Contacts of the helix formed by residues 145 - 157 (chain B) in PDB entry 2Q5E
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 TYR 145 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143B ARG 3.3 0.6 + - - -
144B PRO* 1.3 85.4 - - + +
146B VAL* 1.3 59.5 + - - +
147B ASP 3.4 2.0 - - - -
148B GLU* 3.4 23.0 + - + +
149B PHE* 2.9 29.9 + - - +
240B MET 6.0 0.2 - - - -
242B ASP 3.6 20.6 - - - -
243B THR* 3.9 22.4 - - + +
245B LEU* 4.4 0.9 - - + -
246B LEU* 3.8 55.1 - - + +
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Residues in contact with VAL 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B LEU* 3.8 43.1 - - + +
142B LYS* 3.6 33.4 - - + +
143B ARG 3.3 17.6 + - - +
144B PRO 3.3 0.2 - - - -
145B TYR* 1.3 75.6 - - - +
147B ASP* 1.3 65.0 + - - +
148B GLU* 4.2 0.2 + - - -
149B PHE* 3.5 1.0 - - + +
150B LEU* 2.9 39.8 + - + +
177B LEU* 3.7 14.8 - - + -
245B LEU* 3.7 14.4 - - + -
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Residues in contact with ASP 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B LYS* 2.7 33.7 + - - +
145B TYR 3.4 0.2 - - - -
146B VAL* 1.3 82.4 - - - +
148B GLU* 1.3 72.1 + - - +
150B LEU* 4.0 5.7 - - - +
151B ARG* 3.1 30.3 + - - +
177B LEU* 4.1 15.4 - - - +
179B ARG* 3.0 45.4 + - - +
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Residues in contact with GLU 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B TYR* 3.6 39.6 - - + +
147B ASP* 1.3 83.2 + - - +
149B PHE* 1.3 65.3 + - - +
151B ARG* 3.9 19.7 + - - +
152B ARG* 3.0 24.4 + - - +
246B LEU* 4.6 11.4 - - + -
249B ILE* 4.6 3.9 - - + +
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Residues in contact with PHE 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B ILE* 4.4 4.5 - - + -
112B LEU* 4.3 7.9 - - + -
145B TYR 2.9 18.8 + - - +
146B VAL* 3.5 6.3 - - - +
147B ASP 3.2 0.2 - - - -
148B GLU* 1.3 79.8 - - - +
150B LEU* 1.3 77.8 + - + +
152B ARG* 3.3 2.6 + - - +
153B MET* 3.0 65.3 + - + +
216B LEU* 3.5 33.2 - - + -
245B LEU* 3.5 48.5 - - + +
248B LEU* 4.5 6.3 - - + -
249B ILE* 4.2 16.3 - - + +
252B PHE* 4.3 10.3 - + - -
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Residues in contact with LEU 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B ILE* 4.7 7.9 - - + -
112B LEU* 4.3 14.6 - - + -
146B VAL* 2.9 31.1 + - + +
147B ASP* 4.1 6.3 - - - +
149B PHE* 1.3 94.6 - - + +
151B ARG* 1.3 65.6 + - - +
153B MET* 4.3 4.0 - - + +
154B GLY 2.9 20.3 + - - -
177B LEU* 4.6 24.2 - - + +
178B ASP* 4.7 8.7 - - - +
182B VAL* 3.3 24.4 - - + +
183B PHE* 4.3 28.9 - - + -
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Residues in contact with ARG 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B ASP* 3.1 24.8 + - - +
148B GLU* 3.9 17.1 + - - +
150B LEU* 1.3 78.1 - - - +
152B ARG* 1.3 64.2 + - - +
154B GLY* 3.5 1.0 + - - -
155B GLU* 3.3 35.1 + - + +
179B ARG* 3.9 30.1 - - - +
180B CYS* 5.2 13.2 - - - -
182B VAL* 4.5 8.3 - - + -
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Residues in contact with ARG 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B GLU 3.0 18.6 + - - +
149B PHE 3.7 3.4 - - - +
151B ARG* 1.3 76.4 - - - +
153B MET* 1.4 63.9 + - + +
155B GLU* 2.7 58.1 + - - +
156B LEU* 3.3 44.9 + - + +
249B ILE* 4.2 29.4 - - + -
253B GLU* 2.5 34.3 + - - +
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Residues in contact with MET 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B VAL* 4.3 14.4 - - + -
106B ILE* 4.8 5.2 - - + -
149B PHE* 3.0 50.5 + - + +
150B LEU* 3.3 5.8 + - + +
151B ARG 3.2 0.4 - - - -
152B ARG* 1.4 75.8 - - - +
154B GLY* 1.3 57.1 + - - +
156B LEU* 3.1 3.6 + - - -
157B PHE* 2.6 53.1 + - + +
159B CYS* 3.6 16.8 - - - -
249B ILE* 5.5 5.2 - - - -
252B PHE* 3.4 61.5 - - + -
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Residues in contact with GLY 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B ARG* 2.8 31.9 + - - -
150B LEU 2.9 16.6 + - - -
151B ARG 3.9 2.2 - - - -
153B MET* 1.3 76.5 - - - +
155B GLU* 1.4 49.8 + - - +
157B PHE 4.3 4.0 - - - -
159B CYS* 4.4 1.1 - - - -
182B VAL* 3.8 22.8 - - - +
184B ARG* 3.2 12.7 + - - -
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Residues in contact with GLU 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B ARG* 2.9 24.3 + - - +
151B ARG* 3.3 31.6 + - + +
152B ARG* 2.7 50.6 + - - +
153B MET 3.2 0.8 - - - -
154B GLY* 1.4 74.9 - - - +
156B LEU* 1.3 60.5 + - + +
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Residues in contact with LEU 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B ARG* 3.7 15.6 - - - +
152B ARG* 3.3 46.2 + - + +
153B MET* 3.1 2.3 + - - -
155B GLU* 1.3 80.5 - - - +
157B PHE* 1.3 83.4 + - + +
249B ILE* 5.9 0.2 - - + -
252B PHE* 4.5 3.4 - - + +
253B GLU* 3.5 39.0 - - + +
256B SER* 4.0 28.4 - - - +
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Residues in contact with PHE 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B ARG* 3.0 26.0 + - - +
102B ILE* 3.5 39.9 - - + +
104B VAL* 3.5 21.5 - - + -
153B MET* 2.6 37.6 + - + +
154B GLY 3.6 5.4 - - - +
155B GLU 3.7 0.8 - - - -
156B LEU* 1.3 90.4 - - + +
158B GLU* 1.3 61.3 + - - +
159B CYS* 3.6 15.1 + - - -
184B ARG* 3.7 3.6 + - - -
214B LEU* 4.7 2.5 - - + -
252B PHE* 3.4 53.2 - + + -
255B LEU* 4.5 1.8 - - + -
256B SER* 3.6 20.2 - - - -
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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