Contacts of the helix formed by residues 144 - 163 (chain A) in PDB entry 4E96
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 ASP 144 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A ASN* 3.5 9.0 - - - +
141A LYS* 2.8 50.6 + - - +
142A PRO 3.2 0.5 - - - +
143A GLY* 1.3 80.6 - - - +
145A ASP* 1.3 65.9 + - - +
146A ILE* 4.1 11.4 - - + +
147A VAL* 3.0 20.5 + - + +
148A LEU* 3.1 13.2 + - - +
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Residues in contact with ASP 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 GLY 3.7 2.3 + - - +
144A ASP* 1.3 72.7 - - - +
146A ILE* 1.3 58.1 + - - +
148A LEU* 3.3 20.3 + - - +
149A MET* 2.9 34.1 + - + +
201A 0NS 4.1 19.5 - - + -
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Residues in contact with ILE 146 (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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82A PRO* 3.6 25.6 - - + -
83A PHE* 3.6 23.1 - - + -
136A CYS* 3.9 8.1 - - - -
140A ASN* 3.4 35.2 - - + +
144A ASP* 4.1 7.6 - - + +
145A ASP* 1.3 78.6 - - - +
147A VAL* 1.3 61.9 + - - +
149A MET* 3.1 7.1 + - - +
150A ALA* 2.9 27.0 + - - +
201A 0NS 3.6 61.4 - - + +
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Residues in contact with VAL 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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136A CYS* 4.1 16.8 - - - +
137A TYR* 4.0 14.1 - - + -
140A ASN* 3.5 26.0 - - + +
141A LYS 3.1 27.8 - - - +
142A PRO* 4.3 13.5 - - + -
143A GLY 4.5 2.7 - - - +
144A ASP* 3.0 10.1 + - + +
146A ILE* 1.3 76.8 - - + +
148A LEU* 1.3 56.2 + - + +
150A ALA* 3.4 2.0 + - - +
151A GLU* 2.9 50.6 + - - +
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Residues in contact with LEU 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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79A PHE* 4.4 6.1 - - + -
143A GLY* 4.4 22.7 - - - +
144A ASP 3.1 17.9 + - - +
145A ASP* 3.7 22.9 - - - +
146A ILE 3.3 0.4 - - - -
147A VAL* 1.3 73.1 - - - +
149A MET* 1.3 65.0 + - + +
151A GLU* 3.9 18.4 - - + +
152A ALA* 3.2 23.2 + - - +
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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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79A PHE* 3.5 53.2 - - + -
81A TRP* 3.3 39.9 - - + +
82A PRO* 4.0 8.5 - - + -
83A PHE* 4.0 12.3 - - + -
145A ASP* 2.9 17.2 + - - +
146A ILE* 3.2 9.9 - - - +
148A LEU* 1.3 73.9 - - - +
150A ALA* 1.3 66.0 + - - +
152A ALA* 3.2 5.4 + - - +
153A LEU* 3.1 23.0 + - - +
201A 0NS 3.7 26.7 - - - -
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Residues in contact with ALA 150 (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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83A PHE* 3.8 15.3 - - + -
133A PHE* 3.7 12.6 - - + -
136A CYS* 3.6 28.3 - - + -
137A TYR* 3.4 26.7 - - + +
146A ILE 2.9 10.1 + - - +
147A VAL 3.7 2.0 - - - +
149A MET* 1.3 71.3 - - - +
151A GLU* 1.3 53.6 + - - +
153A LEU* 3.0 5.8 + - - +
154A GLU* 2.7 35.3 + - - +
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Residues in contact with GLU 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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137A TYR* 3.2 26.7 + - + +
147A VAL* 2.9 34.1 + - - +
148A LEU* 3.9 19.0 - - - +
149A MET 3.3 0.2 - - - -
150A ALA* 1.3 75.0 - - - +
152A ALA* 1.3 56.6 + - - +
154A GLU* 3.5 5.9 + - - +
155A LYS* 3.1 33.6 + - + +
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Residues in contact with ALA 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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77A HIS* 4.4 12.5 + - + +
79A PHE* 3.8 21.5 - - + -
148A LEU 3.2 16.5 + - - +
149A MET 3.2 5.3 + - - +
150A ALA 3.2 0.8 - - - -
151A GLU* 1.3 74.6 - - - +
153A LEU* 1.3 63.9 + - - +
155A LYS* 3.7 6.5 + - - +
156A LEU* 3.2 22.0 + - - +
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Residues in contact with LEU 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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74A LEU* 3.6 44.0 - - + +
77A HIS* 3.7 26.9 - - + +
79A PHE 3.6 23.6 - - - +
80A ALA* 4.1 4.7 - - + -
83A PHE* 3.6 28.5 - - + -
107A MET* 4.8 4.7 - - + -
132A MET* 5.5 0.9 - - + -
133A PHE* 3.9 15.3 - - + -
149A MET 3.1 11.7 + - - +
150A ALA* 3.0 7.9 + - - +
152A ALA* 1.3 75.4 - - - +
154A GLU* 1.3 54.2 + - - +
156A LEU* 3.3 4.6 + - - +
157A PHE* 2.7 36.6 + - - +
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Residues in contact with GLU 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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130A ASN* 5.7 0.9 - - - +
133A PHE* 3.7 30.6 - - + +
137A TYR* 2.8 35.0 + - - +
150A ALA 2.7 20.0 + - - +
151A GLU* 3.9 7.9 - - - +
152A ALA 3.3 0.2 - - - -
153A LEU* 1.3 70.4 - - - +
155A LYS* 1.3 64.5 + - - +
157A PHE* 3.6 2.9 - - + +
158A LEU* 3.0 53.4 + - + +
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Residues in contact with LYS 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 GLU* 3.1 22.2 + - + +
152A ALA* 3.8 7.9 - - - +
154A GLU* 1.3 76.4 - - + +
156A LEU* 1.3 62.7 + - - +
158A LEU* 3.5 10.8 + - + +
159A GLN* 3.2 23.4 + - - +
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Residues in contact with LEU 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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73A THR* 3.8 25.1 - - + +
74A LEU* 3.7 20.2 - - + -
77A HIS* 3.8 29.6 - - + +
152A ALA 3.2 15.2 + - - +
153A LEU* 3.5 5.4 - - + +
155A LYS* 1.3 77.8 - - - +
157A PHE* 1.3 64.7 + - - +
159A GLN* 3.3 33.8 + - - +
160A LYS* 3.0 26.5 + - + +
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Residues in contact with PHE 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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66A LEU* 4.7 0.4 - - + -
70A VAL* 3.3 31.2 - - + -
74A LEU* 3.8 22.4 - - + +
126A ILE* 4.3 16.2 - - + -
129A PHE* 3.5 35.9 - + + -
130A ASN* 4.0 19.5 - - - -
133A PHE* 4.0 14.1 - + + -
153A LEU 2.7 21.5 + - - +
154A GLU* 3.6 10.1 - - + +
156A LEU* 1.3 73.7 - - - +
158A LEU* 1.3 64.7 + - + +
160A LYS* 3.0 6.4 + - - +
161A ILE* 2.8 57.7 + - + +
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Residues in contact with LEU 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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130A ASN* 5.9 2.7 - - - +
154A GLU* 3.0 52.3 + - + +
155A LYS* 3.9 9.9 - - + +
157A PHE* 1.3 84.6 - - + +
159A GLN* 1.3 60.7 + - - +
161A ILE* 3.9 10.6 - - + +
162A ASN* 3.1 25.5 + - - +
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Residues in contact with GLN 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 LYS 3.2 13.7 + - - +
156A LEU* 3.5 31.7 - - - +
158A LEU* 1.3 76.6 - - - +
160A LYS* 1.3 75.3 + - + +
162A ASN* 3.4 14.0 + - - +
163A GLU* 3.6 17.5 - - + +
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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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65A TYR* 2.4 33.0 + - - +
69A VAL* 3.9 21.4 - - + +
70A VAL* 4.3 18.6 - - + -
73A THR* 3.9 38.8 + - + +
74A LEU* 5.5 1.3 - - + -
156A LEU* 3.0 24.3 + - + +
157A PHE* 3.7 4.3 - - - +
159A GLN* 1.3 95.0 - - + +
161A ILE* 1.3 63.5 + - - +
163A GLU* 3.4 6.2 + - + -
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Residues in contact with ILE 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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66A LEU* 3.7 16.4 - - + -
70A VAL* 3.3 37.5 - - + -
126A ILE* 4.1 20.4 - - + -
157A PHE* 2.8 37.3 + - + +
158A LEU* 4.1 12.8 - - + +
159A GLN 3.3 0.4 - - - -
160A LYS* 1.3 72.9 - - - +
162A ASN* 1.3 63.3 + - - +
163A GLU 3.1 2.0 - - - -
164A LEU* 3.0 40.0 - - + +
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Residues in contact with ASN 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 LEU 3.1 16.7 + - - +
159A GLN* 3.7 9.0 - - - +
160A LYS 3.3 0.6 - - - -
161A ILE* 1.3 79.4 - - - +
163A GLU* 1.3 71.2 + - - +
164A LEU* 3.1 6.6 + - - +
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Residues in contact with GLU 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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65A TYR* 3.4 26.3 + - + +
159A GLN* 3.6 14.5 - - + +
160A LYS* 3.4 3.5 + - + +
161A ILE 3.1 0.8 - - - -
162A ASN* 1.3 95.4 + - - +
164A LEU* 1.3 63.1 + - - +
165A PRO* 3.3 7.1 - - - +
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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