Contacts of the helix formed by residues 146 - 164 (chain A) in PDB entry 3DEW
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 HIS 146 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A ILE* 5.6 0.2 - - - -
144A ASP 5.2 4.3 + - - -
145A LEU* 1.3 74.9 - - - +
147A ALA* 1.3 65.8 + - - +
148A VAL* 3.4 1.3 - - + +
149A ASN* 3.4 27.7 + - + +
150A SER* 2.9 25.6 + - - -
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Residues in contact with ALA 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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129A ALA* 3.6 14.0 - - + +
132A ILE* 3.8 22.6 - - + +
133A GLU* 3.3 42.4 - - + +
136A MSE 4.6 5.0 - - - -
145A LEU 3.7 3.4 + - - -
146A HIS* 1.3 72.4 - - - +
148A VAL* 1.3 59.1 + - - +
150A SER* 3.3 3.1 + - - -
151A ALA* 2.9 27.4 + - - +
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Residues in contact with VAL 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ILE* 4.1 16.2 - - + -
126A ARG* 6.0 2.5 - - + -
129A ALA* 3.8 21.5 - - + -
133A GLU* 5.0 5.8 - - - +
146A HIS* 3.4 1.6 - - + +
147A ALA* 1.3 73.6 - - - +
149A ASN* 1.3 73.2 + - - +
150A SER 3.1 0.2 + - - -
151A ALA* 3.2 3.2 + - - +
152A LEU* 2.9 37.8 + - + +
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Residues in contact with ASN 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A HIS* 3.4 26.6 + - + +
147A ALA 3.4 0.4 - - - -
148A VAL* 1.3 80.9 - - - +
150A SER* 1.3 56.7 + - - +
152A LEU* 3.4 19.0 + - - +
153A ALA* 3.0 26.2 + - - +
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Residues in contact with SER 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ILE* 3.9 17.7 - - - +
145A LEU* 3.8 25.6 - - - +
146A HIS 2.9 21.4 + - - -
147A ALA* 3.5 7.0 - - - -
149A ASN* 1.3 74.3 - - - +
151A ALA* 1.3 65.1 + - - +
153A ALA* 3.1 7.2 + - - +
154A LEU 3.1 17.7 + - - -
190A PHE* 3.2 23.1 - - - -
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Residues in contact with ALA 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ILE* 3.8 22.7 - - + +
128A LEU* 3.7 30.5 - - + +
129A ALA* 3.8 6.1 - - - +
132A ILE* 3.5 9.1 - - + +
147A ALA 2.9 13.3 + - - +
148A VAL* 3.5 8.3 - - - +
150A SER* 1.3 75.5 - - - +
152A LEU* 1.3 56.9 + - - +
154A LEU* 3.2 7.1 + - - +
155A ALA* 3.0 28.6 + - - +
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Residues in contact with LEU 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ILE* 6.0 1.6 - - + -
125A ILE* 3.8 30.7 - - + -
148A VAL* 2.9 34.8 + - + +
149A ASN* 3.6 19.3 - - - +
151A ALA* 1.3 75.4 - - - +
153A ALA* 1.3 53.2 + - - +
155A ALA* 3.4 5.4 + - + +
156A GLY* 2.8 32.6 + - - -
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Residues in contact with ALA 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 ASN 3.0 14.0 + - - +
150A SER* 3.3 13.0 - - - +
152A LEU* 1.3 75.4 - - - +
154A LEU* 1.4 58.7 + - - +
156A GLY* 3.2 3.1 + - - -
157A MSE 2.9 37.4 + - + +
190A PHE* 4.4 8.5 - - + -
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Residues in contact with LEU 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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81A MSE 3.6 43.1 - - + +
84A TYR* 3.9 24.9 - - + -
85A LEU* 3.8 25.4 - - + -
128A LEU* 4.6 4.7 - - + -
150A SER 3.1 6.3 + - - -
151A ALA* 3.2 8.3 + - - +
153A ALA* 1.4 72.9 - - - +
155A ALA* 1.3 67.9 + - - +
157A MSE 3.2 24.1 + - - +
158A VAL* 3.4 13.5 + - - +
186A TYR 4.7 0.7 - - - +
187A VAL* 5.8 0.4 - - - -
190A PHE* 3.8 42.7 - - + -
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Residues in contact with ALA 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A TYR* 3.4 28.9 - - + +
125A ILE* 3.7 23.1 - - + -
128A LEU* 4.9 0.4 - - + -
151A ALA 3.0 15.9 + - - +
152A LEU* 3.7 5.2 - - + +
154A LEU* 1.3 76.7 - - - +
156A GLY* 1.3 57.3 + - - +
158A VAL* 3.5 0.5 - - - +
159A ASN* 2.8 37.0 + - - +
209A ACY 4.0 7.9 - - + -
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Residues in contact with GLY 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 LEU 2.8 17.0 + - - -
153A ALA* 3.6 2.5 - - - -
154A LEU 3.1 0.2 - - - -
155A ALA* 1.3 74.7 - - - +
157A MSE 1.3 66.5 + - - +
159A ASN* 4.8 3.1 - - - -
160A TYR* 2.8 29.2 + - - +
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Residues in contact with MSE 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 ALA* 2.9 23.9 + - + +
154A LEU* 3.2 13.2 + - + +
156A GLY* 1.3 79.2 - - - +
158A VAL* 1.3 62.6 + - + +
160A TYR* 3.8 3.0 - - - +
161A PHE 3.1 15.8 + - - -
186A TYR* 3.7 58.8 + - + +
189A ILE* 3.7 28.5 - - + -
190A PHE* 3.8 33.9 - - + -
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Residues in contact with VAL 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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84A TYR* 3.8 8.5 - - + +
85A LEU* 3.6 27.1 - - + -
88A THR* 3.8 28.0 - - + -
89A ILE* 3.9 30.1 - - + -
154A LEU 3.4 8.9 + - - +
155A ALA 3.5 10.1 - - - +
157A MSE 1.3 78.3 - - - +
159A ASN* 1.3 69.1 + - - +
161A PHE* 3.3 10.3 + - - +
162A PHE* 3.3 26.8 - - + -
182A LEU* 5.0 5.2 - - + -
186A TYR* 4.3 9.6 - - + -
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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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84A TYR* 3.3 8.1 + - - -
88A THR* 3.9 4.2 - - - +
91A ARG* 4.7 1.2 + - - -
92A HIS* 2.9 34.3 + - - -
99A LEU* 4.1 12.7 - - + +
102A TYR* 4.6 10.9 + - + +
155A ALA* 2.8 29.6 + - - +
156A GLY* 4.4 2.7 - - - +
158A VAL* 1.3 79.3 - - - +
160A TYR* 1.3 57.3 + - - +
162A PHE* 3.3 4.3 + - - +
163A LEU* 2.9 28.6 + - - +
209A ACY 3.1 34.2 + - - +
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Residues in contact with TYR 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 GLY 2.8 20.3 + - - +
157A MSE 3.8 3.6 - - - +
159A ASN* 1.3 77.5 - - - +
161A PHE* 1.3 66.6 + - - +
163A LEU* 4.0 25.4 - - + -
164A SER* 2.9 52.8 + - - -
168A THR* 6.0 1.3 - - + -
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Residues in contact with PHE 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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93A ARG* 4.9 3.8 - - - -
157A MSE 3.1 14.3 + - - +
158A VAL 3.3 10.1 + - - +
160A TYR* 1.3 80.5 - - - +
162A PHE* 1.3 83.6 + + - +
164A SER* 3.4 12.0 + - - -
165A THR* 3.4 10.6 + - - -
172A THR* 4.1 12.1 - - + -
173A SER 3.4 15.0 - - - -
174A HIS* 3.4 34.8 - + + -
179A ASP* 5.2 0.4 - - - -
182A LEU* 3.6 38.8 - - + -
186A TYR* 4.1 17.5 - - + +
206A EDO 3.4 28.7 - - - -
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Residues in contact with PHE 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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89A ILE* 3.8 45.3 - - + -
92A HIS* 3.7 38.1 - + + +
93A ARG* 3.7 36.3 - - - -
99A LEU* 3.8 18.0 - - + +
158A VAL* 3.3 26.2 - - + -
159A ASN 3.3 4.3 + - - +
160A TYR 3.2 0.2 - - - -
161A PHE* 1.3 93.1 - + - +
163A LEU* 1.3 65.4 - - - +
165A THR* 2.8 26.2 + - - -
174A HIS* 6.5 0.4 - - + -
179A ASP* 4.5 1.8 - - - -
182A LEU* 4.8 0.9 - - + -
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Residues in contact with LEU 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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99A LEU* 3.4 19.8 - - + +
103A THR* 4.1 29.4 - - + +
159A ASN 2.9 17.6 + - - +
160A TYR* 3.2 27.1 + - + +
162A PHE* 1.3 79.0 - - - +
164A SER* 1.4 58.8 + - - +
165A THR* 3.4 2.9 + - - -
166A LEU* 4.8 2.6 + - - +
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Residues in contact with SER 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A TYR* 2.9 55.7 + - - -
161A PHE* 3.4 8.7 + - - -
163A LEU* 1.4 76.0 - - - +
165A THR* 1.3 66.4 + - - +
166A LEU 3.3 2.0 - - - -
167A ALA* 2.9 19.9 + - - -
168A THR* 3.0 28.6 + - - +
174A HIS* 5.1 0.2 + - - -
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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
------------------------------------------------------------
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