Contacts of the helix formed by residues 68 - 78 (chain D) in PDB entry 4OA5
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 GLY 68 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65D THR* 3.1 26.4 + - - +
66D CYS 3.4 1.2 + - - -
67D VAL* 1.3 78.7 - - - +
69D PHE* 1.3 58.7 - - - +
70D SER 3.5 2.0 - - - -
71D ALA* 3.3 7.2 + - - +
72D ILE* 2.9 43.5 + - - +
97D ALA* 4.4 5.4 - - - -
101D ILE* 5.3 4.0 - - - -
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Residues in contact with PHE 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D VAL* 4.9 1.1 - - + -
24D ALA* 3.3 35.7 - - + -
25D LEU* 5.0 0.2 - - - -
27D ALA* 4.6 7.1 - - - +
28D HIS* 3.6 26.9 - + + +
39D GLN* 3.6 15.0 + - - +
40D LEU* 3.2 34.3 - - + -
41D GLY 3.6 16.4 - - - -
42D THR* 4.1 20.4 - - + -
45D GLY* 4.9 0.7 - - - -
67D VAL 3.5 3.4 + - - -
68D GLY* 1.3 77.5 - - - +
70D SER* 1.3 69.8 + - - +
72D ILE* 3.3 3.0 + - - +
73D CYS* 3.1 50.1 + - - -
301D SAH 3.4 15.6 + - - +
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Residues in contact with SER 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D LEU* 4.1 12.3 - - - -
48D LEU* 4.7 2.2 - - - +
62D GLU* 2.5 29.0 + - - -
65D THR 4.6 0.7 + - - -
69D PHE* 1.3 84.6 - - - +
71D ALA* 1.3 58.0 + - - +
73D CYS* 3.3 6.3 + - - +
74D MET* 2.9 32.9 + - - +
134D PHE* 4.0 13.0 - - - -
301D SAH 2.7 37.1 + - - -
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Residues in contact with ALA 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D GLU* 3.5 19.9 + - - +
68D GLY* 3.3 14.2 + - - +
69D PHE 3.2 1.0 - - - -
70D SER* 1.3 79.1 + - - +
72D ILE* 1.3 59.9 + - - +
74D MET* 3.4 8.4 + - - -
75D ALA* 2.9 26.9 + - - +
84D ILE* 3.3 15.8 - - + +
86D THR* 4.4 6.7 - - + -
101D ILE* 5.6 0.2 - - + -
110D ILE* 3.8 27.6 - - + -
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Residues in contact with ILE 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D ALA* 4.0 20.2 - - + -
27D ALA* 3.8 26.2 - - + -
68D GLY 2.9 22.9 + - - +
69D PHE* 3.7 3.8 - - - +
71D ALA* 1.3 73.0 - - - +
73D CYS* 1.3 65.2 + - - +
75D ALA* 3.3 2.3 + - - +
76D HIS* 3.2 44.6 + - - +
100D ASN* 4.1 15.9 - - + +
101D ILE* 4.4 7.6 - - + +
104D CYS* 3.9 20.9 - - + -
106D LEU* 3.9 16.8 - - + +
110D ILE* 4.1 12.8 - - + -
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Residues in contact with CYS 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D VAL* 3.8 22.2 - - - -
24D ALA* 4.3 2.9 - - - -
45D GLY* 4.1 21.8 - - - +
48D LEU* 6.0 1.1 - - + -
49D GLN* 2.9 33.5 + - - +
69D PHE* 3.1 55.4 + - - -
70D SER* 3.6 8.1 - - - +
72D ILE* 1.3 76.5 - - - +
74D MET* 1.3 64.9 + - + +
75D ALA 3.4 0.2 + - - -
76D HIS* 3.4 8.4 + - - -
77D ALA 3.7 0.5 + - - -
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Residues in contact with MET 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D LEU* 3.9 27.8 - - + -
49D GLN* 4.8 1.8 - - - -
52D ILE* 3.5 29.1 - - + +
60D ILE* 4.1 26.2 - - + -
62D GLU* 3.3 35.7 - - + +
70D SER 2.9 20.1 + - - +
71D ALA* 4.1 5.2 - - - -
73D CYS* 1.3 77.2 - - + +
75D ALA* 1.3 58.3 + - - +
77D ALA* 3.0 21.7 + - - +
78D LEU* 3.3 13.4 + - - +
84D ILE* 3.7 14.6 - - + -
132D MET* 4.1 12.1 - - - -
134D PHE* 4.0 9.4 - - + -
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Residues in contact with ALA 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71D ALA 2.9 17.5 + - - +
72D ILE 3.3 4.9 + - - +
74D MET* 1.3 76.4 - - - +
76D HIS* 1.3 57.8 + - - +
78D LEU* 3.1 29.5 + - + +
84D ILE* 3.5 14.8 - - + +
106D LEU* 4.1 18.2 - - + +
109D LYS* 4.6 10.8 - - + +
110D ILE* 3.8 20.4 - - + -
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Residues in contact with HIS 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D VAL* 5.9 0.7 - - + -
21D THR* 3.8 31.1 + - + -
24D ALA* 5.1 0.7 - - + -
49D GLN* 3.9 10.5 - - - +
53D ARG* 5.7 1.0 + - - -
72D ILE* 3.2 31.9 + - + +
73D CYS* 3.7 11.4 - - - +
74D MET 3.3 0.2 - - - -
75D ALA* 1.3 74.9 - - - +
77D ALA* 1.3 58.0 + - - +
78D LEU 3.4 3.6 - - - +
104D CYS* 5.2 2.7 - - + -
106D LEU* 3.8 28.6 - - + +
308D IOD 3.7 13.6 - - + +
309D IOD 4.1 22.6 - - + +
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Residues in contact with ALA 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D GLN* 3.7 46.2 - - + +
52D ILE* 3.8 13.8 - - + +
53D ARG* 3.4 28.3 + - + +
73D CYS 3.7 1.4 + - - -
74D MET 3.0 9.8 + - - +
76D HIS* 1.3 78.0 - - - +
78D LEU* 1.3 64.4 + - - +
79D PRO* 3.8 2.4 - - - +
308D IOD 4.0 8.7 - - + +
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Residues in contact with LEU 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D ILE* 3.8 14.8 - - + -
53D ARG* 5.5 2.5 + - - -
57D ILE 3.4 22.9 - - - +
58D HIS 3.6 13.2 - - - +
60D ILE* 3.9 13.2 - - + -
74D MET 3.6 10.1 - - - +
75D ALA* 3.1 19.8 + - + +
76D HIS 4.4 3.5 - - - +
77D ALA* 1.3 78.9 - - - +
79D PRO* 1.3 76.3 - - + +
82D GLY* 4.0 3.4 - - - +
83D HIS* 3.7 22.4 - - - +
84D ILE* 3.6 34.1 - - + -
109D LYS* 5.0 3.8 - - + +
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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