Contacts of the helix formed by residues 149 - 158 (chain A) 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 PHE 149 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A GLU* 3.3 31.9 - - + -
144A VAL* 3.4 41.0 - - + +
145A LYS* 3.9 6.5 - - - -
146A GLY* 2.2 45.5 - - - +
147A LYS 3.2 2.2 - - - -
148A PRO* 1.3 77.4 - - + +
150A GLU* 1.3 114.2 + - + +
151A VAL 3.0 1.3 - - - -
152A LEU* 2.8 18.6 + - - +
153A THR* 3.2 18.7 + - + +
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Residues in contact with GLU 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A GLY 4.7 0.9 - - - +
147A LYS* 3.6 15.4 - - - +
149A PHE* 1.3 110.2 - - + +
151A VAL* 1.3 57.7 + - - +
153A THR* 2.7 23.2 + - - +
154A HIS* 2.7 19.1 + - - +
157A ARG* 4.8 3.1 + - - +
171A ALA 5.0 0.7 - - - +
172A ILE* 3.3 43.2 - - + +
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Residues in contact with VAL 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A LYS 4.9 1.1 - - - +
148A PRO* 3.1 29.4 - - + +
149A PHE 3.0 0.6 - - - -
150A GLU* 1.3 84.2 - - - +
152A LEU* 1.3 76.0 + - + +
154A HIS* 3.1 20.4 + - + +
155A LEU* 3.2 14.4 + - + +
168A LEU* 5.2 15.9 - - + -
172A ILE* 4.1 25.4 - - + -
173A TRP* 6.5 1.8 - - + -
191A ILE* 3.4 40.2 - - + -
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Residues in contact with LEU 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A ILE* 5.0 11.4 - - + -
135A ILE* 4.5 23.8 - - + -
148A PRO 4.2 9.2 - - - +
149A PHE* 2.8 10.4 + - - +
151A VAL* 1.3 83.3 - - - +
153A THR* 1.3 66.2 + - + +
155A LEU* 3.1 36.4 - - + +
156A ALA* 3.2 2.1 + - - +
191A ILE* 4.1 17.7 - - + -
195A MET* 3.9 30.5 - - + -
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Residues in contact with THR 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A ILE* 4.6 15.0 - - + -
130A PRO* 4.3 24.7 - - + -
133A GLU* 6.0 1.6 - - + -
134A LYS 5.3 10.1 - - - +
135A ILE* 5.8 5.6 - - + -
144A VAL* 5.5 6.7 - - + -
149A PHE* 3.2 14.9 + - + +
150A GLU* 2.7 30.7 + - - +
152A LEU* 1.3 79.5 - - + +
154A HIS* 1.3 62.1 + - - +
156A ALA* 3.1 17.1 + - - +
157A ARG* 3.1 25.9 + - - +
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Residues in contact with HIS 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A GLU 2.7 14.8 + - - +
151A VAL* 3.2 15.9 - - + +
152A LEU 3.1 0.2 - - - -
153A THR* 1.3 79.8 + - - +
155A LEU* 1.3 64.5 + - - +
157A ARG* 3.1 25.5 + - - +
158A HIS* 3.0 61.6 + + - +
163A VAL* 5.7 4.2 - - + +
168A LEU* 4.5 18.1 - - + +
171A ALA* 3.9 27.6 - - + +
172A ILE* 4.7 7.9 - - + +
214A PHE* 6.0 1.1 - + - -
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Residues in contact with LEU 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A ILE* 6.1 0.2 - - + -
151A VAL* 3.2 13.9 + - + +
152A LEU* 3.1 39.3 - - + +
154A HIS* 1.3 81.2 - - + +
156A ALA* 1.3 71.9 + - + +
158A HIS* 3.5 3.7 - - - +
159A ARG* 3.0 23.7 + - - +
168A LEU* 6.1 0.7 - - + -
191A ILE* 4.9 9.9 - - + -
195A MET* 6.1 0.2 - - + -
203A THR* 4.7 14.4 - - - +
204A VAL* 4.1 13.0 - - + -
214A PHE* 3.4 53.4 - - + +
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Residues in contact with ALA 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A ILE* 3.8 6.7 - - + +
128A ILE* 3.5 41.1 - - + -
152A LEU 3.2 9.6 + - - +
153A THR* 3.1 15.9 + - - +
154A HIS 3.1 0.6 - - - -
155A LEU* 1.3 87.5 - - + +
157A ARG* 1.3 63.4 + - + +
159A ARG* 3.2 28.8 + - - +
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Residues in contact with ARG 157 (chain A).
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* 6.3 0.4 - - + -
121A ILE* 3.8 21.1 - - + -
130A PRO* 3.9 23.0 - - + +
150A GLU* 4.8 2.4 + - - +
153A THR* 3.1 22.1 + - - +
154A HIS* 3.1 39.2 + - - +
156A ALA* 1.3 72.8 - - + +
158A HIS* 1.3 71.6 + - + +
159A ARG* 2.7 34.8 + - - +
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Residues in contact with HIS 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A HIS* 3.0 55.4 + + + +
155A LEU* 3.5 7.9 - - - -
157A ARG* 1.3 89.6 + - + +
159A ARG* 1.3 68.5 + - - +
161A GLN* 3.0 42.4 + - + +
163A VAL* 4.7 15.5 - - + -
214A PHE* 4.1 7.1 - - + +
159B ARG* 6.1 3.4 - - - -
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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
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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