Contacts of the helix formed by residues 66 - 83 (chain A) in PDB entry 4ORA
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 66 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A ARG* 3.8 21.1 - - - +
38A LEU 3.0 15.8 + - - -
39A THR* 4.0 18.0 - - - +
40A SER* 4.6 2.5 + - - -
65A VAL* 1.3 71.6 - - - +
67A GLU* 1.3 56.7 + - - +
68A GLU* 4.4 6.6 - - + +
69A ILE* 2.8 49.0 + - + +
70A ALA 3.2 3.6 + - - -
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Residues in contact with GLU 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ARG* 4.2 7.0 - - - +
65A VAL 3.2 5.8 + - - -
66A ASP* 1.3 71.3 - - - +
68A GLU* 1.3 69.6 + - + +
70A ALA* 3.1 11.2 + - - +
71A LEU* 3.0 28.6 + - + +
179A TYR* 3.8 17.0 - - + +
180A SER* 2.7 33.5 + - - -
182A ARG* 3.0 33.9 + - - +
183A VAL* 4.3 7.6 - - + +
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Residues in contact with GLU 68 (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 ASP* 3.2 5.3 - - + +
67A GLU* 1.3 82.5 - - + +
69A ILE* 1.3 60.4 + - + +
71A LEU* 3.8 9.6 + - + +
72A ARG* 3.1 26.2 + - - +
182A ARG* 5.3 8.1 - - - +
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Residues in contact with ILE 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LEU 3.2 28.0 - - - +
39A THR 3.3 24.9 - - - +
40A SER* 3.4 18.4 - - - +
43A VAL* 4.2 13.7 - - + -
44A PHE* 3.8 19.5 - - + -
65A VAL* 3.9 9.4 - - + -
66A ASP* 2.8 27.9 + - + +
68A GLU* 1.3 72.1 - - + +
70A ALA* 1.3 64.8 + - - +
71A LEU 3.3 0.2 - - - -
72A ARG* 3.1 6.3 + - - +
73A ILE* 2.8 43.2 + - + +
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Residues in contact with ALA 70 (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 VAL* 3.8 5.9 - - + +
66A ASP 3.2 2.2 + - - -
67A GLU 3.1 9.9 + - - +
69A ILE* 1.3 78.8 - - - +
71A LEU* 1.3 61.6 + - - +
73A ILE* 3.7 1.0 - - - +
74A ILE* 3.0 30.8 + - - +
136A ILE* 6.1 0.2 - - + -
140A LEU* 4.0 20.9 - - + -
179A TYR* 4.0 25.4 - - + -
183A VAL* 3.9 21.8 - - + -
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Residues in contact with LEU 71 (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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67A GLU* 3.0 24.0 + - + +
68A GLU* 4.0 9.2 - - + +
70A ALA* 1.3 75.1 - - - +
72A ARG* 1.3 58.3 + - - +
74A ILE* 4.6 3.1 - - + -
75A ASN* 2.8 48.2 + - - +
182A ARG* 3.4 49.4 - - + +
183A VAL* 3.5 38.6 - - + +
186A ALA* 3.8 12.3 - - + -
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Residues in contact with ARG 72 (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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40A SER* 3.8 13.9 + - - -
44A PHE* 3.6 44.8 - - + +
48A GLY* 3.6 33.7 + - - -
68A GLU 3.1 17.2 + - - +
69A ILE* 3.1 7.7 + - - +
71A LEU* 1.3 79.0 - - - +
73A ILE* 1.3 61.6 + - - +
75A ASN* 4.2 4.1 - - - +
76A GLU* 3.1 31.2 + - + +
147A ILE* 5.0 0.2 - - - +
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Residues in contact with ILE 73 (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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43A VAL* 4.8 7.6 - - + -
44A PHE* 4.1 17.3 - - + -
50A PRO* 5.3 0.4 - - + -
55A LEU* 4.8 11.0 - - + -
65A VAL* 5.5 1.8 - - + -
69A ILE* 2.8 37.0 + - + +
70A ALA* 3.7 3.4 - - - +
72A ARG* 1.3 75.4 - - - +
74A ILE* 1.3 65.6 + - - +
76A GLU 3.3 1.4 + - - -
77A GLY* 3.0 20.8 + - - -
140A LEU* 3.8 40.6 - - + +
143A TRP* 3.8 15.4 - - + -
144A VAL* 3.9 26.0 - - + +
147A ILE* 3.8 13.1 - - + +
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Residues in contact with ILE 74 (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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70A ALA* 3.0 20.1 + - + +
71A LEU 4.0 2.7 - - - +
73A ILE* 1.3 76.7 - - + +
75A ASN* 1.3 56.4 + - - +
78A ALA* 2.9 25.8 + - - +
136A ILE* 4.5 3.6 - - + -
139A VAL* 4.4 10.5 - - + -
140A LEU* 4.2 17.5 - - + -
143A TRP* 3.5 12.6 + - + +
183A VAL* 3.6 24.5 - - + +
186A ALA* 3.4 37.0 - - + +
187A CYS* 3.5 27.8 - - - +
190A ALA* 3.8 10.3 - - + -
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Residues in contact with ASN 75 (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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71A LEU* 2.8 39.0 + - - +
72A ARG* 4.4 3.5 - - - +
74A ILE* 1.3 70.4 - - - +
76A GLU* 1.3 62.0 + - - +
78A ALA* 3.3 7.3 + - - +
79A ALA* 2.8 28.8 + - - +
82A ARG* 5.3 0.2 + - - -
186A ALA* 3.6 24.9 - - - +
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Residues in contact with GLU 76 (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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44A PHE* 5.4 3.6 - - - -
48A GLY 4.8 9.0 - - - +
72A ARG* 3.1 29.0 + - + +
75A ASN* 1.3 73.2 - - - +
77A GLY* 1.3 67.5 + - - +
79A ALA* 3.4 8.1 + - + +
80A ILE* 3.1 32.4 + - + +
147A ILE* 3.8 36.6 - - + +
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Residues in contact with GLY 77 (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 ILE 3.0 10.7 + - - -
76A GLU* 1.3 76.2 - - - +
78A ALA* 1.3 60.5 + - - +
80A ILE* 3.1 8.1 + - - +
81A LEU* 3.0 28.7 + - - +
143A TRP* 3.4 27.6 - - - -
146A LYS* 5.1 4.6 - - - +
147A ILE* 4.1 12.4 - - - +
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Residues in contact with ALA 78 (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 ILE 2.9 18.3 + - - +
75A ASN* 3.3 9.8 + - - +
77A GLY* 1.3 72.4 - - - +
79A ALA* 1.3 65.0 + - - +
81A LEU* 3.2 7.4 + - - +
82A ARG* 2.9 44.6 + - - +
143A TRP* 3.9 1.8 - - - +
186A ALA 5.3 1.1 - - - +
189A GLU* 4.8 0.9 - - + -
190A ALA* 3.6 31.2 - - + +
193A SER* 3.6 3.4 + - - +
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Residues in contact with ALA 79 (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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75A ASN 2.8 20.8 + - - +
76A GLU* 3.4 11.0 - - + +
77A GLY 3.3 0.2 - - - -
78A ALA* 1.3 73.8 - - - +
80A ILE* 1.3 64.4 + - + +
82A ARG* 3.5 24.9 + - - +
83A ARG* 3.7 12.0 + - - +
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Residues in contact with ILE 80 (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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76A GLU* 3.1 28.2 + - + +
77A GLY* 3.1 6.9 + - - +
79A ALA* 1.3 75.4 - - + +
81A LEU* 1.3 65.7 + - - +
83A ARG* 3.2 22.6 - - - +
84A GLU* 3.6 9.6 - - + +
146A LYS* 4.0 28.5 - - + +
147A ILE* 3.9 37.2 - - + +
150A PRO* 4.1 17.7 - - + -
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Residues in contact with LEU 81 (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 GLY 3.0 20.1 + - - +
78A ALA* 3.7 4.7 - - - +
80A ILE* 1.3 75.1 - - - +
82A ARG* 1.3 55.3 + - - +
84A GLU* 2.8 46.2 + - - +
143A TRP* 4.0 20.9 - - + +
146A LYS* 4.1 22.2 - - + +
155A LEU* 4.4 11.9 - - + +
190A ALA 4.0 14.8 - - - +
193A SER* 3.6 15.8 - - - +
194A LEU* 3.6 33.0 - - + -
195A PRO* 4.2 7.2 - - + +
226A ARG* 3.0 11.4 + - - -
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Residues in contact with ARG 82 (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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75A ASN 5.3 0.2 + - - -
78A ALA* 2.9 28.6 + - - +
79A ALA* 3.5 33.3 - - - +
81A LEU* 1.3 77.1 - - - +
83A ARG* 1.3 60.2 + - - +
84A GLU 3.1 2.0 + - - +
189A GLU* 4.2 18.8 + - - +
193A SER* 3.3 27.4 + - - +
226A ARG* 3.6 13.7 + - - +
227A PHE* 3.7 22.5 - - + -
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Residues in contact with ARG 83 (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 ALA 3.7 7.4 + - - +
80A ILE* 3.2 20.1 + - + +
82A ARG* 1.3 77.4 - - - +
84A GLU* 1.3 66.4 + - + +
85A LYS* 4.1 0.7 + - - +
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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