* 4.1 3.6 - - - +
155D TYR* 1.3 102.6 - + - +
157D ASN* 1.3 61.1 + - - +
159D LEU* 3.3 2.6 + - - +
160D PHE* 2.9 47.2 + + - +
164D PHE* 3.6 32.4 - + + +
165D THR 5.8 0.9 - - - +
166D ARG* 3.7 22.7 - - + -
176D LEU* 3.4 28.3 - - + -
180D TYR* 3.7 22.0 - + - -
226D ASP* 4.3 2.0 - - - -
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Residues in contact with ASN 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 ARG* 2.5 47.9 + - - +
154D SER* 3.2 6.9 + - - +
156D PHE* 1.3 75.9 - - - +
158D THR* 1.3 57.5 + - - +
161D GLY* 2.6 43.0 + - - -
162D ASN* 3.3 31.7 + - - +
164D PHE 3.2 24.0 + - - -
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Residues in contact with THR 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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120D LEU* 3.8 15.2 - - + +
125D TYR* 3.5 53.6 + - + -
128D LYS* 3.9 33.7 + - + +
154D SER* 2.8 23.5 + - - -
155D TYR* 3.5 6.2 - - - -
157D ASN* 1.3 79.7 - - - +
159D LEU* 1.3 60.2 + - - +
161D GLY 4.4 1.4 + - - -
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Residues in contact with LEU 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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119D HIS* 3.7 19.1 - - + +
120D LEU* 3.8 20.4 - - + -
123D ARG* 4.2 19.1 - - + -
125D TYR* 4.7 7.3 + - + -
155D TYR* 3.1 50.4 + - + +
156D PHE 3.9 0.2 - - - +
157D ASN 3.3 0.2 - - - -
158D THR* 1.3 82.6 - - - +
160D PHE* 1.3 88.9 + - + +
161D GLY 3.6 0.2 - - - -
226D ASP* 5.1 2.2 - - + -
230D TYR* 3.4 40.7 + - + -
233D ARG* 4.9 2.8 + - - -
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Residues in contact with PHE 160 (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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156D PHE* 2.9 35.4 + + - +
159D LEU* 1.3 94.7 - - + +
161D GLY* 1.3 63.7 + - - +
163D ASP* 5.1 2.1 + - - +
164D PHE* 3.5 41.7 + + + +
172D ILE* 3.7 44.6 - - + -
176D LEU* 4.6 4.0 - - + -
226D ASP* 5.1 3.6 - - + -
229D ILE* 4.5 7.2 - - + -
230D TYR* 3.9 33.0 - + + -
233D ARG* 4.1 17.9 - - + +
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Residues in contact with GLY 161 (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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157D ASN* 2.6 31.0 + - - +
158D THR 4.4 1.6 + - - -
159D LEU 3.6 2.2 + - - -
160D PHE* 1.3 74.7 - - - +
162D ASN* 1.3 61.9 + - - -
163D ASP* 3.2 7.4 - - - -
164D PHE* 3.2 15.6 + - - +
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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