Contacts of the helix formed by residues 144 - 162 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143A LEU* 1.3 81.9 - - + +
145A GLU* 1.3 64.9 + - - +
146A GLU* 3.5 9.4 + - - +
147A GLN* 2.9 43.1 + - - +
148A ARG* 3.0 20.3 + - - +
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Residues in contact with GLU 145 (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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143A LEU 3.7 1.0 + - - -
144A THR* 1.3 72.6 - - - +
146A GLU* 1.3 56.3 + - - +
148A ARG* 3.1 23.2 + - - +
149A MET* 2.9 65.5 + - + +
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Residues in contact with GLU 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A THR* 3.5 8.0 + - - +
145A GLU* 1.3 78.7 - - - +
147A GLN* 1.3 57.4 + - + +
149A MET* 3.2 9.7 + - + +
150A MET* 2.9 34.6 + - + +
263A TYR* 5.3 5.5 + - - +
368A GLN* 5.5 2.8 - - - +
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Residues in contact with GLN 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A LEU 2.8 33.6 + - - +
144A THR* 2.9 42.3 + - - +
146A GLU* 1.3 72.9 - - + +
148A ARG* 1.3 64.3 + - + +
150A MET* 3.2 9.0 + - - +
151A ILE* 3.0 32.4 + - + +
371A ILE* 3.9 18.8 - - - +
372A THR* 3.8 26.4 + - + +
375A SER* 3.3 26.4 + - - -
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Residues in contact with ARG 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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143A LEU* 3.7 38.7 + - - +
144A THR 3.0 16.5 + - - +
145A GLU* 3.1 30.5 + - - +
147A GLN* 1.3 77.1 - - - +
149A MET* 1.3 61.7 + - + +
151A ILE* 3.5 9.3 + - + +
152A ARG* 3.0 28.2 + - - +
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Residues in contact with MET 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 GLU* 2.9 44.7 + - + +
146A GLU* 3.5 10.5 - - + +
148A ARG* 1.3 80.4 - - + +
150A MET* 1.3 60.3 + - - +
152A ARG* 3.4 15.6 + - + +
153A GLU* 3.0 29.6 + - - +
263A TYR* 5.4 1.3 - - - +
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Residues in contact with MET 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A GLU* 2.9 18.0 + - + +
147A GLN* 3.2 10.5 + - - +
149A MET* 1.3 73.4 - - - +
151A ILE* 1.3 65.4 + - - +
153A GLU* 3.4 6.2 + - - +
154A LEU* 3.1 29.5 + - + +
263A TYR* 4.1 33.8 + - + +
365A LEU* 6.2 1.3 - - + -
368A GLN* 3.9 27.4 - - + +
369A PHE* 3.4 42.2 - - + -
372A THR* 3.1 30.3 - - + +
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Residues in contact with ILE 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 GLN* 3.0 19.1 + - + +
148A ARG* 3.8 8.1 - - + +
150A MET* 1.3 71.6 - - - +
152A ARG* 1.3 61.9 + - - +
154A LEU* 3.1 9.3 + - - +
155A MET* 2.8 35.9 + - + +
338A GLU* 3.8 30.1 - - + -
341A VAL* 5.3 2.5 - - + -
342A LEU* 4.3 12.1 - - + -
372A THR* 3.7 25.6 - - + -
376A TYR* 3.8 28.9 - - + -
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Residues in contact with ARG 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 ARG 3.0 17.7 + - - +
149A MET* 3.6 19.9 - - + +
150A MET 3.3 0.2 - - - -
151A ILE* 1.3 78.0 - - - +
153A GLU* 1.3 57.4 + - - +
155A MET* 3.8 7.8 - - - -
156A ASP* 2.9 38.8 + - + +
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Residues in contact with GLU 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 MET 3.0 17.1 + - - +
150A MET* 3.7 5.6 - - - +
151A ILE 3.3 0.2 - - - -
152A ARG* 1.3 76.5 - - - +
154A LEU* 1.3 58.9 + - + +
156A ASP* 3.5 7.5 + - - +
157A ALA* 3.0 26.9 + - - +
260A VAL 3.8 7.7 - - - +
261A ILE* 3.9 12.9 - - + +
262A SER* 2.9 48.2 + - - -
263A TYR* 2.9 28.1 - - + -
265A ARG* 4.8 1.4 + - - -
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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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150A MET 3.1 17.6 + - - +
151A ILE* 3.4 7.2 - - - +
153A GLU* 1.3 76.1 - - + +
155A MET* 1.3 58.5 + - - +
157A ALA* 3.2 4.0 + - - +
158A GLN 2.9 23.7 + - - -
257A PHE* 4.7 6.3 - - + -
261A ILE* 3.8 26.9 - - + -
263A TYR* 5.9 0.2 - - + -
341A VAL* 3.4 31.6 - - + +
342A LEU* 3.5 35.0 - - + -
345A ALA* 3.9 24.5 - - + -
349A PHE* 6.0 0.4 - - + -
369A PHE* 3.9 23.6 - - + -
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Residues in contact with MET 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 ILE* 2.8 36.8 + - + +
152A ARG* 3.8 9.9 - - - +
154A LEU* 1.3 67.6 - - - +
156A ASP* 1.3 59.2 + - - +
158A GLN* 3.3 9.6 + - - +
159A MET* 2.9 31.0 + - - +
337A GLU* 3.5 30.1 - - + +
338A GLU* 3.8 28.5 - - + +
341A VAL* 3.9 21.8 - - + -
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Residues in contact with ASP 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 ARG* 2.9 26.1 + - + +
153A GLU* 3.6 9.6 - - - +
155A MET* 1.3 74.1 - - - +
157A ALA* 1.3 61.9 + - - +
159A MET* 3.4 14.8 + - - +
160A LYS* 2.7 67.7 + - - +
260A VAL* 5.9 1.7 - - - +
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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 GLU 3.0 8.0 + - - +
154A LEU 3.4 6.7 - - - +
156A ASP* 1.3 78.3 + - - +
158A GLN* 1.3 55.8 + - - +
160A LYS* 3.4 2.2 + - - -
161A THR* 2.7 38.1 + - - +
257A PHE* 3.7 9.0 - - + -
260A VAL* 3.2 24.0 - - + -
261A ILE* 3.2 36.1 - - + -
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Residues in contact with GLN 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 LEU 2.9 13.5 + - - +
155A MET* 3.3 13.7 + - - +
157A ALA* 1.3 76.7 - - - +
159A MET* 1.3 56.6 + - - +
161A THR* 4.1 0.7 - - - -
162A PHE* 2.9 56.5 + - + +
257A PHE* 3.8 4.2 - - - -
287A ARG* 2.8 32.0 + - - +
290A THR* 5.8 3.0 - - - +
337A GLU* 5.2 12.2 + - + +
340A TYR* 5.0 6.1 - - - +
341A VAL* 4.0 19.4 - - + +
344A GLN* 2.8 38.0 + - - -
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Residues in contact with MET 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 MET 2.9 17.4 + - - +
156A ASP* 3.5 27.6 - - - +
158A GLN* 1.3 76.1 - - - +
160A LYS* 1.3 86.2 + - + +
161A THR 3.5 0.2 + - - -
162A PHE 4.2 9.8 + - - +
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Residues in contact with LYS 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 ASP* 2.7 54.4 + - - +
157A ALA* 3.9 6.3 - - - +
158A GLN 3.2 0.2 - - - -
159A MET* 1.3 95.1 - - + +
161A THR* 1.3 66.0 + - + +
162A PHE 3.8 0.2 - - - -
260A VAL* 5.1 13.2 - - + -
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Residues in contact with THR 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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157A ALA 2.7 21.7 + - - +
160A LYS* 1.3 87.8 - - + +
162A PHE* 1.3 59.6 + - - +
163A ASP* 3.8 3.0 + - - +
253A GLY* 3.7 21.5 - - - +
256A SER* 3.5 36.6 - - - +
257A PHE* 3.5 7.7 - - - +
260A VAL* 4.5 8.7 - - + -
287A ARG* 2.9 29.2 + - - -
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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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158A GLN* 2.9 37.3 + - + +
159A MET* 4.2 7.7 + - - +
160A LYS 3.8 0.6 - - - -
161A THR* 1.3 77.3 - - - +
163A ASP* 1.3 70.2 + - - +
164A THR* 3.0 41.3 + - + +
166A PHE* 4.7 9.0 - + - -
250A MET* 4.6 11.4 - - + -
287A ARG* 3.6 55.4 - - + +
290A THR* 3.4 28.7 - - + -
291A VAL* 4.5 9.0 - - + -
337A GLU* 6.1 2.2 - - - -
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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
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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