Contacts of the helix formed by residues 144 - 158 (chain D) in PDB entry 2Q2U
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 144 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20D PHE* 3.4 17.8 - - - -
142D ILE 3.7 0.2 - - - -
143D ASN* 1.3 82.0 - - - +
145D ILE* 1.3 67.1 + - - +
146D THR* 3.0 37.4 + - - +
147D GLU* 2.7 41.1 + - - +
148D LEU* 3.0 9.2 + - - +
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Residues in contact with ILE 145 (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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15D ILE* 3.8 42.2 - - + +
16D GLU* 5.0 12.1 - - + -
20D PHE* 3.3 26.0 - - + -
144D ASN* 1.3 71.1 - - - +
146D THR* 1.3 57.0 + - - +
148D LEU* 3.2 6.0 + - - +
149D LEU* 2.8 50.6 + - + +
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Residues in contact with THR 146 (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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144D ASN* 2.8 23.4 + - - +
145D ILE* 1.3 78.1 - - - +
147D GLU* 1.3 66.7 + - + +
149D LEU* 3.2 8.3 + - - +
150D GLN* 2.9 23.9 + - + +
153D ARG* 5.2 2.3 + - - +
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Residues in contact with GLU 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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141D GLU 4.3 9.4 - - - +
142D ILE* 4.3 8.2 - - + +
143D ASN* 3.3 44.6 + - - +
144D ASN* 2.7 28.3 + - - +
146D THR* 1.3 78.0 - - + +
148D LEU* 1.3 62.6 + - - +
150D GLN* 3.1 9.8 + - - +
151D TYR* 2.8 22.5 + - - +
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Residues in contact with LEU 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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15D ILE* 3.5 28.3 - - + -
18D VAL* 4.1 17.0 - - + -
20D PHE* 4.6 4.9 - - + -
22D CYS* 5.4 1.3 - - - -
24D ALA* 5.4 1.1 - - + -
142D ILE* 3.8 24.7 - - + +
144D ASN 3.0 9.0 + - - +
145D ILE* 3.3 9.9 - - - +
147D GLU* 1.3 74.7 - - - +
149D LEU* 1.3 57.3 + - + +
151D TYR* 2.7 31.2 + - + +
152D GLU 2.8 10.6 + - - +
163D VAL* 4.6 9.6 - - + -
165D ILE* 3.9 26.7 - - + -
187D MET* 3.5 25.1 - - + -
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Residues in contact with LEU 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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15D ILE* 4.0 28.0 - - + -
145D ILE* 2.8 37.0 + - + +
146D THR* 3.5 7.0 - - - +
148D LEU* 1.3 72.9 - - - +
150D GLN* 1.3 61.7 + - - +
152D GLU* 3.3 22.3 + - - +
153D ARG* 3.1 37.3 + - - +
187D MET* 5.0 0.9 - - + -
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Residues in contact with GLN 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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146D THR* 2.9 16.3 + - + +
147D GLU* 3.2 13.5 - - - +
149D LEU* 1.3 76.6 - - - +
151D TYR* 1.3 59.3 + - - +
153D ARG* 2.5 52.7 + - - +
154D ASP* 2.7 44.2 + - - +
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Residues in contact with TYR 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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24D ALA* 3.8 11.6 + - + -
25D THR* 3.1 15.4 - - - -
26D PRO* 3.0 29.5 - - - +
140D VAL* 3.6 33.9 - - + +
142D ILE* 4.5 9.9 - - + -
147D GLU 2.8 10.6 + - - +
148D LEU* 2.7 19.3 + - + +
150D GLN* 1.3 71.7 - - - +
152D GLU* 1.3 62.0 + - - +
154D ASP* 3.0 25.0 + - + +
155D VAL* 3.0 36.9 + - + +
163D VAL* 3.5 34.3 - - + -
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Residues in contact with GLU 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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148D LEU 2.8 7.1 + - - +
149D LEU* 3.5 21.0 - - - +
150D GLN 3.2 0.2 - - - -
151D TYR* 1.3 78.9 - - - +
153D ARG* 1.3 64.4 + - + +
155D VAL* 3.2 8.1 - - + +
156D LEU* 3.0 50.4 + - + +
162D GLY* 6.0 0.9 - - - -
163D VAL* 4.7 6.1 - - + +
187D MET* 3.0 43.3 - - + +
189D GLN* 3.0 39.6 + - - +
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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 THR* 5.2 2.4 + - - +
149D LEU* 3.1 28.8 + - - +
150D GLN* 2.5 59.5 + - - +
152D GLU* 1.3 75.9 - - - +
154D ASP* 1.3 64.3 + - - +
156D LEU* 3.8 7.1 - - + +
157D SER* 3.0 25.3 + - - -
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Residues in contact with ASP 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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150D GLN* 2.7 35.3 + - - +
151D TYR* 3.0 21.6 + - + +
153D ARG* 1.3 75.7 - - - +
155D VAL* 1.3 66.8 + - + +
157D SER* 2.6 26.5 + - - -
158D LYS* 3.0 18.4 + - - +
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Residues in contact with VAL 155 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26D PRO* 3.7 17.3 - - + -
151D TYR* 3.0 46.4 + - + +
152D GLU* 3.2 19.1 - - - +
154D ASP* 1.3 77.4 - - + +
156D LEU* 1.3 70.1 + - + +
158D LYS* 3.1 10.5 + - + -
160D PHE* 3.1 39.8 + - + -
162D GLY 3.9 22.7 - - - +
163D VAL* 4.5 4.9 - - + -
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Residues in contact with LEU 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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152D GLU* 3.0 52.1 + - + +
153D ARG* 3.8 6.5 - - + +
155D VAL* 1.3 78.1 - - + +
157D SER* 1.3 57.4 + - - +
159D GLY* 2.6 26.3 + - - -
160D PHE 3.4 21.7 + - - +
161D GLU 4.4 10.1 - - - +
162D GLY* 4.4 10.1 - - - -
189D GLN* 5.4 8.7 - - + +
276D PHE* 6.2 0.9 - - + -
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Residues in contact with SER 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 3.0 14.2 + - - -
154D ASP* 2.6 22.2 + - - -
156D LEU* 1.3 76.1 - - - +
158D LYS* 1.3 61.9 + - - +
159D GLY 3.1 3.8 + - - -
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Residues in contact with LYS 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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154D ASP* 3.0 20.0 + - + +
155D VAL* 3.5 11.7 - - + +
156D LEU 3.0 1.4 - - - -
157D SER* 1.3 82.4 + - - +
159D GLY* 1.3 62.6 + - - +
160D PHE* 3.7 26.2 - - + -
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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