Contacts of the helix formed by residues 154 - 173 (chain B) in PDB entry 2QB0
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 ASP 154 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B HIS* 3.2 21.7 + - + +
33B ASP* 3.6 1.4 - - - +
36B GLN* 3.7 22.2 + - - +
152B THR* 3.4 14.8 - - - +
153B LYS* 1.3 72.9 + - - +
155B GLU* 1.3 61.5 + - - +
157B GLU* 3.1 18.2 + - - +
158B LYS* 3.0 22.7 + - - +
257B MN 2.3 34.3 + - - -
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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
----------------------------------------------------------
143B ILE* 3.5 32.4 - - + +
145B ARG* 2.8 42.1 + - - +
151B ILE* 3.4 10.5 - - + +
152B THR* 2.9 33.7 + - - +
154B ASP* 1.3 77.0 - - + +
156B ALA* 1.3 61.1 + - - +
158B LYS* 3.5 11.3 - - + +
159B LEU* 3.1 32.6 + - - +
228D LYS* 3.5 26.6 + - - +
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Residues in contact with ALA 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B LEU* 4.5 15.9 - - + -
108B LEU* 5.1 0.9 - - + -
121B GLY* 4.1 17.3 - - - -
122B ILE* 4.9 8.5 + - + +
151B ILE* 3.8 18.1 - - + +
152B THR 3.2 13.5 + - - +
153B LYS 3.2 15.5 - - - +
155B GLU* 1.3 78.4 - - - +
157B GLU* 1.3 56.1 + - - +
159B LEU* 3.5 5.8 + - - +
160B PHE* 3.0 28.6 + - - +
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Residues in contact with GLU 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B HIS* 3.5 14.1 - - + +
24B LEU* 3.6 31.4 - - + +
28B TYR* 5.3 3.1 - - - +
33B ASP* 4.8 3.3 - - - +
97B PHE* 4.4 11.7 - - + -
153B LYS* 3.2 35.3 + - + +
154B ASP* 3.1 19.4 + - - +
155B GLU 3.3 0.2 - - - -
156B ALA* 1.3 76.8 - - - +
158B LYS* 1.3 58.9 + - - +
160B PHE* 3.6 6.5 - - - +
161B CYS* 3.0 35.2 + - - -
257B MN 2.4 33.9 + - - -
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Residues in contact with LYS 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ALA* 3.8 30.2 - - + +
21B HIS* 4.3 4.0 - - + +
142B ALA 3.8 19.3 - - - +
143B ILE* 4.3 17.7 - - + +
154B ASP 3.0 17.9 + - - +
155B GLU* 3.5 14.6 - - + +
157B GLU* 1.3 74.8 - - - +
159B LEU* 1.3 61.5 + - + +
161B CYS* 3.4 2.9 + - - +
162B GLN* 3.0 62.1 + - - +
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Residues in contact with LEU 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B ILE* 4.3 10.5 - - + +
121B GLY* 5.5 1.6 - - - -
122B ILE 6.3 0.4 - - - +
124B HIS* 3.9 34.1 - - + +
139B LEU* 4.2 12.3 - - + -
142B ALA* 3.8 29.6 - - + +
143B ILE* 3.8 20.2 - - + -
151B ILE* 4.0 18.4 - - + -
155B GLU 3.1 20.8 + - - +
156B ALA* 3.8 4.5 - - - +
158B LYS* 1.3 75.7 - - + +
160B PHE* 1.3 56.9 + - - +
162B GLN* 3.3 16.0 + - - +
163B ASP* 2.9 37.0 + - - +
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Residues in contact with PHE 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LEU* 3.9 17.0 - - + -
96B ILE* 3.7 28.0 - - + -
97B PHE* 3.6 34.3 - + + -
100B LEU* 3.5 32.3 - - + -
122B ILE* 3.9 33.0 - - + +
156B ALA 3.0 19.5 + - - +
157B GLU* 3.6 5.8 - - - +
159B LEU* 1.3 76.6 - - - +
161B CYS* 1.3 59.6 + - - +
163B ASP* 3.2 8.6 + - - +
164B VAL* 2.9 52.8 + - + +
197B PHE* 4.2 8.3 - + - -
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Residues in contact with CYS 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ALA* 3.4 24.2 - - + +
23B ARG* 3.7 31.2 - - - +
24B LEU* 3.4 33.0 - - - -
157B GLU 3.0 15.0 + - - +
158B LYS 3.9 2.9 - - - +
160B PHE* 1.3 74.9 - - - +
162B GLN* 1.3 60.2 + - - +
164B VAL* 3.3 7.9 + - - +
165B ASP* 2.9 34.1 + - - +
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Residues in contact with GLN 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ALA* 5.1 2.4 - - + +
23B ARG* 4.3 12.8 - - - +
124B HIS* 5.9 1.4 - - + -
142B ALA* 4.4 12.7 + - - +
158B LYS* 3.0 53.0 + - + +
159B LEU* 3.6 24.4 - - - +
161B CYS* 1.3 75.9 - - - +
163B ASP* 1.3 59.6 + - - +
165B ASP* 3.7 4.7 + - - +
166B ALA* 3.1 25.6 + - - +
169B ARG* 4.7 2.6 + - - -
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Residues in contact with ASP 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B ILE 4.9 0.3 - - - +
124B HIS* 2.8 46.9 + - - +
159B LEU 2.9 19.5 + - - +
160B PHE* 3.5 6.4 - - - +
161B CYS 3.2 0.2 - - - -
162B GLN* 1.3 79.0 - - - +
164B VAL* 1.3 54.8 + - - +
165B ASP 3.2 0.2 - - - -
166B ALA* 3.1 8.2 + - - +
167B ALA* 2.8 34.5 + - - +
197B PHE* 3.6 27.0 - - + -
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Residues in contact with VAL 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B PRO* 6.3 2.5 - - + -
96B ILE* 4.4 14.6 - - + -
100B LEU* 5.0 1.1 - - + -
160B PHE* 2.9 52.1 + - + +
161B CYS* 3.3 6.9 + - - +
163B ASP* 1.3 74.1 - - - +
165B ASP* 1.3 58.2 + - - +
167B ALA* 3.2 7.2 + - - +
168B VAL* 2.8 52.7 + - + +
193B ILE* 4.6 14.8 - - + -
197B PHE* 4.6 7.9 - - + -
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Residues in contact with ASP 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ARG* 5.1 4.9 + - - -
23B ARG* 2.8 33.8 + - - -
161B CYS 2.9 16.6 + - - +
162B GLN* 3.9 4.7 - - - +
164B VAL* 1.3 82.2 - - - +
166B ALA* 1.3 56.5 + - - +
168B VAL* 4.1 6.9 - - - +
169B ARG* 3.1 53.7 + - - +
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Residues in contact with ALA 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B GLN 3.1 18.4 + - - +
163B ASP* 3.1 10.3 + - - +
165B ASP* 1.3 75.2 - - - +
167B ALA* 1.3 58.3 + - - +
169B ARG* 3.9 14.3 - - - +
170B GLY* 3.0 24.3 + - - -
173B ARG* 4.6 3.6 + - - -
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Residues in contact with ALA 167 (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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163B ASP 2.8 15.9 + - - +
164B VAL* 3.5 5.4 - - - +
166B ALA* 1.3 75.4 - - - +
168B VAL* 1.3 58.3 + - - +
170B GLY* 3.2 1.6 + - - -
171B ILE* 2.8 36.4 + - - +
193B ILE* 4.0 21.5 - - + +
196B VAL* 3.9 24.9 - - + +
197B PHE* 4.8 9.2 - - + +
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Residues in contact with VAL 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B PRO* 5.9 1.8 - - + -
164B VAL* 2.8 31.6 + - + +
165B ASP* 4.1 8.3 - - - +
167B ALA* 1.3 72.5 - - - +
169B ARG* 1.3 53.9 + - + +
171B ILE* 3.1 10.8 + - + +
172B LEU* 2.7 59.2 + - + +
181B TYR* 4.2 17.9 - - + +
193B ILE* 4.1 26.7 - - + -
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Residues in contact with ARG 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B GLN* 4.7 2.8 + - - +
165B ASP* 3.1 50.4 + - - +
166B ALA* 3.9 12.5 - - - +
168B VAL* 1.3 78.1 - - + +
170B GLY* 1.3 56.5 + - - +
172B LEU* 4.3 12.3 - - + -
173B ARG* 3.0 56.5 + - + +
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Residues in contact with GLY 170 (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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166B ALA 3.0 17.7 + - - -
167B ALA* 3.5 4.5 - - - -
168B VAL 3.2 0.6 - - - -
169B ARG* 1.3 78.2 - - - +
171B ILE* 1.3 59.4 + - - +
173B ARG* 3.6 12.1 + - - +
174B ASN* 3.6 7.1 + - - +
196B VAL* 5.8 0.4 - - - -
201B GLU* 3.1 44.8 - - - +
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Residues in contact with ILE 171 (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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167B ALA 2.8 21.3 + - - +
168B VAL* 3.4 9.0 - - - +
170B GLY* 1.3 77.7 - - - +
172B LEU* 1.3 59.6 + - + +
174B ASN* 3.1 26.5 + - - +
177B LEU* 3.7 26.0 - - + +
178B LYS* 3.3 5.7 + - - +
181B TYR* 3.6 42.2 - - + -
192B LEU* 4.5 6.1 - - + -
193B ILE* 4.0 28.5 - - + +
196B VAL* 3.7 33.0 - - + -
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Residues in contact with LEU 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B VAL* 2.7 40.1 + - + +
169B ARG* 4.1 12.8 - - + +
171B ILE* 1.3 74.2 - - + +
173B ARG* 1.3 60.7 + - + +
174B ASN 3.3 1.1 - - - -
178B LYS* 3.3 46.6 - - + +
181B TYR* 4.4 24.0 - - + -
182B ASP* 4.5 7.2 - - - +
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Residues in contact with ARG 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B ALA 4.6 3.6 + - - -
169B ARG* 3.0 53.1 + - + +
170B GLY* 3.6 8.3 + - - +
171B ILE 3.2 0.4 - - - -
172B LEU* 1.3 79.2 - - + +
174B ASN* 1.3 57.8 + - - +
175B ALA 4.2 0.9 + - - -
201B GLU* 4.2 18.4 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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