Contacts of the helix formed by residues 136 - 155 (chain D) in PDB entry 3MA2
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 GLY 136 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131D TYR* 3.6 12.3 - - - -
132D THR 2.9 10.0 + - - -
133D PRO* 3.7 7.8 + - - -
135D VAL* 1.3 77.4 - - - +
137D GLU* 1.3 62.4 + - - -
138D TYR 3.6 1.3 - - - -
139D ALA 4.2 1.8 - - - -
140D THR* 2.7 32.1 + - - -
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Residues in contact with GLU 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D TYR* 3.4 49.5 + - + -
136D GLY* 1.3 73.2 - - - +
138D TYR* 1.3 66.6 + - - +
140D THR* 3.8 0.2 - - - -
141D TYR* 3.1 49.5 + - + -
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Residues in contact with TYR 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D GLY 3.6 0.2 - - - -
137D GLU* 1.3 79.1 - - - +
139D ALA* 1.4 64.5 + - + +
141D TYR* 3.4 3.1 + - - +
142D GLU* 3.0 56.8 + - + +
145D ARG* 5.0 11.9 - - - -
224D ARG* 4.1 20.2 + - - -
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Residues in contact with ALA 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D VAL* 3.5 31.1 - - + +
136D GLY 3.6 2.2 + - - -
137D GLU 3.3 0.6 - - - -
138D TYR* 1.4 88.7 - - + +
140D THR* 1.3 63.5 + - - +
142D GLU* 3.8 2.2 - - - +
143D ALA* 2.9 25.3 + - - +
223D VAL* 4.1 15.6 - - + +
224D ARG* 4.5 13.8 + - - +
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Residues in contact with THR 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D ASN 4.3 2.9 - - - +
131D TYR* 3.7 17.3 - - + -
132D THR* 3.6 11.8 + - - +
135D VAL* 3.6 19.2 - - - +
136D GLY 2.7 24.2 + - - -
137D GLU 3.8 0.2 - - - -
139D ALA* 1.3 76.3 - - - +
141D TYR* 1.3 65.5 + - + +
143D ALA* 3.0 12.6 + - - +
144D ILE* 3.1 23.5 + - + +
181D PHE* 3.4 37.7 - - + -
233D ILE* 4.2 6.7 - - + -
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Residues in contact with TYR 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D ILE* 2.6 60.7 + - + +
129D GLN 3.5 4.9 + - - -
130D ASN* 3.5 26.0 + - - -
131D TYR* 4.2 7.4 - + + -
137D GLU* 3.1 52.4 + - + +
138D TYR* 4.0 3.4 - - - +
140D THR* 1.3 78.8 - - - +
142D GLU* 1.3 62.5 + - - +
144D ILE* 3.3 4.0 + - - +
145D ARG* 3.0 61.3 + - - +
161D GLU* 3.9 7.0 - - - -
164D TYR* 5.7 0.3 - - - +
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Residues in contact with GLU 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138D TYR* 3.0 50.4 + - + +
139D ALA 4.1 2.2 - - - +
141D TYR* 1.3 75.5 - - - +
143D ALA* 1.3 64.7 + - - +
145D ARG* 4.1 11.8 + - - +
146D LYS* 2.9 31.9 + - + +
149D ARG* 2.7 41.6 + - - -
224D ARG* 3.7 20.0 + - - +
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Residues in contact with ALA 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139D ALA 2.9 19.5 + - - +
140D THR 3.0 5.3 + - - +
142D GLU* 1.3 77.4 - - - +
144D ILE* 1.3 63.9 + - - +
146D LYS* 3.5 5.3 + - - -
147D ALA* 3.1 18.0 + - - +
223D VAL* 3.9 22.4 - - + -
233D ILE* 4.1 6.7 - - + -
234D PHE* 3.4 40.0 - - + +
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Residues in contact with ILE 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D ILE* 3.8 40.8 - - + -
140D THR* 3.1 32.8 + - + +
141D TYR 3.9 0.9 - - - +
142D GLU 3.2 0.2 - - - -
143D ALA* 1.3 77.1 - - - +
145D ARG* 1.4 63.4 + - - +
147D ALA* 3.1 4.3 + - - +
148D PHE* 3.1 28.5 + - + -
179D ILE* 4.1 33.9 - - + -
181D PHE* 4.4 3.8 - - + -
215D PHE* 4.2 9.9 - - + -
233D ILE* 4.3 13.2 - - + -
237D ALA* 4.3 13.5 - - + -
241D LEU* 4.3 8.3 - - + -
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Residues in contact with ARG 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D PHE* 4.5 10.8 - - + -
128D ILE* 4.7 3.4 - - + -
138D TYR* 5.0 13.1 - - - -
141D TYR* 3.0 51.1 + - - +
142D GLU* 3.2 12.6 + - - +
144D ILE* 1.4 75.3 - - - +
146D LYS* 1.3 57.6 + - - +
148D PHE* 3.2 12.2 + - - +
149D ARG* 2.9 47.6 + - + +
161D GLU* 2.7 41.3 + - - +
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Residues in contact with LYS 146 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142D GLU* 2.9 25.5 + - + +
143D ALA* 3.5 7.4 - - - +
145D ARG* 1.3 77.1 - - - +
147D ALA* 1.3 60.4 + - - +
149D ARG* 3.3 28.8 + - + +
150D VAL* 3.1 25.9 + - + +
224D ARG* 6.1 4.0 - - - +
234D PHE* 3.6 28.3 - - + +
266D THR* 2.9 40.2 + - - -
267D GLU* 4.7 6.1 + - - +
269D PHE* 5.4 1.3 - - - -
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Residues in contact with ALA 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143D ALA 3.1 9.0 + - - +
144D ILE 3.1 10.1 + - - +
146D LYS* 1.3 76.6 - - - +
148D PHE* 1.3 62.2 + - - +
150D VAL* 3.2 17.3 + - - +
151D TRP* 3.4 13.2 + - - -
234D PHE* 3.5 10.5 - - + -
237D ALA* 3.7 16.8 - - + -
238D VAL* 3.4 36.0 - - + +
241D LEU* 4.0 6.1 - - + -
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Residues in contact with PHE 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D PHE* 3.3 55.6 - + + -
144D ILE* 3.1 26.2 + - + -
145D ARG* 3.2 8.3 + - - +
147D ALA* 1.3 73.2 - - - +
149D ARG* 1.3 63.8 + - + +
151D TRP* 3.0 8.6 + + - +
152D GLU* 3.0 26.8 + - - +
159D PHE* 3.4 52.5 - + + -
177D ILE* 4.1 10.3 - - + -
179D ILE* 3.7 13.0 - - + -
241D LEU* 3.6 36.5 - - + +
245D LEU* 5.5 1.1 - - + -
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Residues in contact with ARG 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D GLU* 2.7 40.6 + - - -
145D ARG* 2.9 26.2 + - + +
146D LYS* 3.4 35.8 - - + +
147D ALA 3.3 0.4 - - - -
148D PHE* 1.3 75.8 - - + +
150D VAL* 1.3 62.9 + - - +
152D GLU* 3.4 20.5 + - - +
153D SER* 3.1 23.7 + - - -
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Residues in contact with VAL 150 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146D LYS* 3.1 15.8 + - + +
147D ALA* 3.3 9.4 - - - +
149D ARG* 1.3 76.2 - - - +
151D TRP* 1.3 66.2 + - + +
153D SER* 3.0 23.2 + - - +
154D ALA* 3.6 6.4 + - - +
234D PHE* 3.8 25.8 - - + -
238D VAL* 4.4 8.7 - - + -
269D PHE* 3.9 19.3 - - + -
271D LEU* 4.0 34.4 - - + +
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Residues in contact with TRP 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D ALA 3.4 17.7 + - - -
148D PHE* 3.0 9.9 + + - +
150D VAL* 1.3 76.2 - - + +
152D GLU* 1.3 64.0 + - - +
154D ALA* 3.1 10.7 + - - +
155D THR* 3.0 22.4 + - - +
159D PHE* 4.4 7.0 - - + -
238D VAL* 3.0 47.1 + - + +
241D LEU* 4.0 13.3 - - + +
242D GLY* 3.5 19.3 - - - +
245D LEU* 3.7 28.5 - - + -
247D LEU* 3.5 19.1 - - + -
256D ILE* 4.5 2.9 - - + -
257D MET* 4.4 4.3 - - - -
271D LEU* 3.9 30.5 - - + -
275D ASP* 4.1 9.9 - - + -
279D ILE* 3.3 41.7 - - + -
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Residues in contact with GLU 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148D PHE* 3.0 10.5 + - - +
149D ARG* 3.5 24.7 - - - +
151D TRP* 1.3 77.1 - - - +
153D SER* 1.3 58.4 + - - +
155D THR* 3.0 23.5 - - - +
157D LEU 3.3 23.3 - - - +
158D ARG* 3.5 25.6 + - - +
159D PHE* 2.9 51.7 + - + +
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Residues in contact with SER 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149D ARG 3.1 13.0 + - - -
150D VAL* 3.0 18.1 + - - +
152D GLU* 1.3 77.4 - - - +
154D ALA* 1.3 59.8 + - - +
155D THR 4.8 0.4 - - - -
271D LEU* 6.0 0.3 - - - +
285D GLY 5.6 0.2 - - - +
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Residues in contact with ALA 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150D VAL 4.3 2.9 - - - +
151D TRP* 3.1 6.5 + - - +
153D SER* 1.3 83.7 + - - +
155D THR* 1.3 56.7 + - - +
271D LEU* 4.0 20.0 - - + -
276D ARG* 4.8 6.3 - - + -
279D ILE* 3.6 22.0 - - + -
280D GLN* 2.9 37.9 - - - +
285D GLY* 3.6 8.5 - - - -
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Residues in contact with THR 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151D TRP* 3.0 17.4 + - + +
152D GLU* 3.0 15.8 + - - +
153D SER 3.6 0.5 - - - -
154D ALA* 1.3 85.5 - - - +
156D PRO* 1.4 74.4 - - - +
157D LEU* 3.0 29.3 + - + +
158D ARG* 3.3 4.9 + - - -
279D ILE* 3.6 35.9 - - + -
283D TYR* 4.3 9.4 - - + -
284D GLY 3.6 7.9 - - - +
285D GLY 3.8 8.4 - - - +
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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