Contacts of the helix formed by residues 57 - 77 (chain A) in PDB entry 3ABD
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 HIS 57 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ILE* 4.1 22.0 + - + +
55A SER* 3.1 11.5 + - - +
56A CYS* 1.3 76.9 - - - +
58A PRO* 1.4 74.2 - - + +
59A GLU* 3.3 37.0 + - + -
60A LEU* 3.3 10.8 + - + -
61A ASN* 3.0 25.2 + - - +
1890X ILE* 3.6 40.1 - - + +
1893X THR* 4.0 22.1 + - - +
1894X LEU* 4.9 5.2 - - + -
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Residues in contact with PRO 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A CYS 3.5 8.3 - - - +
57A HIS* 1.4 95.0 - - + +
59A GLU* 1.3 57.6 + - - +
61A ASN* 3.8 7.6 - - + +
62A GLN* 2.9 30.8 + - - +
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Residues in contact with GLU 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A HIS* 3.4 20.7 + - + -
58A PRO* 1.3 76.0 - - - +
60A LEU* 1.3 65.8 + - - +
62A GLN* 3.3 6.1 + - - +
63A TYR* 3.0 21.7 + - - +
1885X PRO* 3.5 30.0 - - + +
1889X GLU* 4.7 6.8 - - - +
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Residues in contact with LEU 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LEU* 4.2 7.0 - - + -
37A TYR* 3.7 50.9 - - + +
41A ILE* 3.7 14.6 - - + -
42A PHE* 5.1 1.3 - - + -
55A SER* 3.7 22.9 - - - +
57A HIS* 3.3 19.5 + - + +
59A GLU* 1.3 78.6 - - - +
61A ASN* 1.3 61.8 + - - +
63A TYR* 3.0 13.7 + - + +
64A ILE* 3.1 31.4 + - + +
146A PHE* 4.0 15.7 - - + -
1884X PRO* 4.6 0.9 - - + -
1885X PRO* 3.8 17.6 - - + +
1890X ILE* 4.7 2.2 - - + -
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Residues in contact with ASN 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A GLU* 5.0 3.5 - - - +
28A HIS* 3.1 23.7 + - + +
55A SER* 2.7 42.7 + - - -
56A CYS* 3.9 7.9 - - - +
57A HIS 3.0 19.4 + - - +
58A PRO* 3.8 6.7 - - + +
60A LEU* 1.3 76.4 - - - +
62A GLN* 1.3 63.4 + - - +
64A ILE* 3.4 6.8 + - - +
65A GLN* 3.0 29.8 + - + +
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Residues in contact with GLN 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A PRO 2.9 18.8 + - - +
59A GLU* 3.8 6.1 - - + +
61A ASN* 1.3 79.3 - - - +
63A TYR* 1.3 56.3 + - - +
65A GLN* 3.3 21.4 + - - +
66A ASP* 2.8 67.2 + - - +
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Residues in contact with TYR 63 (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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59A GLU* 3.0 14.5 + - + +
60A LEU* 3.0 9.8 + - - +
62A GLN* 1.3 75.4 - - - +
64A ILE* 1.3 60.3 + - + +
66A ASP* 3.3 7.7 + - - +
67A THR* 2.8 43.9 + - + -
146A PHE* 4.2 18.2 - + - -
147A THR* 4.9 6.1 + - - -
148A VAL* 5.8 2.2 - - + -
169A PHE* 3.6 26.8 - + - -
1880X PRO* 3.4 15.0 - - + +
1882X MET* 2.6 32.8 + - + -
1883X SER 3.4 12.8 - - - -
1884X PRO* 3.3 43.7 - - + +
1885X PRO* 4.4 8.5 - - + -
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Residues in contact with ILE 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A GLU* 4.2 14.8 - - + -
27A VAL* 3.8 34.8 - - + -
28A HIS* 3.7 26.0 - - + +
31A LEU* 3.9 17.0 - - + -
60A LEU* 3.1 22.8 + - + +
61A ASN 3.8 5.8 - - - +
62A GLN 3.3 0.2 - - - -
63A TYR* 1.3 73.4 - - - +
65A GLN* 1.3 67.2 + - - +
67A THR* 3.3 7.4 + - - -
68A LEU* 3.0 41.4 + - + +
146A PHE* 4.3 14.6 - - + -
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Residues in contact with GLN 65 (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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24A GLU* 3.7 26.4 + - - +
61A ASN* 3.0 19.4 + - + +
62A GLN* 3.5 25.3 + - - +
64A ILE* 1.3 75.5 - - - +
66A ASP* 1.3 66.5 + - - +
68A LEU* 3.1 6.9 + - - +
69A HIS* 2.9 25.2 + - - +
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Residues in contact with ASP 66 (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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62A GLN* 2.8 55.1 + - - +
63A TYR* 3.7 4.9 + - - +
65A GLN* 1.3 73.2 - - - +
67A THR* 1.3 62.6 - - - +
69A HIS* 3.3 7.7 + - - +
70A CYS* 3.2 26.9 + - - -
169A PHE* 3.8 33.6 - - + -
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Residues in contact with THR 67 (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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63A TYR* 2.8 33.5 + - - -
64A ILE* 3.5 8.3 - - - -
65A GLN 3.2 0.2 - - - -
66A ASP* 1.3 73.0 - - - +
68A LEU* 1.3 63.4 + - + +
70A CYS* 3.0 19.1 + - - +
71A VAL* 3.2 18.2 + - + +
148A VAL* 4.0 31.4 - - + -
169A PHE* 3.3 23.3 - - - -
171A TRP* 3.6 23.6 - - + -
1880X PRO* 4.1 3.8 - - + +
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Residues in contact with LEU 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A CYS* 3.6 26.8 - - + +
23A LEU* 3.7 31.9 - - + +
24A GLU* 3.4 46.0 - - + +
27A VAL* 5.2 6.1 - - + -
64A ILE* 3.0 28.0 + - + +
65A GLN* 3.1 4.0 + - - +
67A THR* 1.3 79.2 - - + +
69A HIS* 1.3 66.1 + - - +
70A CYS 3.0 1.3 - - - -
71A VAL* 3.2 13.8 + - + +
72A LYS* 3.0 19.4 + - - +
83A VAL* 5.5 4.5 - - + -
148A VAL* 6.0 2.7 - - + -
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Residues in contact with HIS 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A GLN 2.9 17.0 + - - +
66A ASP* 3.6 9.9 - - - +
68A LEU* 1.3 77.5 - - - +
70A CYS* 1.3 63.1 + - - +
72A LYS* 3.6 20.4 + - + +
73A PRO* 3.3 17.3 - - - +
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Residues in contact with CYS 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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66A ASP 3.2 15.7 + - - -
67A THR 3.0 10.0 + - - +
69A HIS* 1.3 79.6 - - - +
71A VAL* 1.3 64.0 + - - +
73A PRO* 3.3 15.8 - - - +
74A LEU* 3.8 12.1 - - - +
169A PHE* 4.1 21.8 - - - -
171A TRP* 3.3 35.2 - - + +
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Residues in contact with VAL 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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20A CYS* 5.1 0.4 - - - -
23A LEU* 5.1 0.7 - - + -
67A THR* 3.4 19.5 - - + +
68A LEU* 3.2 23.0 + - + +
70A CYS* 1.3 76.3 - - - +
72A LYS* 1.3 66.6 + - - +
74A LEU* 3.0 21.2 + - + +
75A LEU* 3.0 34.2 + - + +
80A VAL* 4.6 7.2 - - + -
83A VAL* 4.3 19.7 - - + -
148A VAL* 5.5 2.0 - - + -
150A VAL* 3.7 27.4 - - + -
171A TRP* 3.9 9.2 - - + -
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Residues in contact with LYS 72 (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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16A ALA* 4.2 10.1 - - + -
17A ASP* 2.2 41.9 + - - +
20A CYS* 3.5 26.9 - - - -
68A LEU 3.0 11.2 + - - +
69A HIS* 3.7 24.0 - - + +
71A VAL* 1.3 76.8 - - - +
73A PRO* 1.3 72.6 - - + +
75A LEU* 3.0 6.3 + - - +
76A GLU* 3.0 37.5 + - - +
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Residues in contact with PRO 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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69A HIS 3.3 13.9 - - - +
70A CYS* 3.3 15.3 - - - +
72A LYS* 1.3 95.5 - - + +
74A LEU* 1.3 62.0 + - + +
76A GLU* 3.4 19.6 + - - +
77A LYS* 3.2 31.0 + - + +
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Residues in contact with LEU 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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70A CYS 3.8 18.8 - - - +
71A VAL* 3.0 12.7 + - + +
73A PRO* 1.3 77.4 - - + +
75A LEU* 1.3 62.8 + - - +
77A LYS* 3.3 4.9 + - - -
78A ASN 3.1 3.5 + - - -
79A ASP* 2.9 46.7 + - + +
80A VAL* 3.6 15.5 - - + -
150A VAL* 4.7 16.4 - - + -
152A THR* 4.7 14.6 - - + -
1878X LEU* 5.1 8.5 - - + -
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Residues in contact with LEU 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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12A GLY 4.6 0.5 - - - +
16A ALA* 3.9 14.1 - - + +
19A LEU* 3.8 41.1 - - + -
20A CYS* 3.9 23.8 - - - -
23A LEU* 4.8 7.2 - - + -
71A VAL* 3.0 25.0 + - + +
72A LYS 3.0 7.6 + - - +
74A LEU* 1.3 75.5 - - - +
76A GLU* 1.3 56.3 + - - +
78A ASN* 2.8 19.3 + - - +
80A VAL* 3.7 29.4 - - + -
83A VAL* 5.3 0.2 - - + -
102A ILE* 4.5 10.3 - - + -
104A GLN* 2.8 28.7 + - - +
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Residues in contact with GLU 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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12A GLY* 3.6 31.2 - - - +
13A GLN* 4.2 25.3 + - + +
16A ALA* 3.3 21.0 - - + +
17A ASP* 5.1 0.9 - - - +
72A LYS* 3.0 32.3 + - - +
73A PRO* 3.5 19.1 - - - +
75A LEU* 1.3 77.4 - - - +
77A LYS* 1.3 62.9 + - + +
78A ASN* 3.4 2.8 + - - +
104A GLN* 4.9 0.9 - - - +
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Residues in contact with LYS 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 PRO* 3.2 18.5 + - - +
74A LEU* 4.0 1.3 - - - +
75A LEU 3.2 0.6 - - - -
76A GLU* 1.3 78.5 - - + +
78A ASN* 1.3 70.2 + - - +
79A ASP* 3.1 27.6 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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