Contacts of the helix formed by residues 149 - 162 (chain N) in PDB entry 5A31
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 LEU 149 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148N GLY* 1.3 80.2 - - - +
150N ARG* 1.3 84.4 + - - +
151N GLU* 3.1 10.0 - - + +
152N GLU* 2.7 35.3 + - - +
153N VAL 3.3 3.6 + - - -
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Residues in contact with ARG 150 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74N TRP* 3.7 35.2 - - - -
76N VAL* 4.9 3.8 - - - +
148N GLY 4.5 4.8 + - - -
149N LEU* 1.3 105.9 + - - +
151N GLU* 1.3 58.8 + - - +
152N GLU* 3.2 0.6 - - - +
153N VAL* 3.4 33.7 - - + +
154N HIS* 2.9 44.9 + - + +
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Residues in contact with GLU 151 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1841A ASN 6.0 2.0 - - - +
149N LEU* 4.4 7.8 - - + +
150N ARG* 1.3 75.9 - - - +
152N GLU* 1.3 64.3 + - + +
154N HIS* 3.2 15.7 + - - +
155N THR* 2.9 39.9 + - + +
158N ARG* 4.3 17.5 + - - -
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Residues in contact with GLU 152 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1821A PHE* 4.2 34.9 - - + +
1822A SER* 5.9 2.1 - - - -
1841A ASN 5.8 4.0 - - - +
77N GLU* 5.4 1.3 - - - -
148N GLY* 3.0 45.7 + - - +
149N LEU 2.7 15.9 + - - +
150N ARG* 5.9 0.2 - - - +
151N GLU* 1.3 78.5 - - + +
153N VAL* 1.3 60.3 + - - -
155N THR* 3.0 23.5 + - + +
156N MET* 3.2 17.7 - - - +
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Residues in contact with VAL 153 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76N VAL* 5.9 2.5 - - + -
77N GLU* 3.0 35.2 - - + +
80N GLN* 3.9 13.6 + - - +
149N LEU 3.3 1.0 + - - -
150N ARG* 3.3 57.1 + - + +
152N GLU* 1.3 74.3 - - - +
154N HIS* 1.3 69.6 + - + +
156N MET* 3.3 13.5 + - - +
157N LEU* 3.3 13.4 + - + +
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Residues in contact with HIS 154 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150N ARG* 2.9 31.7 + - + +
151N GLU* 3.5 16.4 + - - +
153N VAL* 1.3 79.4 - - + +
155N THR* 1.3 58.0 + - + +
157N LEU* 3.1 19.2 - - + +
158N ARG* 3.0 40.3 + - - +
250N LEU 4.9 14.8 + - - -
251N SER 5.4 5.8 - - - +
252N LEU* 5.0 17.3 - - + +
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Residues in contact with THR 155 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1821A PHE* 6.2 0.3 - - - -
1841A ASN 5.0 9.6 - - - +
1842A SER* 6.2 0.2 - - - -
1843A GLU* 3.9 28.0 - - + +
1846A PRO* 4.1 16.0 - - - +
151N GLU* 2.9 30.7 + - + +
152N GLU* 3.0 25.0 + - + +
154N HIS* 1.3 73.1 - - - +
156N MET* 1.3 64.4 + - - +
158N ARG* 3.7 24.0 - - - +
159N GLY* 2.9 22.7 + - - -
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Residues in contact with MET 156 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1846A PRO* 4.4 13.7 - - - +
1849A LYS* 3.0 41.5 - - - +
1850A CYS* 4.9 2.1 - - - -
77N GLU* 3.7 46.2 - - + +
78N VAL* 5.3 1.3 - - + -
81N ASN* 3.3 27.6 - - + +
84N GLN* 3.9 8.5 - - - +
152N GLU 3.2 17.4 + - - +
153N VAL 3.3 6.9 + - - +
155N THR* 1.3 77.7 + - - +
157N LEU* 1.3 59.6 + - - +
159N GLY* 3.5 1.2 + - - -
160N VAL* 3.1 32.7 + - - +
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Residues in contact with LEU 157 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80N GLN* 5.7 1.1 - - - +
84N GLN* 3.3 27.6 - - + +
153N VAL* 3.3 7.9 + - + +
154N HIS* 3.1 24.0 - - + +
156N MET* 1.3 76.5 - - - +
158N ARG* 1.3 75.5 + - + +
160N VAL* 3.4 4.2 + - - +
161N LEU* 3.2 36.0 + - + +
162N PHE* 6.0 2.0 - - + -
250N LEU* 5.1 13.5 - - + +
251N SER* 4.6 23.6 - - - +
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Residues in contact with ARG 158 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1728A SER* 4.6 28.1 + - - +
1843A GLU* 5.5 8.7 - - + +
151N GLU* 4.3 16.7 + - - -
154N HIS* 3.0 24.8 + - - +
155N THR* 3.7 23.2 - - - +
157N LEU* 1.3 85.2 - - + +
159N GLY* 1.3 55.7 + - - +
161N LEU* 3.2 1.0 + - - +
162N PHE* 2.6 48.3 + - + +
251N SER 4.7 12.4 + - - +
252N LEU* 3.6 32.5 - - - +
254N ALA* 5.0 2.2 - - - +
255N ARG* 4.4 38.6 - - + +
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Residues in contact with GLY 159 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1843A GLU* 5.3 3.3 - - - +
1846A PRO* 5.5 0.7 - - - -
1847A VAL* 3.7 34.2 - - - +
1850A CYS* 5.0 4.7 - - - -
155N THR 2.9 16.2 + - - -
156N MET* 3.9 2.2 - - - -
157N LEU 3.3 0.2 - - - -
158N ARG* 1.3 77.4 - - - +
160N VAL* 1.3 62.6 + - - +
162N PHE 4.2 4.0 - - - -
163N PHE* 3.5 17.7 + - - +
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Residues in contact with VAL 160 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1850A CYS* 4.0 22.2 - - + -
1854A ASN* 6.0 0.4 - - - +
81N ASN* 4.2 9.0 - - - +
84N GLN* 3.9 27.1 - - + +
85N ALA* 4.0 22.2 - - + +
88N SER* 3.8 23.3 + - - +
156N MET 3.1 18.9 + - - +
157N LEU 3.4 3.6 + - - +
158N ARG 3.2 0.4 - - - -
159N GLY* 1.3 77.6 - - - +
161N LEU* 1.3 65.5 + - + +
163N PHE 4.9 3.8 - - - +
164N ALA* 5.9 0.3 - - - +
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Residues in contact with LEU 161 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84N GLN* 5.1 3.8 - - + +
87N ILE* 6.1 1.8 - - + -
88N SER* 3.3 31.9 - - - +
91N PHE* 2.4 61.0 - - + -
157N LEU* 3.2 26.4 + - + +
158N ARG* 3.2 2.7 + - - +
160N VAL* 1.3 82.0 - - + +
162N PHE* 1.3 88.6 + - + +
163N PHE 4.1 0.7 - - - -
164N ALA* 3.5 21.8 + - - +
251N SER* 6.1 2.9 - - - -
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Residues in contact with PHE 162 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1847A VAL* 5.5 0.3 - - - +
91N PHE* 3.8 28.7 - + - -
157N LEU* 6.0 2.0 - - + -
158N ARG* 2.6 34.4 + - + +
159N GLY* 3.8 3.0 - - - -
161N LEU* 1.3 94.9 - - + +
163N PHE* 1.3 65.5 + - - +
164N ALA* 3.6 1.6 - - + +
165N ALA* 4.7 16.6 - - + -
169N PHE* 4.1 26.5 - + - -
251N SER* 5.4 11.0 - - - -
252N LEU 6.1 0.2 - - - -
255N ARG* 4.1 36.3 + - + +
256N VAL* 3.7 30.3 - - + -
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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