Contacts of the helix formed by residues 149 - 161 (chain D) in PDB entry 5UQ9
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 ALA 149 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97D ILE* 3.7 37.5 - - + -
122D LEU* 3.7 18.6 - - + +
124D VAL* 3.7 9.9 - - + -
146D ASN* 3.1 12.1 + - - +
147D LYS 3.0 0.8 - - - -
148D GLU* 1.3 77.0 - - - +
150D TRP* 1.3 64.6 + - - +
151D PRO* 3.5 1.3 - - - -
152D HIS* 3.3 5.8 + - - +
153D ILE* 3.3 25.1 + - - +
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Residues in contact with TRP 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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143D PRO* 3.6 20.6 - - + -
146D ASN 4.1 1.4 + - - -
147D LYS* 2.9 28.5 + - + +
149D ALA* 1.3 77.0 - - - +
151D PRO* 1.3 61.5 - - + +
152D HIS 3.0 0.6 + - - -
153D ILE* 3.3 19.7 + - + -
154D LYS* 2.8 63.5 + - + +
157D PHE* 4.5 1.6 - - + -
158D GLN* 3.2 32.3 - - + -
171D CYS* 4.1 21.1 - - - -
172D ASP* 3.9 6.2 + - - -
173D TRP* 3.5 62.3 - + + +
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Residues in contact with PRO 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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147D LYS* 3.4 11.9 - - + +
148D GLU* 3.7 11.4 - - - +
149D ALA 3.7 1.6 - - - -
150D TRP* 1.3 94.9 - - + +
152D HIS* 1.3 69.1 + - + +
154D LYS* 4.1 31.5 - - + +
155D THR* 5.1 3.8 + - - -
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Residues in contact with HIS 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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68D PRO* 3.3 31.5 - - + +
70D ARG* 3.4 35.9 + - - +
95D GLY 5.8 0.4 + - - -
97D ILE* 3.6 26.9 - - + -
122D LEU* 5.1 4.4 - - + +
148D GLU* 3.6 23.9 + - - +
149D ALA* 3.3 0.9 + - - +
150D TRP 3.1 0.8 - - - -
151D PRO* 1.3 89.9 + - + +
153D ILE* 1.3 61.3 + - - +
154D LYS 3.3 1.0 + - - -
155D THR* 4.6 6.1 + - - -
156D ILE* 5.1 2.1 + - - +
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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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6D ILE* 5.8 1.3 - - + -
70D ARG* 4.5 11.0 - - + +
97D ILE* 4.2 13.7 - - + -
99D ILE* 4.1 23.3 - - + -
124D VAL* 4.0 31.2 - - + -
143D PRO* 4.5 1.8 - - + -
149D ALA 3.3 17.4 + - - +
150D TRP* 3.7 24.9 - - + -
152D HIS* 1.3 76.0 - - - +
154D LYS* 1.3 65.0 + - - +
155D THR 3.3 2.0 - - - -
156D ILE* 4.1 5.6 - - - +
157D PHE* 3.0 55.8 + - + +
173D TRP* 4.7 1.8 - - + -
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Residues in contact with LYS 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 TRP* 2.8 43.6 + - + +
151D PRO* 4.1 26.4 - - + +
152D HIS 3.3 1.8 - - - -
153D ILE* 1.3 77.9 - - - +
155D THR* 1.3 65.9 + - - +
158D GLN* 3.1 55.6 + - - +
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Residues in contact with THR 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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27D PHE* 4.3 19.6 - - + -
151D PRO 5.1 0.4 + - - -
152D HIS 4.6 5.6 + - - -
153D ILE 3.3 0.4 - - - -
154D LYS* 1.3 83.3 - - - +
156D ILE* 1.3 61.1 + - - +
158D GLN* 4.4 1.2 - - - +
159D GLY* 2.9 28.8 + - - -
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Residues in contact with ILE 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 ASP* 4.6 3.1 - - + -
6D ILE* 3.9 35.4 - - + -
22D MET* 3.8 33.7 - - + -
27D PHE* 3.6 41.3 - - + -
70D ARG* 3.5 29.8 - - - +
152D HIS 5.2 2.0 - - - +
153D ILE* 3.6 7.8 + - - +
154D LYS 3.5 0.4 - - - -
155D THR* 1.3 76.6 - - - +
157D PHE* 1.3 70.6 + - + +
159D GLY* 3.3 0.7 + - - -
160D ILE* 3.1 30.3 + - + +
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Residues in contact with PHE 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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6D ILE* 4.8 6.3 - - + -
72D ILE* 4.3 20.4 - - + -
99D ILE* 3.5 27.8 - - + -
126D SER* 3.7 24.7 - - - -
141D LEU* 3.5 32.8 - - + +
143D PRO* 4.5 8.1 - - + -
150D TRP* 4.5 3.6 - - + -
153D ILE* 3.0 55.9 + - + +
154D LYS 4.3 0.9 - - - +
156D ILE* 1.3 84.3 - - + +
158D GLN* 1.3 57.7 + - - +
160D ILE* 3.4 6.5 + - + +
161D ALA* 2.9 30.5 + - - +
171D CYS* 3.6 15.5 - - - -
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Residues in contact with GLN 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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150D TRP* 3.2 32.9 - - + -
154D LYS* 3.1 33.3 + - - +
155D THR* 4.4 1.1 - - - +
157D PHE* 1.3 75.2 - - - +
159D GLY* 1.3 57.2 + - - +
161D ALA* 3.8 7.8 + - - +
163D LYS* 3.0 28.4 + - - -
169D PRO* 3.7 25.9 - - + +
171D CYS* 3.3 25.4 + - + +
172D ASP* 4.5 4.9 + - - -
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Residues in contact with GLY 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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25D HIS* 3.1 26.7 + - - -
27D PHE* 5.5 4.3 - - - -
155D THR 2.9 19.7 + - - -
156D ILE* 3.8 1.1 - - - -
157D PHE 3.1 0.4 - - - -
158D GLN* 1.3 78.6 - - - +
160D ILE* 1.3 58.0 + - - +
163D LYS* 3.0 19.1 + - - -
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Residues in contact with ILE 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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18D LEU* 4.3 22.9 - - + +
21D ASN* 3.4 28.5 + - - +
22D MET* 3.6 47.3 - - + -
25D HIS* 3.9 12.9 - - + -
27D PHE* 4.9 2.7 - - + -
72D ILE* 6.1 3.1 - - + -
137D TYR 4.5 1.0 - - - +
138D GLY* 3.6 5.5 - - - -
139D PRO* 3.3 17.4 - - + +
141D LEU* 4.2 14.6 - - + -
156D ILE* 3.1 20.5 + - + +
157D PHE* 3.5 8.7 - - + +
159D GLY* 1.3 72.0 - - - +
161D ALA* 1.3 69.3 + - - +
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Residues in contact with ALA 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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137D TYR 5.2 0.5 - - - +
138D GLY* 4.4 1.2 - - - -
139D PRO* 3.2 14.8 - - - +
141D LEU* 4.3 4.0 - - + -
157D PHE 2.9 18.9 + - - +
158D GLN 4.0 6.7 - - - +
159D GLY 3.3 1.8 - - - +
160D ILE* 1.3 83.4 - - - +
162D ALA* 1.3 66.1 + - - +
163D LYS* 2.8 23.7 + - - +
170D CYS 4.4 5.2 - - - +
171D CYS* 3.6 26.0 - - + -
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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