Contacts of the helix formed by residues 57 - 77 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B ILE* 4.1 22.7 + - + +
55B SER* 3.0 10.5 + - - +
56B CYS* 1.3 78.2 - - - +
58B PRO* 1.3 74.6 - - + +
59B GLU* 3.3 34.6 + - + -
60B LEU* 3.5 10.3 + - + -
61B ASN* 3.0 24.9 + - - +
1885Y PRO* 5.2 0.4 - - + -
1890Y ILE* 3.9 41.6 - - + +
1893Y THR* 4.3 14.9 + - - +
1894Y LEU* 5.8 3.8 - - + -
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Residues in contact with PRO 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B CYS 3.5 8.5 - - - +
57B HIS* 1.3 95.7 - - + +
59B GLU* 1.3 59.2 + - - +
61B ASN* 3.8 7.4 - - + +
62B GLN* 2.9 30.5 + - - +
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Residues in contact with GLU 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B HIS* 3.3 19.0 + - + -
58B PRO* 1.3 79.0 - - - +
60B LEU* 1.3 68.3 + - - +
62B GLN* 3.2 7.5 + - + +
63B TYR* 2.9 22.8 + - + +
1885Y PRO* 3.9 29.2 - - + +
1889Y GLU* 4.5 7.8 - - - +
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Residues in contact with LEU 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU* 4.5 7.0 - - + -
37B TYR* 3.8 50.3 - - + +
41B ILE* 3.8 13.7 - - + -
42B PHE* 5.2 1.6 - - + -
55B SER* 3.8 22.0 - - - +
57B HIS* 3.5 18.4 + - + +
59B GLU* 1.3 80.1 - - - +
61B ASN* 1.3 61.8 + - - +
63B TYR* 3.1 5.6 + - + +
64B ILE* 3.1 37.0 + - + +
146B PHE* 4.1 12.3 - - + -
1884Y PRO* 4.6 1.1 - - + -
1885Y PRO* 3.8 18.9 - - + +
1890Y ILE* 4.6 2.0 - - + -
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Residues in contact with ASN 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B GLU* 4.9 4.5 - - - +
28B HIS* 3.2 13.3 + - + +
55B SER* 2.6 51.9 + - - -
56B CYS* 4.0 3.6 - - - +
57B HIS 3.0 19.0 + - - +
58B PRO* 3.8 6.5 - - + +
60B LEU* 1.3 77.7 - - - +
62B GLN* 1.3 57.6 + - - +
64B ILE* 3.4 7.7 + - - +
65B GLN* 2.9 33.0 + - - +
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Residues in contact with GLN 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B PRO 2.9 18.1 + - - +
59B GLU* 3.6 7.9 - - + +
61B ASN* 1.3 75.2 - - - +
63B TYR* 1.3 58.2 - - - +
65B GLN* 4.3 17.2 + - - +
66B ASP* 2.8 68.8 + - - +
69B HIS* 5.4 2.2 + - - -
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Residues in contact with TYR 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B GLU* 2.9 13.6 + - + +
60B LEU* 3.4 10.3 - - + +
62B GLN* 1.3 75.2 - - - +
64B ILE* 1.3 60.7 + - + +
66B ASP* 3.6 6.7 - - - +
67B THR* 2.9 44.4 + - - -
146B PHE* 4.1 20.6 - + - -
147B THR* 4.7 7.1 + - - -
148B VAL* 5.8 2.7 - - + -
169B PHE* 3.5 27.2 - + - -
1880Y PRO* 3.6 15.2 - - + +
1882Y MET* 2.7 32.3 + - + -
1883Y SER 3.5 12.3 - - - -
1884Y PRO* 3.5 39.2 - - + +
1885Y PRO* 4.4 9.2 - - + -
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Residues in contact with ILE 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B GLU* 4.3 8.7 - - + +
27B VAL* 4.0 24.5 - - + -
28B HIS* 3.7 35.7 - - + +
31B LEU* 4.0 16.8 - - + -
60B LEU* 3.1 32.6 + - + +
61B ASN 3.8 5.4 - - - +
63B TYR* 1.3 75.2 - - - +
65B GLN* 1.3 65.0 + - - +
67B THR* 3.3 8.1 + - - -
68B LEU* 3.0 39.7 + - + +
146B PHE* 4.3 14.6 - - + -
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Residues in contact with GLN 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B GLU* 4.5 18.4 + - - +
61B ASN* 2.9 19.8 + - - +
62B GLN* 3.7 18.0 - - - +
64B ILE* 1.3 78.2 - - - +
66B ASP* 1.3 55.9 + - - +
68B LEU* 3.1 7.3 + - - +
69B HIS* 2.8 64.8 + - + +
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Residues in contact with ASP 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B GLN* 2.8 56.5 + - - +
63B TYR* 3.6 5.0 - - - +
65B GLN* 1.3 72.9 - - - +
67B THR* 1.3 64.0 + - - +
69B HIS* 3.5 8.6 + - - +
70B CYS* 3.1 28.8 + - - -
166B ILE* 4.0 21.2 - - + +
168B ASP* 6.2 0.2 - - - +
169B PHE* 3.8 30.2 - - + +
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Residues in contact with THR 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B TYR* 2.9 26.8 + - - -
64B ILE* 3.5 11.0 - - - -
66B ASP* 1.3 75.6 - - - +
68B LEU* 1.3 65.5 + - + +
70B CYS* 3.2 7.3 + - - +
71B VAL* 3.1 27.6 + - + +
148B VAL* 4.1 31.2 - - + -
169B PHE* 3.2 23.5 - - - -
171B TRP* 3.6 22.9 - - + -
1880Y PRO* 4.1 2.8 - - + +
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Residues in contact with LEU 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B CYS* 3.7 25.3 - - + +
23B LEU* 4.0 28.0 - - + +
24B GLU* 3.5 44.2 - - + +
27B VAL* 5.3 5.6 - - + -
64B ILE* 3.0 25.0 + - + +
65B GLN* 3.8 5.2 - - - +
67B THR* 1.3 81.2 - - + +
69B HIS* 1.3 65.7 + - - +
70B CYS 3.1 1.3 - - - -
71B VAL* 3.1 14.6 + - + +
72B LYS* 3.0 25.2 + - - +
83B VAL* 5.7 4.5 - - + -
148B VAL* 6.0 2.0 - - + -
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Residues in contact with HIS 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ASP* 3.3 26.8 + - - -
62B GLN* 5.5 2.0 - - - -
65B GLN* 2.8 60.5 + - + +
66B ASP* 3.5 16.0 + - - +
68B LEU* 1.3 74.8 - - - +
70B CYS* 1.3 58.8 + - - +
72B LYS* 3.6 17.1 + - + +
73B PRO* 3.3 17.7 - - - +
165B VAL* 5.6 2.8 - - - +
166B ILE* 4.3 11.0 - - + +
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Residues in contact with CYS 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B ASP 3.1 16.7 + - - -
67B THR 3.4 6.5 - - - +
68B LEU 3.1 0.4 - - - -
69B HIS* 1.3 78.9 - - - +
71B VAL* 1.3 62.5 + - - +
73B PRO* 3.2 16.0 - - - +
74B LEU* 4.6 1.7 + - - +
163B ILE* 3.4 33.2 - - + +
165B VAL* 4.6 6.3 - - - -
166B ILE* 3.7 24.9 - - - -
169B PHE* 4.1 11.4 - - - -
171B TRP* 3.3 34.1 - - + +
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Residues in contact with VAL 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B LEU* 5.6 0.7 - - + -
67B THR* 3.1 22.0 + - + +
68B LEU* 3.1 18.6 + - + +
70B CYS* 1.3 74.8 - - - +
72B LYS* 1.3 66.4 + - - +
73B PRO 3.4 0.2 - - - -
74B LEU* 3.0 8.9 + - + +
75B LEU* 2.9 40.3 + - + +
80B VAL* 4.4 13.2 - - + -
83B VAL* 4.4 16.4 - - + -
148B VAL* 5.4 1.8 - - + -
150B VAL* 3.8 27.1 - - + -
163B ILE* 4.8 4.9 - - + -
171B TRP* 4.1 9.0 - - + -
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Residues in contact with LYS 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A ASP* 3.9 27.1 + - + +
13B GLN* 4.5 8.7 - - - +
16B ALA* 3.7 15.9 - - + +
17B ASP* 3.0 30.2 + - - +
20B CYS* 3.8 32.3 - - - +
68B LEU 3.0 14.7 + - - +
69B HIS* 3.7 15.8 - - + +
71B VAL* 1.3 77.5 - - - +
73B PRO* 1.3 68.0 - - + +
75B LEU* 3.1 5.5 + - - +
76B GLU* 2.9 26.8 + - + +
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Residues in contact with PRO 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B HIS 3.3 13.0 - - - +
70B CYS 3.2 17.0 - - - +
72B LYS* 1.3 94.1 - - + +
74B LEU* 1.3 59.6 + - - +
76B GLU* 3.4 9.1 + - + +
77B LYS* 3.2 35.4 + - + +
162B LYS* 3.8 23.1 - - + +
165B VAL* 4.7 11.2 - - + -
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Residues in contact with LEU 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B CYS 4.7 2.7 - - - +
71B VAL* 3.0 10.4 + - - +
73B PRO* 1.3 77.3 - - - +
75B LEU* 1.3 63.2 + - - +
77B LYS* 3.4 2.3 + - - +
78B ASN 3.3 2.9 + - - -
79B ASP* 2.8 41.0 + - + +
80B VAL* 3.6 17.7 - - + -
150B VAL* 4.7 3.6 - - + -
152B THR* 4.4 22.0 - - + -
161B GLU 5.6 0.9 - - - +
162B LYS* 3.1 47.3 - - + +
163B ILE* 3.6 40.8 - - + -
1878Y LEU* 4.6 1.3 - - + -
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Residues in contact with LEU 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B GLY 4.6 0.7 - - - +
16B ALA* 3.8 13.0 - - + +
19B LEU* 4.1 36.3 - - + -
20B CYS* 3.7 29.6 - - - +
23B LEU* 5.0 5.4 - - + -
71B VAL* 2.9 26.2 + - + +
72B LYS* 3.1 5.8 + - - +
74B LEU* 1.3 77.1 - - - +
76B GLU* 1.3 64.2 + - - +
78B ASN 3.0 3.6 + - - -
79B ASP 4.8 0.2 - - - +
80B VAL* 3.8 28.0 - - + -
83B VAL* 5.2 1.1 - - + -
102B ILE* 4.3 11.0 - - + -
104B GLN* 2.8 33.5 + - - +
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Residues in contact with GLU 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A GLN* 5.3 3.3 + - - -
10B ASN* 4.9 14.6 + - - +
12B GLY* 3.7 39.1 - - - +
13B GLN* 3.8 21.9 + - + +
16B ALA* 3.8 4.9 - - + +
72B LYS* 2.9 16.5 + - + +
73B PRO* 3.8 8.9 - - + +
74B LEU 3.3 0.4 - - - -
75B LEU* 1.3 77.9 - - - +
77B LYS* 1.3 75.3 + - - +
78B ASN 3.5 0.7 + - - -
104B GLN* 5.0 0.7 - - - +
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Residues in contact with LYS 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B PRO* 3.2 22.7 + - - +
74B LEU 3.4 0.9 + - - +
75B LEU 3.2 0.4 - - - -
76B GLU* 1.3 88.2 - - - +
78B ASN* 1.3 67.9 + - - +
79B ASP* 3.3 23.1 + - - +
162B LYS* 2.9 47.9 - - + +
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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
------------------------------------------------------------
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