Contacts of the helix formed by residues 146 - 158 (chain B) in PDB entry 2HQR
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 GLY 146 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145B LYS* 1.3 78.4 - - - +
147B LYS* 1.3 62.2 + - - -
148B PRO* 3.2 9.2 - - - -
149B PHE* 3.6 6.3 + - - +
150B GLU* 3.0 26.7 + - - +
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Residues in contact with LYS 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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146B GLY* 1.3 73.4 - - - -
148B PRO* 1.3 76.6 - - + +
150B GLU* 3.1 30.1 + - - +
151B VAL* 3.5 8.7 + - - +
172B ILE* 5.6 4.0 - - + +
177B GLU* 4.0 36.1 - - + +
179B VAL* 4.7 17.0 - - - -
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Residues in contact with PRO 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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146B GLY* 3.2 8.7 - - - -
147B LYS* 1.3 104.0 - - + +
149B PHE* 1.3 74.1 + - + +
151B VAL* 3.2 21.5 - - + +
152B LEU* 4.0 3.5 + - - +
191B ILE* 5.5 1.7 - - - +
194B LYS* 5.6 8.3 - - - +
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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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142B VAL* 6.5 1.3 - - + -
143B GLU 4.8 6.5 - - - -
144B VAL* 3.6 40.2 - - + -
145B LYS* 4.3 16.2 - - + +
146B GLY* 3.6 9.8 + - - +
147B LYS 3.2 0.4 - - - -
148B PRO* 1.3 92.5 - - + +
150B GLU* 1.3 67.0 + - - +
151B VAL 3.2 0.4 - - - -
152B LEU* 2.9 28.0 + - + +
153B THR* 2.8 18.9 + - - -
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Residues in contact with GLU 150 (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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146B GLY 3.0 16.3 + - - +
147B LYS* 3.1 20.0 + - - +
149B PHE* 1.3 77.6 - - - +
151B VAL* 1.3 64.0 + - - +
153B THR* 3.0 18.9 + - - -
154B HIS* 3.1 10.4 + - + +
171B ALA 4.4 3.8 - - - +
172B ILE* 3.5 42.9 - - + +
177B GLU* 4.0 9.6 - - - +
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Residues in contact with VAL 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 LYS 3.5 4.1 + - - +
148B PRO* 3.2 21.1 - - + +
150B GLU* 1.3 80.2 - - - +
152B LEU* 1.3 63.9 + - + +
154B HIS* 2.7 32.2 + - + +
155B LEU* 3.3 10.3 + - + +
168B LEU* 4.8 16.4 - - + -
172B ILE* 3.6 28.4 - - + +
191B ILE* 3.6 39.0 - - + -
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Residues in contact with LEU 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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135B ILE* 4.2 23.3 - - + -
137B TYR* 3.3 33.6 + - + +
148B PRO 4.3 2.7 - - - +
149B PHE* 2.9 34.6 + - + +
151B VAL* 1.3 83.5 - - + +
153B THR* 1.3 57.4 + - - +
155B LEU* 2.6 35.2 - - + +
156B ALA* 3.2 8.4 - - + +
191B ILE* 5.5 5.6 - - + -
195B MET* 4.3 23.6 - - + -
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Residues in contact with THR 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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128B ILE* 4.7 11.2 - - + -
130B PRO* 3.8 31.9 - - + -
133B GLU* 6.2 1.3 - - - -
135B ILE* 4.5 17.0 - - + +
144B VAL* 5.1 4.4 - - + +
149B PHE* 2.8 17.4 + - - +
150B GLU* 3.0 9.1 + - - -
152B LEU* 1.3 75.9 - - - +
154B HIS* 1.3 66.1 + - - +
156B ALA* 3.4 6.8 - - - +
157B ARG* 3.3 25.7 + - + +
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Residues in contact with HIS 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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150B GLU 3.1 6.2 + - - +
151B VAL* 2.7 21.9 + - + +
153B THR* 1.3 78.7 - - - +
155B LEU* 1.3 58.6 + - - +
157B ARG* 3.1 5.9 + - + +
158B HIS* 2.6 77.0 + + + +
167B GLN* 3.9 15.5 + - + +
168B LEU* 3.6 20.2 - - + +
171B ALA* 2.9 40.3 - - + +
172B ILE* 4.9 5.8 - - + +
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Residues in contact with LEU 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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151B VAL* 3.3 7.7 + - + +
152B LEU* 2.6 49.6 - - + +
154B HIS* 1.3 79.0 - - - +
156B ALA* 1.3 75.0 + - + +
157B ARG 3.2 0.3 + - - -
158B HIS* 3.4 19.0 - - + +
159B ARG* 3.1 20.6 + - + +
163B VAL* 6.1 0.4 - - + -
168B LEU* 5.9 3.4 - - + -
195B MET* 4.1 17.7 - - + -
214B PHE* 3.0 47.8 - - + -
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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
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121B ILE* 3.3 25.8 - - - +
123B ILE* 5.1 1.4 - - - +
128B ILE* 3.4 41.1 - - + -
137B TYR* 6.0 0.2 - - - +
152B LEU* 3.2 16.6 - - + +
153B THR* 3.4 9.0 - - - +
154B HIS 3.0 0.4 - - - -
155B LEU* 1.3 91.1 - - + +
157B ARG* 1.3 62.6 + - + +
159B ARG* 3.9 4.9 - - - +
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Residues in contact with ARG 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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120A VAL* 4.9 20.5 - - - +
120B VAL* 4.6 15.4 - - - +
121B ILE* 4.2 16.6 - - + +
130B PRO* 3.5 40.9 - - + +
153B THR* 3.4 14.8 - - - +
154B HIS* 3.1 6.0 + - + +
156B ALA* 1.3 77.5 - - + +
158B HIS* 1.3 54.5 + - - +
159B ARG* 2.4 40.2 + - - +
161B GLN* 4.6 0.3 + - - -
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Residues in contact with HIS 158 (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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154B HIS* 2.6 76.1 + + + +
155B LEU* 3.4 18.7 - - + +
157B ARG* 1.3 76.2 - - - +
159B ARG* 1.3 54.9 + - - +
161B GLN* 2.8 48.2 - - - +
163B VAL* 3.2 37.2 - - + +
167B GLN* 4.8 7.0 - - + -
168B LEU* 4.6 1.6 - - + -
214B PHE* 4.9 0.2 - - - +
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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