Contacts of the helix formed by residues 146 - 160 (chain A) in PDB entry 6EVP
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 146 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145A LEU* 1.3 78.2 - - - +
147A VAL* 1.3 65.5 + - - +
148A ASP* 3.4 6.8 + - - +
149A ASP* 3.1 33.9 + - - -
150A CYS* 2.8 22.7 + - - +
176A GLN* 3.8 1.6 - - - -
181A GLU* 5.5 1.8 - - - -
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Residues in contact with VAL 147 (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 SER* 1.3 73.6 - - - +
148A ASP* 1.3 60.1 + - - +
150A CYS* 3.3 5.5 + - - +
151A PHE* 2.9 26.3 + - - +
173A VAL* 3.9 20.0 - - + +
176A GLN* 3.4 39.4 + - + +
177A LEU* 3.9 13.2 - - + -
181A GLU* 3.8 24.1 + - + +
182A GLU 4.2 6.7 + - - +
183A ALA* 3.3 30.5 - - + -
185A THR* 5.1 3.8 - - - -
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Residues in contact with ASP 148 (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 SER* 3.2 7.1 + - - +
147A VAL* 1.3 74.9 - - - +
149A ASP* 1.3 63.1 + - - +
151A PHE* 3.4 6.3 + - + +
152A GLY* 2.9 24.8 + - - -
183A ALA* 3.9 7.3 - - - +
184A THR* 3.0 33.7 + - - -
185A THR* 2.6 39.2 + - - -
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Residues in contact with ASP 149 (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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145A LEU* 4.0 21.9 - - + +
146A SER* 3.1 35.8 + - - +
148A ASP* 1.3 77.5 - - - +
150A CYS* 1.3 57.5 + - - +
152A GLY* 3.1 3.1 + - - -
153A MET* 2.9 35.7 + - + +
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Residues in contact with CYS 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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144A MET* 5.6 1.8 - - - -
145A LEU* 3.8 19.5 - - - -
146A SER 2.8 22.3 + - - +
147A VAL* 3.7 2.7 - - - +
149A ASP* 1.3 72.6 - - - +
151A PHE* 1.3 58.3 + - - +
153A MET* 3.1 4.8 + - - +
154A GLY 2.8 24.9 + - - -
169A TRP* 3.7 33.4 - - + +
172A GLN* 4.0 11.9 - - - -
173A VAL* 3.6 20.8 - - + +
176A GLN* 4.0 21.8 - - - -
303A DMS 4.6 0.7 - - - -
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Residues in contact with PHE 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 VAL 2.9 17.5 + - - +
148A ASP* 3.6 5.8 - - - +
149A ASP 3.3 0.2 - - - -
150A CYS* 1.3 77.4 - - - +
152A GLY* 1.3 57.9 + - - +
154A GLY* 3.2 2.5 + - - +
155A ARG* 2.9 48.3 + - - +
170A MET* 3.6 32.5 - - + -
173A VAL* 3.4 9.7 - - + +
185A THR* 3.5 44.9 - - + +
189A GLN* 4.4 7.9 - - + -
190A VAL* 4.1 14.4 - - + -
193A TYR* 3.8 26.2 - + - -
304A DMS 4.3 11.2 - - - -
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Residues in contact with GLY 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 ASP 2.9 15.5 + - - -
149A ASP* 3.1 4.2 + - - -
151A PHE* 1.3 79.4 - - - +
153A MET* 1.3 57.5 + - - +
155A ARG* 3.4 14.3 + - - +
156A SER* 2.9 30.0 + - - -
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Residues in contact with MET 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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145A LEU* 4.2 23.8 - - + -
149A ASP* 2.9 20.5 + - + +
150A CYS 3.1 7.8 + - - +
152A GLY* 1.3 76.6 - - - +
154A GLY* 1.3 57.6 + - - +
156A SER* 3.3 8.8 + - - -
157A ALA* 3.0 27.9 + - - +
169A TRP* 3.4 46.9 + - + +
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Residues in contact with GLY 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 CYS 2.8 16.1 + - - -
151A PHE 3.2 2.4 + - - -
153A MET* 1.3 73.6 - - - +
155A ARG* 1.3 57.7 + - - +
157A ALA* 3.4 0.7 + - - +
158A TYR* 3.0 27.5 + - - +
166A THR* 3.6 12.2 + - - +
169A TRP* 3.4 23.5 - - - +
170A MET* 3.7 16.2 - - - -
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Residues in contact with ARG 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 PHE* 2.9 36.5 + - - +
152A GLY* 3.8 11.9 - - - +
154A GLY* 1.3 72.2 - - - +
156A SER* 1.3 60.3 + - - +
158A TYR* 3.2 5.2 + - - +
159A ASN* 2.9 43.0 + - - +
170A MET* 3.7 4.8 - - + +
193A TYR* 2.7 42.4 - - + +
304A DMS 5.2 1.8 - - - -
9C GLY 3.5 17.6 + - - +
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Residues in contact with SER 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 GLY 2.9 18.9 + - - -
153A MET* 3.4 12.3 - - - -
155A ARG* 1.3 76.3 - - - +
157A ALA* 1.3 62.0 + - - +
159A ASN* 3.3 6.9 + - - +
160A GLU* 3.1 34.1 + - - +
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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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153A MET 3.0 16.0 + - - +
154A GLY 3.8 2.2 - - - +
155A ARG 3.3 0.2 - - - -
156A SER* 1.3 76.0 + - - +
158A TYR* 1.3 60.6 + - - +
160A GLU* 3.2 10.4 + - - -
162A ASP* 2.8 47.1 + - + +
165A HIS* 3.9 16.2 - - + +
166A THR* 3.6 16.4 - - - +
169A TRP* 4.5 2.9 - - + +
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Residues in contact with TYR 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 GLY 3.0 17.7 + - - +
155A ARG 3.2 4.2 + - - +
157A ALA* 1.3 75.8 - - - +
159A ASN* 1.3 75.0 + - - +
161A GLY* 2.9 15.2 + - - -
162A ASP 4.6 2.2 - - - +
163A TYR* 3.9 14.7 - + - -
166A THR* 3.1 20.5 + - + +
193A TYR* 3.5 40.8 - + + -
196A TYR* 3.7 27.4 - + - -
302A DMS 3.1 43.6 + - + +
6C GLY* 3.4 7.3 - - - -
7C PRO* 2.8 48.2 + - + +
9C GLY* 4.5 1.6 - - - -
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Residues in contact with ASN 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 ARG* 2.9 32.1 + - - +
156A SER* 3.3 6.3 + - - +
157A ALA 3.2 0.2 - - - -
158A TYR* 1.3 91.5 - - - +
160A GLU* 1.3 63.2 + - + +
161A GLY 3.2 0.9 + - - -
302A DMS 4.6 11.2 - - - +
8C PRO 4.8 0.7 - - - +
9C GLY* 3.3 36.1 + - - +
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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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156A SER* 3.1 22.2 + - - +
157A ALA* 3.2 9.6 + - - +
159A ASN* 1.3 78.7 - - - +
161A GLY* 1.3 60.4 + - - +
162A ASP* 3.5 7.9 + - + +
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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