Contacts of the helix formed by residues 58 - 80 (chain A) in PDB entry 1AR5
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 ILE 58 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A LEU* 3.9 25.1 - - + -
55A PHE* 3.1 42.7 + - + +
56A GLY 3.3 3.1 - - - +
57A ALA* 1.3 75.3 - - - +
59A ASN* 1.3 72.0 + - - +
61A LEU* 4.5 4.9 - - + +
62A GLU* 2.9 55.6 + - + +
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Residues in contact with ASN 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A GLY 5.0 0.6 + - - -
57A ALA 3.1 0.8 + - - -
58A ILE* 1.3 93.1 - - - +
60A LYS* 1.3 62.4 + - - +
62A GLU* 3.7 5.0 + - - +
63A LYS* 3.4 21.5 + - - +
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Residues in contact with LYS 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ALA* 3.0 23.1 + - + +
59A ASN* 1.3 78.9 - - - +
61A LEU* 1.3 65.8 + - + +
63A LYS* 3.2 6.0 + - - +
64A ASP* 2.9 56.8 + - - +
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Residues in contact with LEU 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ALA* 4.3 7.6 - - - +
45A LYS* 3.7 45.5 - - + +
46A LEU* 3.8 32.3 - - + +
49A ALA* 4.8 8.7 - - + -
55A PHE* 6.6 0.2 - - - -
57A ALA* 2.9 28.4 + - + +
58A ILE* 3.9 4.0 - - + +
60A LYS* 1.3 89.0 - - + +
62A GLU* 1.3 57.0 + - - +
64A ASP* 3.6 17.0 - - + +
65A LEU* 2.9 29.6 + - - +
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Residues in contact with GLU 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LEU* 4.8 8.3 - - - +
58A ILE* 2.9 46.4 + - + +
59A ASN* 4.2 4.5 - - - +
61A LEU* 1.3 76.4 - - - +
63A LYS* 1.3 56.7 + - - +
65A LEU* 3.7 19.4 + - - +
66A ALA* 3.1 27.2 + - - +
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Residues in contact with LYS 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 ASN 3.4 14.9 + - - +
60A LYS* 3.2 6.1 + - - +
62A GLU* 1.3 76.1 - - - +
64A ASP* 1.3 62.1 + - - +
65A LEU 3.2 0.2 - - - -
66A ALA* 4.5 4.3 - - + -
67A PHE* 2.8 32.8 + - + +
147A GLN* 4.6 15.5 - - + +
122B GLN* 3.4 35.2 + - - +
144B TYR* 3.3 41.2 + - - -
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Residues in contact with ASP 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A GLY 5.3 0.4 - - - +
42A ALA* 4.2 13.8 - - + +
60A LYS* 2.9 56.3 + - - +
61A LEU* 3.6 12.8 - - - +
63A LYS* 1.3 76.3 - - - +
65A LEU* 1.3 62.3 + - - +
68A ASN* 2.9 37.2 + - - +
122B GLN* 3.0 28.5 + - - +
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Residues in contact with LEU 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A TYR* 4.9 2.0 - - - +
39A ALA* 4.3 16.6 - - + +
42A ALA* 3.8 10.1 - - + +
43A LEU* 4.1 24.7 - - + -
46A LEU* 4.0 21.5 - - + -
61A LEU 2.9 18.4 + - - +
62A GLU* 3.8 16.2 - - - +
64A ASP* 1.3 77.1 - - - +
66A ALA* 1.3 57.8 + - - +
68A ASN* 5.2 0.9 - - - -
69A LEU* 2.9 59.2 + - + +
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Residues in contact with ALA 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 GLU 3.1 18.6 + - - +
63A LYS* 4.0 5.2 - - + +
65A LEU* 1.3 78.7 - - - +
67A PHE* 1.3 57.4 + - - +
69A LEU* 4.9 2.2 - - - -
70A ALA* 2.9 34.1 + - - +
147A GLN* 3.6 19.1 - - + +
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Residues in contact with PHE 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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35A TYR* 3.9 21.3 - + - -
63A LYS* 2.8 24.4 + - + +
64A ASP 4.2 1.1 - - - +
66A ALA* 1.3 73.8 - - - +
68A ASN* 1.3 70.3 + - - +
70A ALA* 3.8 1.2 - - - +
71A GLY 3.0 21.8 + - - -
145A ASP* 4.8 2.2 - - + -
146A HIS* 3.5 28.6 + - - -
147A GLN* 3.4 34.4 - - - +
163A TRP* 3.9 24.7 - + - -
122B GLN* 3.9 59.0 - - + +
123B GLY* 4.1 0.4 - - - -
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Residues in contact with ASN 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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34A ALA 3.9 2.3 - - - +
35A TYR* 3.4 49.2 - - - +
38A GLY* 3.7 23.4 + - - -
39A ALA* 3.4 11.0 - - - +
64A ASP* 2.9 32.0 + - - +
67A PHE* 1.3 91.7 - - - +
69A LEU* 1.3 61.8 + - - +
71A GLY 3.2 0.7 + - - -
72A HIS* 2.9 25.6 + - - +
122B GLN* 4.5 4.4 - - - +
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Residues in contact with LEU 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 TYR* 3.6 47.3 - - + +
39A ALA* 4.0 7.5 - - + +
65A LEU* 2.9 39.9 + - + +
66A ALA* 4.4 2.2 - - - +
68A ASN* 1.3 72.5 - - - +
70A ALA* 1.3 58.0 + - - +
72A HIS* 3.2 9.5 + - - +
73A VAL* 2.9 49.4 + - + +
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Residues in contact with ALA 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 ALA 2.9 21.7 + - - +
69A LEU* 1.3 77.1 - - - +
71A GLY* 1.3 57.8 + - - +
73A VAL* 3.8 6.0 - - - +
74A ASN* 2.9 38.0 + - - +
146A HIS* 3.5 34.3 - - + +
147A GLN* 3.7 7.6 - - + -
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Residues in contact with GLY 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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35A TYR* 3.9 9.6 - - - -
67A PHE 3.0 12.2 + - - -
68A ASN 3.2 4.2 + - - -
70A ALA* 1.3 78.3 - - - +
72A HIS* 1.3 59.9 + - - +
74A ASN* 4.6 0.2 - - - -
75A HIS* 2.7 34.2 + - - +
146A HIS* 3.6 32.5 - - - +
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Residues in contact with HIS 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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3A TYR* 3.8 39.7 - + + +
4A THR 3.2 26.6 + - - -
6A PRO* 4.0 2.2 - - - +
32A HIS* 3.0 35.8 + - - -
35A TYR* 3.9 8.0 - - + +
36A VAL* 3.7 13.4 - - + +
39A ALA* 5.4 1.1 - - + +
68A ASN 2.9 13.7 + - - +
69A LEU* 3.5 15.2 - - - +
71A GLY* 1.3 73.5 - - - +
73A VAL* 1.3 65.1 + - - +
76A SER* 2.9 41.1 + - - -
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Residues in contact with VAL 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 LEU* 2.9 37.6 + - + +
70A ALA* 3.8 6.7 - - - +
72A HIS* 1.3 77.0 - - + +
74A ASN* 1.3 69.8 + - - +
76A SER* 3.3 5.1 + - - -
77A VAL* 3.1 39.2 + - + +
156A PRO* 4.7 13.0 - - + -
159A GLN* 5.7 0.2 - - - +
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Residues in contact with ASN 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 ALA* 2.9 22.9 + - - +
71A GLY 4.0 2.2 - - - +
73A VAL* 1.3 83.1 - - - +
75A HIS* 1.3 57.5 + - - +
77A VAL 3.5 0.5 + - - -
78A PHE* 3.0 26.9 + - - +
126A TRP* 3.4 44.0 - - + +
143A PHE* 3.9 14.6 - - - -
146A HIS* 3.1 29.7 + - - +
156A PRO* 5.9 0.2 - - - +
159A GLN* 3.3 29.3 + - - +
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Residues in contact with HIS 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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27A HIS* 3.0 22.5 + + - -
32A HIS* 3.5 28.5 - + + +
35A TYR* 3.3 29.1 - + - -
71A GLY 2.7 27.5 + - - +
74A ASN* 1.3 75.8 - - - +
76A SER* 1.3 66.6 + - - +
78A PHE* 3.3 6.0 - + - +
79A TRP* 3.0 40.2 + + - +
126A TRP* 3.6 19.0 - + - -
146A HIS* 3.6 8.5 - - - -
161A ASP* 3.2 3.7 + - - -
165A HIS* 4.0 0.2 + - - -
202A FE 2.1 32.4 - - - -
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Residues in contact with SER 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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6A PRO* 3.8 11.1 - - - +
32A HIS* 3.5 10.1 - - - -
72A HIS* 2.9 44.3 + - - -
73A VAL* 3.7 6.5 - - - -
75A HIS* 1.3 78.0 - - - +
77A VAL* 1.3 64.6 + - - +
79A TRP* 3.8 7.1 + - - +
80A LYS* 3.7 26.4 + - - +
194A ARG* 5.0 0.4 - - - -
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Residues in contact with VAL 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 VAL* 3.1 23.8 + - + +
74A ASN 3.7 4.5 - - - +
76A SER* 1.3 75.5 - - - +
78A PHE* 1.3 66.2 + - - +
80A LYS* 3.2 4.7 + - - +
81A ASN* 2.9 49.5 + - - +
156A PRO* 4.1 25.4 - - + -
157A LEU 4.6 1.8 - - - +
159A GLN* 4.2 16.2 - - + +
194A ARG* 4.0 32.5 - - - +
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Residues in contact with PHE 78 (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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19A ILE* 5.2 3.8 - - + -
24A MET* 5.9 0.9 - - - -
27A HIS* 3.8 25.6 - + - -
74A ASN 3.0 18.9 + - - +
75A HIS* 3.1 8.9 + + - +
77A VAL* 1.3 76.6 - - - +
79A TRP* 1.3 88.7 + + - +
81A ASN* 3.3 19.9 + - + +
82A MET* 3.6 32.9 + - + +
126A TRP* 4.0 8.5 - + + -
159A GLN* 3.2 22.9 - - - +
160A LEU* 3.9 1.1 - - + -
161A ASP* 3.5 26.7 - - + -
166A ALA* 5.5 0.2 - - + -
178A TYR* 3.8 20.0 - - - -
182A TRP* 3.7 19.5 - + - -
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Residues in contact with TRP 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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6A PRO* 4.5 7.9 - - + -
7A GLU 5.6 1.1 - - - +
8A LEU* 3.6 22.9 - - + -
9A PRO* 4.3 10.8 - - + -
10A TYR* 2.9 23.7 + - - +
24A MET* 3.9 24.0 - - + -
27A HIS* 3.5 37.9 - + + -
28A HIS* 3.4 40.4 + + + -
32A HIS* 2.8 31.3 + + - -
75A HIS* 3.0 30.8 + + - +
76A SER* 4.1 7.2 - - - +
77A VAL 3.3 0.2 - - - -
78A PHE* 1.3 98.8 - + - +
80A LYS* 1.3 64.4 + - + +
82A MET* 3.3 14.8 + - + +
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Residues in contact with LYS 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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6A PRO* 6.1 5.2 - - - -
9A PRO* 4.7 16.2 - - + -
76A SER* 3.7 11.6 + - - +
77A VAL 3.2 3.4 + - - +
79A TRP* 1.3 75.9 - - + +
81A ASN* 1.3 59.6 + - - +
82A MET 3.1 12.5 + - - +
187A ASN* 3.7 4.9 - - - +
190A ASP* 3.2 29.4 - - - +
194A ARG* 3.2 32.3 - - - +
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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