Contacts of the helix formed by residues 72 - 87 (chain D) in PDB entry 3X0Y
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 72 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61D LEU* 4.5 1.3 - - - -
70D GLY 4.0 0.8 + - - -
71D ALA* 1.3 78.0 - - - +
73D TRP* 1.3 64.3 + - - +
74D PRO* 3.8 15.1 - - + +
75D THR* 2.9 35.2 + - - -
76D ALA* 3.1 18.2 + - - +
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Residues in contact with TRP 73 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61D LEU* 3.5 37.0 - - + +
72D ASP* 1.3 70.0 - - - +
74D PRO* 1.3 70.1 - - + +
76D ALA* 3.8 4.7 - - + +
77D ILE* 2.9 54.6 + - + +
98D LEU* 4.3 8.3 - - + -
99D THR* 5.6 5.6 - - + -
102D PRO* 4.3 22.0 - - + -
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Residues in contact with PRO 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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72D ASP* 3.6 17.7 - - + +
73D TRP* 1.3 95.0 - - + +
75D THR* 1.3 58.0 + - - +
77D ILE* 3.5 9.9 + - + +
78D GLU* 3.0 28.2 + - - +
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Residues in contact with THR 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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19D ASP* 5.5 0.7 - - - +
20D PRO* 3.7 29.8 - - + -
21D VAL* 4.3 11.0 - - + -
60D LEU* 5.4 0.2 - - + -
71D ALA* 4.2 13.0 - - + -
72D ASP* 2.9 27.1 + - - -
74D PRO* 1.3 74.5 - - - +
76D ALA* 1.3 65.3 + - - +
78D GLU* 3.2 12.2 + - - +
79D VAL* 3.1 23.2 + - - +
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Residues in contact with ALA 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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60D LEU* 3.6 24.9 - - + +
61D LEU* 3.5 36.8 - - + -
71D ALA* 4.8 1.0 - - + +
72D ASP 3.1 9.7 + - - +
73D TRP* 3.4 7.4 + - + +
75D THR* 1.3 76.2 - - - +
77D ILE* 1.3 57.9 + - + +
79D VAL* 3.3 5.4 + - - +
80D VAL* 3.1 30.8 + - - +
98D LEU* 4.3 7.4 - - + +
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Residues in contact with ILE 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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73D TRP* 2.9 45.2 + - + +
74D PRO* 3.7 7.9 - - + +
76D ALA* 1.3 73.9 - - - +
78D GLU* 1.3 60.1 + - - +
80D VAL* 3.1 13.5 + - + +
81D ARG* 2.9 43.4 + - + +
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Residues in contact with GLU 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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21D VAL* 3.7 34.8 - - + +
25D ARG* 4.8 4.3 + - - -
74D PRO 3.0 16.2 + - - +
75D THR* 3.2 15.1 + - - +
77D ILE* 1.3 77.1 - - - +
79D VAL* 1.3 57.8 + - - +
81D ARG* 3.4 14.9 + - + +
82D GLU* 3.1 30.0 + - - +
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Residues in contact with VAL 79 (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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20D PRO* 3.7 31.4 - - + +
21D VAL* 3.9 10.3 - - + +
24D ALA* 4.0 18.6 - - + -
57D LEU* 4.4 10.5 - - + -
60D LEU* 3.9 17.9 - - + -
75D THR 3.1 13.2 + - - +
76D ALA 3.5 7.2 - - - +
77D ILE 3.2 0.4 - - - -
78D GLU* 1.3 73.2 - - - +
80D VAL* 1.3 65.4 + - - +
82D GLU* 3.5 2.4 + - - +
83D ILE* 3.2 26.5 + - + +
94D PHE* 3.7 25.1 - - + -
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Residues in contact with VAL 80 (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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76D ALA 3.1 16.7 + - - +
77D ILE* 3.1 13.2 + - + +
79D VAL* 1.3 76.9 - - - +
81D ARG* 1.3 57.9 + - + +
83D ILE* 3.5 2.7 + - - +
84D ALA* 2.9 32.0 + - + +
91D GLY* 4.1 18.2 - - - +
94D PHE* 4.2 10.8 - - + -
95D GLY* 4.2 16.8 - - - -
98D LEU* 3.9 22.2 - - + -
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Residues in contact with ARG 81 (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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77D ILE* 2.9 31.8 + - + +
78D GLU* 3.6 18.6 - - + +
79D VAL 3.3 0.2 - - - -
80D VAL* 1.3 77.9 - - + +
82D GLU* 1.3 63.4 + - - +
84D ALA* 3.2 7.7 + - - +
85D ALA* 3.0 24.8 + - - +
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Residues in contact with GLU 82 (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 VAL* 4.8 6.2 - - + +
24D ALA* 4.3 11.2 - - + +
25D ARG* 3.4 55.2 + - + +
28D ALA* 4.3 7.4 - - + +
32D ARG* 4.7 9.5 + - - -
78D GLU* 3.1 16.7 + - - +
79D VAL* 3.8 4.5 - - - +
80D VAL 3.4 0.2 - - - -
81D ARG* 1.3 79.7 - - - +
83D ILE* 1.3 61.9 + - - +
85D ALA* 3.4 7.5 + - - +
86D ALA* 3.3 18.7 + - - +
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Residues in contact with ILE 83 (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* 3.7 36.6 - - + +
27D LEU* 4.8 4.9 - - + -
28D ALA 4.9 0.9 - - - +
31D TRP* 3.6 37.7 - - + -
52D LEU* 5.4 4.5 - - + -
57D LEU* 5.6 0.4 - - + -
79D VAL* 3.2 23.2 + - + +
80D VAL* 3.8 3.8 - - - +
82D GLU* 1.3 74.6 - - - +
84D ALA* 1.3 55.0 + - - +
86D ALA* 3.0 6.9 + - - +
87D ASP 2.8 31.4 + - - +
90D LEU* 3.6 11.7 - - + +
91D GLY* 3.6 23.1 - - - +
94D PHE* 4.9 12.3 - - + -
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Residues in contact with ALA 84 (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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80D VAL* 2.9 22.8 + - + +
81D ARG* 3.5 7.0 - - - +
83D ILE* 1.3 76.3 - - - +
85D ALA* 1.3 61.6 + - - +
87D ASP 3.4 9.4 + - - -
88D GLY* 3.4 24.7 + - - +
91D GLY* 3.8 13.0 - - - -
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Residues in contact with ALA 85 (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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32D ARG* 3.6 21.0 + - - +
81D ARG 3.0 13.4 + - - +
82D GLU* 3.6 13.7 - - - +
83D ILE 3.2 0.2 - - - -
84D ALA* 1.3 77.4 - - - +
86D ALA* 1.3 60.9 + - - +
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Residues in contact with ALA 86 (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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28D ALA* 3.7 40.8 - - + +
31D TRP* 4.6 9.3 - - + +
32D ARG* 3.7 22.3 - - + +
35D ALA* 4.1 18.7 - - - +
82D GLU 3.3 3.0 + - - +
83D ILE 3.0 8.8 + - - +
84D ALA 4.1 0.2 - - - -
85D ALA* 1.3 80.9 - - - +
87D ASP* 1.3 63.5 + - + +
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Residues in contact with ASP 87 (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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31D TRP* 4.9 1.3 - - + -
35D ALA* 4.9 6.3 - - - +
38D ARG* 2.6 39.3 + - - +
39D ASP 5.9 0.2 + - - -
83D ILE 2.8 12.9 + - - +
84D ALA* 3.4 4.5 + - - -
86D ALA* 1.3 79.2 - - + +
88D GLY* 1.3 58.3 + - - +
89D SER* 2.9 22.9 + - - -
90D LEU* 3.0 31.3 + - + +
91D GLY 2.9 25.1 + - - -
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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