Contacts of the helix formed by residues 147 - 161 (chain C) in PDB entry 2PGW
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 THR 147 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146C GLU* 1.3 85.9 - - + +
148C ALA* 1.3 64.8 + - - +
149C GLU* 3.5 8.9 + - - +
150C GLU* 3.0 35.3 + - - +
151C LEU* 3.1 29.7 + - - +
176C LEU* 5.4 2.7 - - - -
180C ILE* 4.3 1.6 - - - -
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Residues in contact with ALA 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C THR* 1.3 74.3 - - - +
149C GLU* 1.3 57.1 + - - +
151C LEU* 3.4 2.0 + - - +
152C ALA* 2.9 34.1 + - - +
176C LEU* 5.1 3.6 - - + +
179C GLU* 4.1 9.9 - - + +
180C ILE* 3.8 29.3 - - + +
183C ALA* 3.9 21.4 - - + +
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Residues in contact with GLU 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C THR* 3.2 8.9 + - - +
148C ALA* 1.3 79.4 - - - +
150C GLU* 1.3 65.7 + - - +
152C ALA* 3.9 3.7 - - - +
153C ARG* 3.1 53.4 + - - +
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Residues in contact with GLU 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C GLN 4.0 3.4 - - - +
145C GLY* 3.7 10.6 - - - -
146C GLU* 2.8 35.2 + - - +
147C THR* 3.0 25.7 + - - +
149C GLU* 1.3 79.6 - - - +
151C LEU* 1.3 58.2 + - - +
153C ARG* 3.4 29.9 + - - +
154C ASP* 3.0 29.1 + - - +
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Residues in contact with LEU 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143C LEU* 4.0 20.3 - - + +
144C GLN* 3.6 28.3 - - - +
145C GLY 3.6 18.4 - - - +
147C THR 3.1 21.4 + - - +
148C ALA* 3.8 3.8 - - - +
150C GLU* 1.3 78.0 - - - +
152C ALA* 1.3 57.6 + - - +
154C ASP* 3.4 3.0 + - - +
155C ALA* 2.9 28.6 + - - +
168C LEU* 3.8 18.8 - - + -
172C ARG* 3.8 17.7 - - - +
180C ILE* 3.7 30.3 - - + -
184C VAL* 4.0 13.6 - - + +
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Residues in contact with ALA 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148C ALA 2.9 18.3 + - - +
149C GLU* 3.9 4.7 - - - +
151C LEU* 1.3 73.5 - - - +
153C ARG* 1.3 56.2 + - - +
155C ALA* 3.2 7.5 + - - +
156C ALA* 2.8 34.7 + - - +
183C ALA* 3.6 29.6 - - + +
184C VAL* 4.4 2.9 - - - +
187C GLU* 3.5 16.3 - - + +
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Residues in contact with ARG 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149C GLU* 3.1 45.3 + - + +
150C GLU* 3.5 37.7 + - - +
152C ALA* 1.3 76.2 - - - +
154C ASP* 1.3 62.4 + - - +
156C ALA* 3.2 8.6 + - + +
157C VAL* 3.1 34.0 + - + +
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Residues in contact with ASP 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141C TYR* 2.7 31.8 + - - -
142C PHE 4.4 1.4 - - - +
143C LEU* 3.5 12.3 - - + +
144C GLN* 3.0 38.4 + - - +
150C GLU 3.0 17.7 + - - +
151C LEU 3.7 3.8 - - - +
152C ALA 3.3 0.2 - - - -
153C ARG* 1.3 76.5 - - - +
155C ALA* 1.3 58.3 + - - +
157C VAL* 3.3 8.0 + - - +
158C GLY 2.9 24.4 + - - -
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Residues in contact with ALA 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143C LEU* 3.6 18.6 - - + +
151C LEU 2.9 18.1 + - - +
152C ALA* 3.2 8.3 + - - +
154C ASP* 1.3 77.2 - - - +
156C ALA* 1.3 63.6 + - - +
158C GLY 3.4 0.2 + - - -
159C HIS* 2.9 26.3 + - - +
166C PHE* 3.7 7.1 - - + -
184C VAL* 4.0 15.5 - - + +
187C GLU* 4.4 4.0 - - + -
188C ILE* 3.8 20.8 - - + +
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Residues in contact with ALA 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152C ALA 2.8 17.0 + - - +
153C ARG* 3.2 14.3 + - + +
155C ALA* 1.3 74.3 - - - +
157C VAL* 1.3 63.4 + - + +
159C HIS* 3.4 2.8 + - - +
160C ALA* 3.1 23.0 + - - +
187C GLU* 4.1 28.2 - - + +
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Residues in contact with VAL 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141C TYR* 5.1 3.6 - - - +
153C ARG* 3.1 22.8 + - + +
154C ASP* 3.6 11.2 - - - +
155C ALA 3.3 0.2 - - - -
156C ALA* 1.3 74.4 - - + +
158C GLY* 1.3 66.4 + - - +
160C ALA* 3.1 8.1 + - + +
161C GLN* 3.0 49.7 + - + +
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Residues in contact with GLY 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141C TYR* 3.9 16.1 + - - -
154C ASP 2.9 15.8 + - - -
155C ALA 3.8 1.6 - - - -
157C VAL* 1.3 77.0 - - - +
159C HIS* 1.3 59.7 + - - +
161C GLN* 3.3 12.3 + - - +
162C GLY 3.3 0.2 + - - -
163C GLU* 2.9 46.9 + - - +
166C PHE* 4.0 2.0 - - - -
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Residues in contact with HIS 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155C ALA 2.9 17.9 + - - +
156C ALA 3.6 4.7 - - - +
158C GLY* 1.3 74.1 - - - +
160C ALA* 1.3 68.5 + - - +
162C GLY* 3.0 13.7 + - - -
163C GLU 4.5 6.2 - - - +
166C PHE* 3.6 13.3 - + + -
187C GLU 4.1 9.0 + - - +
188C ILE* 3.3 41.7 + - + -
189C GLY* 4.4 4.1 + - - -
190C ASP 5.3 0.2 + - - -
191C ALA* 3.9 13.8 + - + +
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Residues in contact with ALA 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156C ALA 3.1 14.2 + - - +
157C VAL* 3.1 11.0 + - - +
159C HIS* 1.3 78.8 + - - +
161C GLN* 1.3 61.7 + - + +
162C GLY 3.4 0.7 + - - -
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Residues in contact with GLN 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141C TYR* 4.6 9.9 + - - -
157C VAL* 3.0 37.0 + - + +
158C GLY* 3.7 11.9 - - - +
159C HIS 3.1 0.4 - - - -
160C ALA* 1.3 78.7 - - + +
162C GLY* 1.3 58.6 + - - +
163C GLU* 4.9 7.3 - - + +
344C LYS* 4.3 11.4 - - - +
345C ASN* 3.3 14.6 + - - +
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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