Contacts of the helix formed by residues 155 - 165 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150A GLY* 3.3 26.9 - - - -
151A HIS 3.5 3.5 + - - -
152A SER 2.7 21.3 + - - -
154A GLY* 1.3 76.8 - - - +
156A HIS* 1.3 59.6 + - - +
158A ALA* 3.4 6.6 - - - +
159A GLY 3.1 19.8 + - - -
174A GLY* 3.9 18.4 - - - -
175A LEU 4.3 0.9 - - - -
177A PRO* 3.1 27.4 - - - +
191A LEU* 3.7 15.6 - - - +
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Residues in contact with HIS 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 VAL* 4.0 8.8 - - + +
152A SER 4.1 2.5 - - - -
153A LEU* 3.0 16.0 + - - +
155A SER* 1.3 77.4 - - - +
157A ALA* 1.3 57.9 + - - +
159A GLY* 3.4 2.1 + - - +
160A GLU* 3.1 25.5 + - - +
177A PRO* 3.9 9.2 - - + -
178A ALA* 2.8 39.0 + - + -
182A PHE* 3.5 51.9 - + + -
189A VAL 4.9 4.4 - - - +
190A ARG* 4.2 5.9 - - + -
191A LEU* 3.5 26.3 + - + +
217A MET* 3.7 22.2 - - + -
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Residues in contact with ALA 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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74A ILE* 4.3 9.4 - - + +
106A TRP* 5.7 1.1 - - + -
121A VAL* 3.7 35.8 - - + +
124A VAL* 4.1 24.0 - - + -
125A GLY* 3.5 10.1 - - - +
153A LEU 3.4 3.2 + - - -
154A GLY* 3.3 13.8 + - - +
156A HIS* 1.3 73.6 - - - +
158A ALA* 1.3 65.5 + - - +
160A GLU* 3.1 2.2 + - - +
161A ALA* 3.0 20.4 + - - +
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Residues in contact with ALA 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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74A ILE* 3.9 5.1 - - + +
148A ILE* 3.6 31.8 - - + +
150A GLY* 4.5 6.5 - - - +
154A GLY 3.1 13.4 + - - +
155A SER* 3.4 13.0 - - - +
157A ALA* 1.3 77.2 - - - +
159A GLY* 1.3 59.6 + - - +
161A ALA* 3.4 5.8 + - - +
162A GLY 3.1 17.7 + - - -
172A ILE* 3.4 28.1 - - + +
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Residues in contact with GLY 159 (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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155A SER 3.1 11.8 + - - -
156A HIS 3.4 3.6 + - - -
157A ALA 3.3 0.4 - - - -
158A ALA* 1.3 71.9 - - - +
160A GLU* 1.3 60.1 + - - +
162A GLY 3.4 0.3 + - - -
163A ARG* 2.9 30.3 + - - +
172A ILE* 4.2 1.6 - - - -
190A ARG 5.2 3.1 - - - -
191A LEU* 3.9 18.6 - - - +
195A ASP* 3.4 24.9 - - - -
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Residues in contact with GLU 160 (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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17A TRP* 3.5 18.4 - - - -
121A VAL* 4.5 4.3 - - + +
122A ARG* 3.9 24.3 + - + +
125A GLY* 3.9 16.2 - - - -
156A HIS 3.1 13.8 + - - +
157A ALA* 3.1 10.3 + - - +
159A GLY* 1.3 75.6 - - - +
161A ALA* 1.3 57.4 + - - +
163A ARG* 2.9 46.1 + - - +
164A ARG* 2.9 58.1 + - - +
188A LEU 4.1 4.2 - - - +
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Residues in contact with ALA 161 (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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125A GLY* 3.5 22.0 - - - +
128A VAL* 4.0 15.3 - - + -
129A ALA* 4.0 8.6 - - - +
132A VAL* 6.3 0.2 - - + -
148A ILE* 3.8 19.1 - - + -
157A ALA 3.0 11.4 + - - +
158A ALA* 3.6 8.5 - - - +
160A GLU* 1.3 76.0 - - - +
162A GLY* 1.3 64.3 + - - +
164A ARG* 3.2 3.3 + - - +
165A THR* 3.0 30.0 + - + +
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Residues in contact with GLY 162 (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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148A ILE* 4.5 1.2 - - - +
158A ALA 3.1 13.9 + - - -
159A GLY 3.8 2.5 - - - -
161A ALA* 1.3 76.5 - - - +
163A ARG* 1.3 57.8 + - - +
165A THR* 2.7 22.1 + - - -
167A GLY 2.9 17.0 + - - -
169A VAL* 4.5 7.4 - - - -
172A ILE* 4.1 6.3 - - - -
195A ASP 3.1 24.7 - - - -
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Residues in contact with ARG 163 (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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17A TRP* 3.6 13.9 - - - -
159A GLY 2.9 17.5 + - - +
160A GLU* 2.9 45.7 + - - +
162A GLY* 1.3 73.3 - - - +
164A ARG* 1.3 81.5 + - - +
166A ASN* 3.1 17.8 + - - +
167A GLY 4.7 2.2 - - - +
187A GLU 5.0 1.6 - - - -
188A LEU* 3.7 47.0 + - - +
194A SER 5.8 0.2 - - - -
195A ASP* 3.7 16.2 + - - +
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Residues in contact with ARG 164 (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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8A LEU* 3.1 26.7 + - - +
10A CYS 5.3 3.0 + - - -
11A PHE* 3.8 21.8 - - - -
122A ARG* 6.0 0.4 - - - +
125A GLY 4.6 0.2 - - - -
126A ALA* 3.7 29.8 + - - +
129A ALA* 3.7 20.4 - - + +
160A GLU* 2.9 55.5 + - - +
161A ALA 3.2 0.4 + - - -
163A ARG* 1.3 93.0 - - - +
165A THR* 1.3 59.2 + - - +
166A ASN* 3.1 13.6 + - - -
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Residues in contact with THR 165 (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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129A ALA* 4.3 15.7 - - + +
132A VAL* 4.2 19.7 - - + -
143A PRO* 5.4 2.2 - - + -
161A ALA 3.0 13.9 + - - +
162A GLY* 2.7 19.1 + - - -
164A ARG* 1.3 76.2 - - - +
166A ASN* 1.3 70.6 + - - +
167A GLY 3.7 2.3 + - - -
168A ALA* 3.0 24.4 + - - +
169A VAL* 3.3 33.3 + - + +
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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