Contacts of the helix formed by residues 73 - 87 (chain D) in PDB entry 3OX4
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 THR 73 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71D ASN 3.7 11.0 - - - +
72D PRO* 1.3 76.9 - - + +
74D VAL* 1.3 64.8 + - - +
75D THR* 2.8 21.0 + - - -
76D ALA* 3.1 25.3 + - - +
77D VAL* 3.2 16.1 + - - +
152D ILE* 3.7 3.8 - - - -
153D THR* 3.6 16.4 - - + +
154D ASP 5.7 1.1 - - - +
155D GLU* 3.2 13.9 - - - +
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Residues in contact with VAL 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73D THR* 1.3 72.9 - - - +
75D THR* 1.3 61.4 + - - +
77D VAL* 3.2 6.3 + - - +
78D LEU* 3.0 38.7 + - + +
117D VAL* 4.4 15.9 - - + +
118D LYS* 4.7 12.8 - - - +
152D ILE* 3.8 9.6 - - + -
153D THR 3.2 16.5 + - - +
154D ASP* 4.3 2.7 - - - -
155D GLU* 2.7 27.3 + - + +
161D MET* 3.5 27.8 - - + -
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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
----------------------------------------------------------
73D THR* 2.8 17.8 + - - +
74D VAL* 1.3 74.7 - - - +
76D ALA* 1.3 58.0 + - - +
78D LEU* 3.1 18.1 + - + +
79D GLU* 2.8 44.0 + - - +
155D GLU* 3.0 34.9 + - + +
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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
----------------------------------------------------------
65D TYR* 3.2 28.1 + - + +
68D VAL* 5.4 7.6 - - + -
69D MET* 6.2 2.0 - - + +
72D PRO* 4.9 2.5 - - + -
73D THR* 3.1 30.9 + - - +
75D THR* 1.3 77.3 + - - +
77D VAL* 1.3 63.0 + - - +
79D GLU* 3.3 4.3 + - - +
80D GLY* 3.0 19.1 + - - -
103D CYS* 4.0 15.7 - - - -
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Residues in contact with VAL 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73D THR 3.2 13.6 + - - +
74D VAL 3.4 7.4 - - - +
76D ALA* 1.3 76.5 - - - +
78D LEU* 1.3 59.3 + - + +
80D GLY 3.4 0.7 + - - -
81D LEU* 2.8 41.8 + - + +
103D CYS* 4.0 9.6 - - - +
106D ALA* 3.6 33.2 - - + +
107D ILE* 3.8 23.6 - - + +
110D VAL* 4.9 0.9 - - + -
117D VAL* 3.8 25.4 - - + -
152D ILE* 4.0 15.7 - - + -
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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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74D VAL* 3.0 35.0 + - + +
75D THR* 3.1 22.9 + - + +
77D VAL* 1.3 78.5 - - + +
79D GLU* 1.3 64.5 + - + +
81D LEU* 3.1 25.9 + - + +
82D LYS* 3.3 17.6 + - - +
117D VAL* 5.9 3.1 - - + -
155D GLU* 6.1 0.2 - - + -
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Residues in contact with GLU 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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65D TYR* 3.6 32.0 + - + +
75D THR* 2.8 34.5 + - - +
76D ALA* 4.2 1.7 + - - -
78D LEU* 1.3 73.2 - - + +
80D GLY* 1.3 59.0 + - - +
82D LYS* 2.9 43.7 - - + +
83D ILE* 3.4 7.2 + - - +
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Residues in contact with GLY 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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35D LEU* 3.6 9.6 - - - +
65D TYR* 3.7 31.7 - - - -
76D ALA 3.0 12.2 + - - -
77D VAL 3.7 2.5 - - - -
79D GLU* 1.3 77.1 - - - +
81D LEU* 1.3 62.3 + - - +
83D ILE* 3.3 6.3 + - - +
84D LEU 3.1 17.7 + - - -
107D ILE* 3.9 11.9 - - - -
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Residues in contact with LEU 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 VAL* 2.8 25.1 + - + +
78D LEU* 3.1 19.0 + - + +
80D GLY* 1.3 77.6 - - - +
82D LYS* 1.3 61.2 + - - +
84D LEU* 3.3 12.2 - - + +
85D LYS* 3.1 20.3 + - - +
107D ILE* 3.6 34.5 - - + +
110D VAL* 3.5 30.3 - - + -
111D ALA* 4.4 15.5 - - + +
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Residues in contact with LYS 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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78D LEU* 3.3 8.3 + - - +
79D GLU* 2.9 50.7 + - - +
81D LEU* 1.3 74.0 - - - +
83D ILE* 1.3 67.9 + - + +
84D LEU 3.0 1.3 - - - -
85D LYS* 3.0 13.7 + - - +
86D ASP* 2.7 49.6 + - - +
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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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35D LEU* 3.6 22.4 - - + -
63D ALA* 3.9 9.0 - - + -
64D VAL 4.6 12.3 - - - +
65D TYR* 4.5 13.2 - - + -
79D GLU 3.6 13.2 - - - +
80D GLY* 3.3 12.3 + - - +
82D LYS* 1.3 87.7 - - + +
84D LEU* 1.3 62.6 + - - +
86D ASP* 4.5 4.5 - - + +
87D ASN* 2.9 46.2 + - - +
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Residues in contact with LEU 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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35D LEU* 3.8 12.8 - - + +
80D GLY 3.1 13.0 + - - +
81D LEU* 3.3 15.7 - - + +
82D LYS 3.0 0.6 - - - -
83D ILE* 1.3 78.1 - - - +
85D LYS* 1.3 68.3 + - + +
87D ASN 3.4 0.5 + - - -
88D ASN* 3.2 3.8 + - - -
89D SER* 3.1 56.8 + - - +
92D VAL* 4.3 6.3 - - + -
107D ILE* 3.8 24.2 - - + -
111D ALA* 4.3 17.5 - - + -
131D LEU* 3.8 24.0 - - + -
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Residues in contact with LYS 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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81D LEU 3.1 9.4 + - - +
82D LYS* 3.0 13.9 + - - +
84D LEU* 1.3 82.7 - - + +
86D ASP* 1.3 82.6 + - - +
87D ASN 3.1 9.3 + - - -
88D ASN* 3.5 9.6 + - - +
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Residues in contact with ASP 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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82D LYS* 2.7 40.3 + - - +
83D ILE* 4.1 7.9 + - + +
85D LYS* 1.3 91.0 + - - +
87D ASN* 1.3 66.2 + - - +
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Residues in contact with ASN 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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33D ASN* 3.8 17.6 + - + +
61D ASN* 5.6 4.5 + - - -
62D SER 5.8 0.2 - - - -
63D ALA* 3.4 28.1 - - + +
83D ILE* 2.9 35.0 + - - +
85D LYS 3.1 0.4 - - - -
86D ASP* 1.3 87.3 - - - +
88D ASN* 1.3 70.9 + - - +
89D SER* 3.1 11.1 + - - +
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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