Contacts of the helix formed by residues 149 - 160 (chain A) in PDB entry 2HPC
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 ARG 149 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145A VAL* 3.6 27.5 + - - +
146A ASP* 4.1 3.4 - - - +
148A LYS* 1.3 82.1 - - - +
150A LEU* 1.3 58.2 + - - +
151A GLU 2.8 1.1 - - - -
152A VAL* 3.2 1.0 + - - +
153A ASP* 2.6 38.4 + - - +
424B TRP* 2.9 58.4 + - - -
425B ASP* 3.6 5.9 - - - +
426B MET* 2.9 30.7 - - - +
427B ALA 3.2 19.6 + - - +
428B LYS* 4.9 8.3 + - - +
429B HIS 5.3 1.2 - - - -
430B GLY* 4.4 7.5 - - - +
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Residues in contact with LEU 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 ASP* 2.8 22.3 + - - +
147A MET* 3.9 11.7 - - + -
149A ARG* 1.3 76.5 - - - +
151A GLU* 1.3 66.9 + - - +
153A ASP* 4.1 14.1 - - - +
154A ILE* 2.8 44.0 + - + +
182B LEU* 5.1 5.4 - - + +
121C ILE* 3.7 25.6 - - + -
124C LEU* 4.0 25.4 - - + +
125C LYS* 3.6 34.1 - - - +
128C VAL* 5.2 1.3 - - + -
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Residues in contact with GLU 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 MET 3.0 23.6 + - - +
148A LYS* 4.2 5.4 - - - +
149A ARG 2.8 0.2 - - - -
150A LEU* 1.3 76.4 - - - +
152A VAL* 1.3 61.3 + - + +
154A ILE* 2.6 28.3 + - - +
155A ASP* 2.8 21.0 + - - +
171A ARG* 4.1 0.3 + - - -
173A VAL* 2.7 48.3 - - + +
175A LEU* 4.8 7.9 - - + -
178A TYR* 4.1 12.2 - - + -
181B LYS* 5.5 1.6 - - - +
182B LEU* 3.2 46.5 - - + +
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Residues in contact with VAL 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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148A LYS 3.0 24.9 - - - +
149A ARG 3.2 0.9 + - - +
151A GLU* 1.3 87.2 - - + +
153A ASP* 1.3 62.1 + - - +
155A ASP* 3.3 13.9 - - - +
156A ILE* 3.1 25.8 + - + +
175A LEU* 4.8 7.2 - - + -
417B TYR* 3.8 31.6 - - + +
426B MET* 3.6 45.3 - - + +
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Residues in contact with ASP 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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149A ARG 2.6 23.0 + - - +
150A LEU* 4.0 15.9 - - + +
152A VAL* 1.3 71.7 - - - +
154A ILE* 1.3 67.5 + - - +
156A ILE* 3.3 5.5 - - - +
157A LYS* 2.9 45.2 + - - +
415B ARG* 2.8 30.0 + - - +
426B MET 4.7 2.6 + - - +
428B LYS* 4.4 23.9 - - + +
128C VAL* 4.7 5.4 - - - +
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Residues in contact with ILE 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 LEU* 2.8 30.4 + - + +
151A GLU* 2.6 16.5 + - - +
153A ASP* 1.3 72.3 - - - +
155A ASP* 1.3 63.0 + - - +
157A LYS* 3.2 5.0 + - - +
158A ILE* 3.0 31.0 + - + +
171A ARG* 3.8 7.1 + - - +
182B LEU* 3.6 40.8 - - + +
185B ASP* 6.4 0.9 - - + -
186B VAL* 4.3 18.4 - - + +
124C LEU* 5.3 3.1 - - + -
128C VAL* 3.2 46.9 - - + -
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Residues in contact with ASP 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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151A GLU* 2.8 32.3 + - - +
152A VAL* 3.3 18.5 - - - +
154A ILE* 1.3 74.9 - - - +
156A ILE* 1.3 66.1 + - - +
158A ILE* 3.0 24.3 - - - +
159A ARG* 3.4 27.5 + - - +
171A ARG* 2.9 23.8 + - - +
173A VAL* 4.0 13.8 - - + +
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Residues in contact with ILE 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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152A VAL* 3.1 16.1 + - + +
153A ASP* 3.3 16.4 - - - +
155A ASP* 1.3 81.4 - - - +
157A LYS* 1.3 73.8 + - + +
158A ILE 3.1 4.7 - - - -
159A ARG* 3.4 11.2 + - + +
160A SER* 3.2 16.6 + - - -
258B GLY* 5.3 1.2 - - - -
415B ARG* 3.5 30.5 - - + +
416B TYR* 2.9 56.5 - - + +
417B TYR* 4.6 13.5 - - + -
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Residues in contact with LYS 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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153A ASP* 2.9 40.5 + - - +
154A ILE* 3.2 6.9 + - - +
156A ILE* 1.3 83.8 - - + +
158A ILE* 1.3 61.3 + - - +
160A SER* 2.9 39.5 + - - -
161A CYS* 3.9 9.4 - - - -
261B ASP* 3.7 22.4 + - - +
415B ARG* 4.4 12.0 - - - +
128C VAL* 4.8 14.1 - - + -
131C LEU* 3.9 11.0 - - + +
132C GLU* 3.4 42.9 + - + +
136C GLN* 4.6 0.4 + - - -
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Residues in contact with ILE 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 ILE* 3.0 9.8 + - + +
155A ASP 3.0 16.4 - - - +
156A ILE 3.1 0.6 - - - -
157A LYS* 1.3 76.8 - - - +
159A ARG* 1.3 75.0 + - + +
160A SER 2.8 6.0 + - - -
161A CYS* 3.1 13.2 + - - +
162A ARG 4.3 0.3 + - - -
168A ALA* 6.1 1.1 - - + -
169A LEU 5.1 7.0 - - - +
171A ARG* 3.5 35.0 - - - +
185B ASP* 4.2 9.4 - - + +
186B VAL* 5.0 5.6 - - + -
189B GLN* 3.4 58.5 + - + +
131C LEU* 4.1 24.0 - - + -
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Residues in contact with ARG 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 ASP* 3.4 25.6 + - - +
156A ILE* 3.4 11.8 + - + +
158A ILE* 1.3 87.5 - - - +
160A SER* 1.3 49.7 + - - +
161A CYS 2.6 11.1 + - - -
162A ARG* 3.3 40.1 + - - +
168A ALA* 5.9 1.6 - - - -
169A LEU 5.7 2.1 + - - -
170A ALA* 6.0 1.8 - - - +
171A ARG* 4.6 23.0 + - - +
189B GLN* 5.5 0.2 - - - +
258B GLY* 3.6 27.8 - - - +
259B SER* 2.4 30.0 + - - +
416B TYR* 5.0 4.3 + - + -
418B TRP* 2.7 64.2 - - + +
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Residues in contact with SER 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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156A ILE 3.2 7.2 + - - -
157A LYS* 2.9 37.9 + - - -
158A ILE 2.8 0.8 - - - -
159A ARG* 1.3 74.5 - - - +
161A CYS* 1.3 57.0 + - - -
164A SER* 3.5 2.3 + - - -
258B GLY* 4.6 2.4 - - - -
259B SER 3.5 15.9 - - - +
261B ASP* 2.7 38.6 + - - +
132C GLU* 6.2 0.4 - - - -
135C CYS* 3.0 23.4 + - - +
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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