Contacts of the helix formed by residues 155 - 165 (chain B) in PDB entry 1HPL
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 SER 155 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B GLY* 2.9 31.4 + - - -
152B SER 3.2 12.8 + - - -
153B LEU 3.2 0.8 - - - -
154B GLY* 1.3 77.9 - - - +
156B HIS* 1.3 58.5 + - - +
158B ALA* 3.4 5.8 - - - +
159B GLY 3.0 19.6 + - - -
174B GLY* 4.1 9.6 - - - -
175B LEU 3.5 7.4 + - - -
177B PRO* 3.5 34.0 - - - +
191B LEU* 3.8 13.6 - - - +
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Residues in contact with HIS 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 VAL* 4.5 6.9 - - + +
152B SER 4.0 12.1 - - - -
153B LEU* 3.2 8.3 + - - +
155B SER* 1.3 75.3 - - - +
157B ALA* 1.3 60.8 + - - +
159B GLY* 3.7 1.5 - - - +
160B GLU* 2.8 28.1 + - - +
177B PRO* 3.8 9.8 - - + +
178B ALA* 2.8 36.2 + - + -
182B PHE* 3.5 54.0 - + + -
189B VAL 4.6 7.5 - - - +
190B ARG* 3.9 3.9 - - + +
191B LEU* 3.5 25.7 + - + +
217B MET* 3.6 22.0 - - - -
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Residues in contact with ALA 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ILE* 4.3 10.7 - - + +
106B TRP* 5.6 1.1 - - + -
121B VAL* 3.9 32.2 - - + +
124B VAL* 4.2 22.4 - - + -
125B GLY* 3.4 11.3 - - - +
153B LEU 3.5 3.4 + - - -
154B GLY* 3.2 18.1 + - - +
156B HIS* 1.3 77.4 - - - +
158B ALA* 1.3 59.8 + - - +
160B GLU* 3.3 1.7 + - - -
161B ALA* 3.1 19.1 + - - +
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Residues in contact with ALA 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ILE* 3.9 3.5 - - + +
148B ILE* 3.6 32.0 - - + +
150B GLY 4.6 7.6 - - - +
154B GLY 3.0 12.6 + - - +
155B SER* 3.4 12.8 - - - +
157B ALA* 1.3 74.2 - - - +
159B GLY* 1.3 61.1 + - - +
161B ALA* 3.3 6.5 + - - +
162B GLY 3.1 19.1 + - - -
172B ILE* 3.3 28.3 - - + +
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Residues in contact with GLY 159 (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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155B SER 3.0 11.8 + - - -
156B HIS 3.7 3.6 - - - -
157B ALA 3.4 0.4 - - - -
158B ALA* 1.3 75.4 - - - +
160B GLU* 1.3 54.4 + - - +
162B GLY 3.4 0.5 + - - -
163B ARG* 3.0 26.6 + - - +
190B ARG 5.1 3.1 - - - -
191B LEU* 3.8 18.9 - - - +
195B ASP* 3.3 30.7 - - - -
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Residues in contact with GLU 160 (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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17B TRP* 3.9 16.7 - - - -
121B VAL* 4.4 5.4 - - + +
122B ARG* 3.8 24.2 - - + +
125B GLY* 3.8 16.2 - - - -
156B HIS 2.8 17.3 + - - +
157B ALA 3.3 8.9 + - - +
159B GLY* 1.3 71.7 - - - +
161B ALA* 1.3 57.2 + - - +
163B ARG* 2.9 44.1 + - - +
164B ARG* 3.0 52.5 + - - +
188B LEU 4.2 4.4 - - - +
189B VAL 5.7 0.7 - - - +
190B ARG 5.8 0.6 - - - -
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Residues in contact with ALA 161 (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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125B GLY* 3.5 22.9 - - - +
128B VAL* 4.0 25.6 - - + -
129B ALA* 3.6 10.0 - - - +
148B ILE* 4.1 9.4 - - + -
157B ALA 3.1 9.9 + - - +
158B ALA* 3.3 9.6 + - - +
160B GLU* 1.3 75.5 - - - +
162B GLY* 1.3 61.2 + - - +
164B ARG 3.5 0.7 + - - -
165B THR* 2.9 30.1 + - - -
169B VAL* 5.0 0.6 - - + +
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Residues in contact with GLY 162 (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 ILE* 4.9 0.4 - - - +
158B ALA 3.1 10.6 + - - -
159B GLY 3.9 1.6 - - - -
161B ALA* 1.3 77.5 - - - +
163B ARG* 1.3 65.4 + - - +
165B THR* 2.9 17.0 + - - -
167B GLY 2.9 18.5 + - - -
169B VAL* 4.7 8.3 - - - -
172B ILE* 4.2 6.0 - - - +
195B ASP 3.1 24.7 - - - -
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Residues in contact with ARG 163 (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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17B TRP* 3.8 12.9 - - - -
159B GLY 3.0 14.4 + - - +
160B GLU* 2.9 46.8 + - - +
162B GLY* 1.3 73.8 - - - +
164B ARG* 1.3 74.0 + - - +
166B ASN* 2.9 26.0 + - - +
167B GLY 4.7 2.0 - - - +
187B GLU 5.2 1.3 - - - -
188B LEU* 3.6 48.9 + - - +
194B SER 5.6 0.7 - - - -
195B ASP* 3.8 18.1 + - - +
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Residues in contact with ARG 164 (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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8B LEU* 4.6 3.6 - - - +
9B GLY* 4.0 21.8 - - - +
10B CYS 5.3 3.0 + - - -
11B PHE* 3.9 21.8 - - - -
125B GLY 4.3 0.4 - - - -
126B ALA* 3.6 32.7 + - - +
129B ALA* 3.7 18.9 - - + +
160B GLU* 3.0 52.6 + - - +
161B ALA 3.7 0.2 - - - +
162B GLY 3.2 0.2 - - - -
163B ARG* 1.3 89.0 - - - +
165B THR* 1.3 59.7 - - - +
166B ASN* 3.2 7.9 + - - +
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Residues in contact with THR 165 (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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129B ALA* 3.8 6.9 + - - +
132B VAL* 3.8 20.8 - - + +
143B PRO* 4.3 8.7 - - + -
161B ALA 2.9 18.0 + - - -
162B GLY 2.9 6.8 + - - -
164B ARG* 1.3 74.9 - - - +
166B ASN* 1.3 71.2 + - - +
168B ALA* 3.3 18.9 + - + +
169B VAL* 3.5 40.0 - - + +
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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