Contacts of the helix formed by residues 67 - 80 (chain A) in PDB entry 1X3O
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 67 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A GLU* 3.8 13.2 - - - +
29A ALA 3.2 8.5 - - - -
30A ARG* 3.7 25.4 - - + -
31A PHE* 3.3 13.9 - - - -
65A ILE* 3.8 0.3 - - - +
66A ARG* 1.3 85.2 - - + +
68A VAL* 1.3 64.9 + - - +
69A LYS* 3.5 9.6 + - - +
70A ASP* 2.9 33.8 + - - +
71A ALA 3.1 16.3 + - - -
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Residues in contact with VAL 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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7A PHE* 3.8 28.5 - - + -
10A VAL* 4.2 15.5 - - + -
11A LYS 5.6 0.2 - - - +
14A ILE* 3.7 21.1 - - + -
25A VAL* 3.8 12.6 - - + -
26A THR 3.3 27.4 - - - +
27A LEU* 3.4 3.6 + - - +
29A ALA* 3.0 21.3 + - + +
31A PHE* 4.0 9.6 - - + -
35A LEU* 4.6 2.2 - - + -
67A THR* 1.3 74.0 - - - +
69A LYS* 1.3 57.4 + - - +
71A ALA* 3.0 6.2 + - - +
72A VAL* 2.9 27.3 + - + +
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Residues in contact with LYS 69 (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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3A GLU* 6.2 0.2 - - - +
27A LEU* 2.8 41.3 + - + +
28A GLU* 3.9 26.6 + - - +
67A THR* 3.1 7.6 + - - +
68A VAL* 1.3 77.0 - - - +
70A ASP* 1.3 59.2 + - - +
72A VAL* 3.2 2.2 + - + +
73A GLU* 2.8 68.0 + - + +
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Residues in contact with ASP 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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64A LYS 3.8 7.7 - - - +
65A ILE* 3.8 19.7 - - + +
66A ARG* 3.0 25.7 + - - +
67A THR* 2.9 35.0 + - - +
69A LYS* 1.3 75.7 - - - +
71A ALA* 1.3 57.9 + - - +
73A GLU* 3.6 13.6 + - - +
74A TYR* 3.0 30.1 + - - +
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Residues in contact with ALA 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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10A VAL* 4.3 14.4 - - + -
31A PHE* 4.3 9.2 - - + -
49A LEU* 4.3 19.3 - - + -
65A ILE* 3.5 21.9 - - + +
67A THR 3.1 4.7 + - - +
68A VAL 3.0 10.0 + - - +
70A ASP* 1.3 77.3 - - - +
72A VAL* 1.3 66.0 + - - +
74A TYR* 3.3 3.9 + - - +
75A ILE* 3.0 31.7 + - + +
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Residues in contact with VAL 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A GLU* 3.6 44.6 - - + +
6A ILE* 4.1 12.5 - - + +
7A PHE* 3.8 37.7 - - + +
10A VAL* 4.2 11.9 - - + -
27A LEU* 4.7 6.7 - - + -
68A VAL* 2.9 23.3 + - + +
69A LYS* 3.7 6.5 - - + +
71A ALA* 1.3 76.4 - - - +
73A GLU* 1.3 57.8 + - + +
75A ILE* 3.8 1.2 - - - +
76A LYS* 2.9 28.5 + - + +
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Residues in contact with GLU 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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3A GLU* 4.7 11.7 - - - +
69A LYS* 2.8 61.5 + - + +
70A ASP* 4.0 13.4 - - - +
72A VAL* 1.3 70.5 - - + +
74A TYR* 1.3 66.1 + - - +
76A LYS* 3.4 15.1 + - - +
77A ALA* 3.0 24.8 + - - +
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Residues in contact with TYR 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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55A LEU* 4.4 8.1 - - + -
56A GLU 3.6 13.7 + - - -
57A ILE* 3.6 27.1 - - + -
61A GLU* 2.9 48.4 + - + -
65A ILE* 4.1 22.4 - - + -
70A ASP 3.0 19.7 + - - +
71A ALA 3.6 3.6 - - - +
73A GLU* 1.3 74.3 - - - +
75A ILE* 1.3 76.8 + - + +
77A ALA* 3.2 7.3 + - + +
78A LYS* 3.1 55.3 + - + +
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Residues in contact with ILE 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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6A ILE* 3.7 15.0 - - + -
10A VAL* 3.6 16.6 - - + -
49A LEU* 4.2 16.4 - - + -
53A PHE* 3.5 40.6 - - + -
55A LEU* 4.3 12.3 - - + -
57A ILE* 5.8 1.1 - - + -
71A ALA* 3.0 20.0 + - - +
72A VAL 3.8 2.7 - - - +
74A TYR* 1.3 89.4 - - + +
76A LYS* 1.3 61.8 + - - +
78A LYS* 3.3 3.8 + - - +
79A LEU* 2.9 49.1 + - + +
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Residues in contact with LYS 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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1A MET 5.4 2.7 - - - +
3A GLU* 3.1 57.2 + - + +
6A ILE* 3.5 19.0 - - + +
72A VAL* 2.9 18.1 + - + +
73A GLU* 3.9 14.0 + - - +
75A ILE* 1.3 76.2 - - - +
77A ALA* 1.3 62.9 + - - +
79A LEU* 4.9 0.9 - - - -
80A GLY* 3.0 31.3 + - - +
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Residues in contact with ALA 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 GLU 3.0 18.1 + - - +
74A TYR* 3.5 6.5 - - + +
76A LYS* 1.3 80.2 - - - +
78A LYS* 1.3 64.7 + - + +
80A GLY* 3.6 7.8 + - - -
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Residues in contact with LYS 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A LEU* 4.6 20.2 - - + -
56A GLU 4.3 12.2 + - - +
61A GLU* 5.2 4.8 + - - +
74A TYR* 3.1 60.6 + - + +
75A ILE 3.3 3.6 + - - +
77A ALA* 1.3 79.2 - - + +
79A LEU* 1.3 64.2 + - + +
80A GLY* 3.4 0.5 + - - -
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Residues in contact with LEU 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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1A MET* 4.2 24.2 - - + +
6A ILE* 4.5 8.3 - - + -
53A PHE* 4.1 28.5 - - + +
55A LEU* 4.7 13.5 - - + -
75A ILE* 2.9 40.8 + - + +
76A LYS* 4.4 2.2 - - - +
78A LYS* 1.3 79.1 - - + +
80A GLY* 1.3 63.4 + - - +
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Residues in contact with GLY 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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1A MET 4.3 19.1 + - - +
6A ILE* 6.0 0.5 - - - +
76A LYS* 3.0 25.8 + - - +
77A ALA 4.1 6.1 - - - -
78A LYS 3.3 3.7 - - - -
79A LEU* 1.3 83.6 - - - +
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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