Contacts of the helix formed by residues 144 - 162 (chain B) in PDB entry 5A86
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 144 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B LEU* 1.3 76.6 - - - +
145B GLU* 1.3 58.4 + - - +
146B GLU* 3.3 15.1 + - - +
147B GLN* 2.9 46.2 + - + +
148B ARG* 2.9 26.9 + - - +
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Residues in contact with GLU 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B LEU 3.8 0.4 + - - -
144B THR* 1.3 72.0 - - - +
146B GLU* 1.3 70.3 + - - +
148B ARG* 3.4 32.1 + - + +
149B MET* 3.1 47.2 + - + +
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Residues in contact with GLU 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B THR* 3.2 12.1 + - - +
145B GLU* 1.3 89.7 - - - +
147B GLN* 1.3 56.8 + - + +
149B MET* 3.6 7.9 + - - +
150B MET* 3.1 27.9 + - - +
263B TYR* 5.2 1.7 + - - -
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Residues in contact with GLN 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B GLY 4.9 0.3 - - - +
143B LEU* 3.6 16.4 - - + +
144B THR* 2.9 54.4 + - - +
146B GLU* 1.3 76.3 - - + +
148B ARG* 1.3 65.6 + - - +
150B MET* 3.1 8.6 + - - +
151B ILE* 3.0 29.4 + - - +
371B ILE* 3.9 18.8 - - - +
372B THR* 3.8 25.5 + - + +
375B SER* 3.3 31.8 + - - -
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Residues in contact with ARG 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B LEU* 3.9 27.8 + - + +
144B THR 2.9 15.7 + - - +
145B GLU* 3.7 39.0 + - + +
147B GLN* 1.3 74.7 - - - +
149B MET* 1.3 57.6 + - + +
151B ILE* 3.6 6.5 + - - +
152B ARG* 3.0 28.5 + - - +
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Residues in contact with MET 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B GLU* 3.1 36.1 + - + +
146B GLU* 3.8 7.9 - - - +
148B ARG* 1.3 73.8 - - - +
150B MET* 1.3 59.9 + - - +
152B ARG* 3.4 8.1 + - + +
153B GLU* 3.0 29.3 + - - +
263B TYR* 5.4 1.6 - - - +
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Residues in contact with MET 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B GLU 3.1 15.8 + - - +
147B GLN* 3.4 9.2 - - - +
149B MET* 1.3 73.4 - - - +
151B ILE* 1.3 63.7 + - - +
153B GLU* 3.4 6.2 + - - +
154B LEU* 3.1 31.0 + - + +
263B TYR* 4.2 31.8 + - + +
365B LEU* 6.2 1.6 - - + -
368B GLN* 3.9 26.7 - - + +
369B PHE* 3.4 41.7 - - + -
372B THR* 3.2 31.4 - - + +
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Residues in contact with ILE 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B LEU* 3.6 31.2 - - + -
147B GLN 3.0 12.8 + - - +
148B ARG* 3.9 4.9 - - - +
150B MET* 1.3 71.9 - - - +
152B ARG* 1.3 56.0 + - - +
154B LEU* 3.2 8.7 + - - +
155B MET* 2.8 40.8 + - + +
338B GLU* 3.7 29.8 - - + -
341B VAL* 5.3 2.7 - - + -
342B LEU* 4.3 11.2 - - + -
372B THR* 3.6 21.5 - - + -
376B TYR* 3.8 21.8 - - + -
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Residues in contact with ARG 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B ARG 3.0 19.0 + - - +
149B MET* 3.6 10.3 - - + +
150B MET 3.3 0.2 - - - -
151B ILE* 1.3 75.9 - - - +
153B GLU* 1.3 58.5 + - - +
155B MET* 3.8 6.9 - - - +
156B ASP* 2.9 36.3 + - + +
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Residues in contact with GLU 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B MET 3.0 16.5 + - - +
150B MET* 3.7 4.7 - - - +
152B ARG* 1.3 77.0 - - - +
154B LEU* 1.3 55.0 + - + +
156B ASP* 3.3 8.7 + - + +
157B ALA* 2.8 34.4 + - + +
260B VAL 3.9 9.3 - - - +
261B ILE* 3.8 11.4 - - + +
262B SER* 3.0 36.2 + - - -
263B TYR* 3.1 32.3 - - - -
265B ARG* 5.1 0.7 + - - -
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Residues in contact with LEU 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B MET* 3.1 18.8 + - + +
151B ILE* 3.5 7.9 - - - +
153B GLU* 1.3 79.5 - - - +
155B MET* 1.3 55.9 + - - +
157B ALA* 3.2 7.2 + - - +
158B GLN 2.9 24.4 + - - -
257B PHE* 4.7 3.4 - - + -
261B ILE* 3.9 32.8 - - + -
341B VAL* 3.4 30.6 - - + +
342B LEU* 3.5 34.3 - - + -
345B ALA* 3.9 20.9 - - + -
369B PHE* 3.9 22.2 - - + -
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Residues in contact with MET 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B ILE* 2.8 38.1 + - + +
152B ARG* 3.8 9.2 - - - +
154B LEU* 1.3 70.8 - - - +
156B ASP* 1.3 57.2 + - - +
158B GLN* 3.3 8.9 + - - +
159B MET* 2.9 30.7 + - - +
337B GLU* 3.4 30.7 - - + +
338B GLU* 3.8 30.1 - - + +
341B VAL* 3.9 21.1 - - + -
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Residues in contact with ASP 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B ARG* 2.9 25.0 + - + +
153B GLU* 3.5 9.3 - - - +
155B MET* 1.3 75.0 - - - +
157B ALA* 1.3 62.2 + - - +
159B MET* 3.4 22.9 + - - +
160B LYS* 2.7 62.9 + - - +
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Residues in contact with ALA 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B GLU* 2.8 14.1 + - + +
154B LEU 3.4 9.0 - - - +
156B ASP* 1.3 78.9 + - - +
158B GLN* 1.3 55.7 + - - +
160B LYS* 3.4 3.9 + - - -
161B THR* 2.7 38.0 + - - +
257B PHE* 3.8 17.3 - - + +
260B VAL* 3.2 31.9 - - + +
261B ILE* 4.2 9.0 - - + -
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Residues in contact with GLN 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B LEU 2.9 13.9 + - - +
155B MET* 3.5 15.0 - - - +
157B ALA* 1.3 76.4 - - - +
159B MET* 1.3 57.7 - - - +
161B THR* 4.1 0.7 - - - -
162B PHE* 2.9 56.1 + - + +
257B PHE* 3.8 3.8 - - - -
287B ARG* 2.8 32.1 + - - +
290B THR* 5.8 2.4 - - - +
337B GLU* 5.1 13.5 + - + +
340B TYR* 5.0 5.7 - - - +
341B VAL* 4.0 19.2 - - + +
344B GLN* 2.8 39.4 + - - -
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Residues in contact with MET 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B MET 2.9 17.4 + - - +
156B ASP* 3.4 28.5 - - - +
158B GLN* 1.3 76.1 - - - +
160B LYS* 1.3 80.2 + - + +
161B THR 3.5 0.3 + - - -
162B PHE 4.2 10.7 + - - +
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Residues in contact with LYS 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B ASP* 2.7 51.9 + - - +
157B ALA* 3.8 6.5 - - - +
158B GLN 3.2 0.2 - - - -
159B MET* 1.3 93.3 - - + +
161B THR* 1.3 63.1 + - + +
260B VAL* 5.2 12.6 - - + -
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Residues in contact with THR 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157B ALA 2.7 21.3 + - - +
160B LYS* 1.3 87.4 - - + +
162B PHE* 1.3 59.7 + - - +
163B ASP* 3.8 3.0 + - - +
253B GLY* 3.7 22.3 - - - +
256B SER* 3.5 36.8 - - - +
257B PHE* 3.4 7.5 - - - +
260B VAL* 4.4 9.0 - - + -
287B ARG* 2.9 29.9 + - - -
698D SER 5.9 0.2 - - - +
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Residues in contact with PHE 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B GLN* 2.9 34.9 + - + +
159B MET* 4.2 9.5 - - - +
160B LYS 3.8 1.0 - - - -
161B THR* 1.3 77.6 - - - +
163B ASP* 1.3 68.3 + - - +
164B THR* 3.0 41.2 + - + +
166B PHE* 4.6 9.4 - + - -
250B MET* 4.6 10.5 - - + -
287B ARG* 3.6 58.8 - - + +
290B THR* 3.4 27.6 - - + -
291B VAL* 4.5 9.0 - - + -
337B GLU* 5.9 2.7 - - - -
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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