Contacts of the helix formed by residues 63 - 73 (chain D) in PDB entry 5AIS
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 GLN 63 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90C ALA* 3.4 21.1 - - - +
93C ASP* 3.5 19.3 - - + +
94C THR* 3.2 24.4 + - - +
97C ASP* 3.0 22.2 + - - -
52D PRO 4.0 6.3 + - - -
62D HIS* 1.3 98.2 + - - +
64D SER* 1.3 65.9 + - - +
65D LEU* 3.3 2.2 + - - +
66D ALA* 3.3 15.8 + - + +
67D ILE* 3.0 19.7 + - - +
1202D GSH 2.8 36.8 + - - +
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Residues in contact with SER 64 (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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14D ARG* 3.2 31.2 + - - +
17D ILE* 4.4 4.2 - - - +
18D ILE* 4.0 16.7 - - - +
52D PRO* 3.9 11.5 - - - +
63D GLN* 1.3 71.2 - - - +
65D LEU* 1.3 68.9 + - - +
67D ILE* 3.5 3.0 + - - +
68D ALA* 2.9 28.4 + - - +
96D ASP* 5.1 1.9 + - - -
152D TYR* 5.2 1.6 + - - -
1202D GSH 2.8 32.7 + - - -
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Residues in contact with LEU 65 (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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93C ASP* 4.3 14.1 + - - +
17D ILE* 4.6 4.9 - - + -
63D GLN* 3.3 1.8 + - - +
64D SER* 1.3 85.6 - - - +
66D ALA* 1.3 61.4 + - - +
68D ALA* 3.8 3.6 - - - +
69D ARG* 2.9 41.8 + - - +
92D VAL* 3.6 32.5 - - + -
93D ASP* 3.8 13.7 - - - +
96D ASP* 3.5 34.1 - - + +
148D TRP* 3.9 15.4 - - + -
152D TYR* 3.9 22.7 - - + +
1202D GSH 4.9 2.0 + - - +
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Residues in contact with ALA 66 (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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86C CYS* 3.8 14.9 - - - +
89C ASP* 3.7 11.6 - - + +
90C ALA* 3.7 27.8 - - - +
93C ASP* 4.6 3.5 + - - +
62D HIS 4.1 3.6 - - - +
63D GLN* 3.3 19.9 + - + +
65D LEU* 1.3 79.6 - - - +
67D ILE* 1.3 62.2 + - - +
69D ARG* 3.4 15.0 + - - +
70D TYR* 3.1 22.3 + - - +
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Residues in contact with ILE 67 (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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86C CYS* 4.3 8.3 - - - -
18D ILE* 3.9 20.4 - - + -
52D PRO 4.5 5.2 - - - +
53D ILE 4.7 0.2 - - - -
54D LEU* 3.5 46.4 - - + +
61D LEU* 4.0 18.4 - - + +
62D HIS* 3.7 26.5 - - - +
63D GLN 3.0 24.4 + - - +
64D SER* 3.6 4.3 - - - +
66D ALA* 1.3 73.0 - - - +
68D ALA* 1.3 65.7 + - - +
70D TYR* 3.1 5.0 + - + +
71D LEU* 2.9 34.5 + - + +
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Residues in contact with ALA 68 (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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17D ILE* 4.3 9.4 - - + -
18D ILE* 4.7 2.4 - - + +
21D ILE* 3.6 22.9 - - + +
64D SER 2.9 20.0 + - - +
65D LEU* 3.8 2.5 - - - +
67D ILE* 1.3 77.5 - - - +
69D ARG* 1.3 60.2 + - - +
71D LEU* 3.5 2.9 + - - -
72D THR* 2.9 33.3 + - - +
148D TRP* 3.6 28.5 - - + -
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Residues in contact with ARG 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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69C ARG* 3.5 36.3 - - - +
89C ASP* 3.1 38.5 + - - +
93C ASP* 5.4 3.8 + - - -
65D LEU* 2.9 38.1 + - - +
66D ALA* 3.7 6.4 - - - +
68D ALA* 1.3 76.7 - - - +
70D TYR* 1.3 64.0 + - - +
72D THR* 3.1 8.3 + - - +
73D LYS* 3.1 46.5 + - + +
89D ASP* 3.0 35.1 + - - +
92D VAL* 5.7 0.6 - - - +
93D ASP* 4.6 10.9 + - - -
148D TRP* 4.1 18.9 - - + +
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Residues in contact with TYR 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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82C GLU* 3.6 42.2 - - + -
83C MET* 3.2 33.0 - - + +
86C CYS* 3.9 20.6 - - + -
4D TYR* 4.9 12.3 + + - -
54D LEU* 5.9 0.2 - - + -
56D VAL* 5.4 4.5 - - + +
61D LEU* 4.7 13.7 - - + -
66D ALA 3.1 14.3 + - - +
67D ILE* 3.1 8.9 + - + +
69D ARG* 1.3 78.6 - - - +
71D LEU* 1.3 81.4 + - + +
72D THR 3.4 0.2 + - - -
73D LYS* 3.5 25.3 + - + +
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Residues in contact with LEU 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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4D TYR* 3.9 27.4 - - + +
18D ILE* 3.9 10.8 - - + -
21D ILE* 4.0 19.1 - - + -
22D PHE* 3.8 39.5 - - + -
25D LEU* 3.7 17.5 - - + +
27D ILE* 5.3 4.7 - - + -
54D LEU* 4.1 1.8 - - + -
67D ILE* 2.9 39.8 + - + +
68D ALA* 3.9 6.7 - - - +
70D TYR* 1.3 89.1 - - + +
72D THR* 1.3 60.8 + - - +
73D LYS 3.8 1.6 + - - +
75D THR* 3.8 6.4 - - - +
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Residues in contact with THR 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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21D ILE* 3.7 31.4 - - + -
25D LEU* 5.1 0.2 - - - -
68D ALA 2.9 20.9 + - - +
69D ARG* 3.1 9.4 + - - +
71D LEU* 1.3 75.7 - - - +
73D LYS* 1.3 66.2 + - - +
74D ASN 3.4 0.5 + - - -
75D THR* 2.6 30.1 + - - -
77D LEU* 4.0 15.3 - - + -
78D ALA* 3.4 13.1 - - - +
148D TRP* 3.5 35.0 + - + -
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Residues in contact with LYS 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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69C ARG* 6.0 1.9 - - - +
73C LYS* 6.1 4.9 - - - +
82C GLU* 4.4 20.0 + - + +
85C GLN* 2.9 47.0 + - - +
86C CYS* 4.9 0.8 - - - +
89C ASP* 4.8 5.6 + - - -
69D ARG* 3.1 46.2 + - + +
70D TYR* 3.7 16.8 - - + +
71D LEU 3.5 3.1 - - - +
72D THR* 1.3 78.7 - - - +
74D ASN* 1.3 77.2 + - - +
75D THR* 3.4 5.9 + - - +
78D ALA* 4.6 4.9 - - - -
85D GLN* 5.6 9.2 - - - +
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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