Contacts of the helix formed by residues 53 - 73 (chain A) in PDB entry 1HSM
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 PRO 53 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A ASP 3.5 13.7 - - - +
50A ASP* 3.2 27.6 - - - +
51A LYS 3.3 0.2 - - - -
52A GLN* 1.3 94.8 - - + +
54A TYR* 1.3 64.8 - - + +
56A LYS* 4.0 9.3 - - + +
57A LYS* 2.7 32.4 + - - +
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Residues in contact with TYR 54 (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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11A ALA 3.4 18.2 - - - +
14A LEU* 3.2 36.3 - - + +
15A PHE* 4.0 17.0 - + + -
18A GLU* 2.9 37.5 + - - -
43A TRP* 3.9 13.2 - + + -
50A ASP* 3.2 39.4 + - - -
51A LYS 2.7 9.2 + - - +
53A PRO* 1.3 77.8 - - + +
55A GLU* 1.3 67.4 + - - +
57A LYS* 2.9 35.9 + - - +
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Residues in contact with GLU 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A SER 5.2 0.7 - - - +
11A ALA* 3.6 28.2 - - + +
43A TRP* 5.3 0.2 - - - -
51A LYS* 2.8 25.3 + - - +
52A GLN* 2.9 42.9 + - - +
54A TYR* 1.3 77.5 - - - +
56A LYS* 1.3 64.6 + - - +
57A LYS 2.9 1.7 + - - -
58A ALA* 2.9 4.6 + - + +
59A ALA* 2.9 26.0 + - + +
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Residues in contact with LYS 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A GLN* 2.9 21.6 + - + +
53A PRO* 4.0 9.0 - - + +
55A GLU* 1.3 73.4 + - - +
57A LYS* 1.3 63.5 + - + +
59A ALA* 3.6 6.8 - - - +
60A LYS* 3.0 27.7 + - + +
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Residues in contact with LYS 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LEU* 4.2 24.5 - - + -
53A PRO* 2.7 35.5 + - - +
54A TYR* 2.9 23.3 + - - +
56A LYS* 1.3 75.8 - - + +
58A ALA* 1.3 67.8 + - - +
59A ALA 3.0 1.0 + - - -
60A LYS* 3.0 9.7 + - - +
61A LEU* 3.0 34.7 + - + +
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Residues in contact with ALA 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A PRO* 4.3 2.3 - - - +
9A PRO* 3.8 20.5 - - + +
10A SER 3.3 16.8 - - - +
11A ALA* 3.2 35.9 - - + +
14A LEU* 4.1 1.4 - - + +
54A TYR 3.2 1.8 + - - -
55A GLU* 2.9 8.0 + - + +
57A LYS* 1.3 79.9 - - - +
59A ALA* 1.3 63.4 + - - +
61A LEU* 3.4 1.7 + - - +
62A LYS* 2.9 24.9 + - - +
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Residues in contact with ALA 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A GLU* 2.9 14.8 + - + +
56A LYS* 3.6 13.0 - - - +
58A ALA* 1.3 75.9 - - - +
60A LYS* 1.3 66.5 + - - +
61A LEU 3.0 0.5 + - - -
62A LYS* 3.0 7.6 + - - +
63A GLU* 2.9 26.2 + - - +
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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
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56A LYS* 3.0 18.6 + - + +
57A LYS* 3.0 8.8 + - - +
59A ALA* 1.3 78.3 - - - +
61A LEU* 1.3 69.0 + - + +
63A GLU* 3.3 16.4 - - - +
64A LYS* 3.0 26.6 + - + +
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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
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8A PRO* 3.4 20.1 - - + +
9A PRO* 3.7 26.0 - - + -
14A LEU* 6.1 0.4 - - + -
57A LYS* 3.0 20.2 + - + +
58A ALA 3.7 3.8 - - - +
60A LYS* 1.3 89.6 - - + +
62A LYS* 1.3 69.7 + - - +
63A GLU 3.0 1.6 - - - -
64A LYS* 2.9 17.8 + - + +
65A TYR* 2.9 22.0 + - - +
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Residues in contact with LYS 62 (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 ARG* 3.6 28.4 - - - +
8A PRO* 3.1 21.6 - - + +
9A PRO 5.3 2.9 - - - +
58A ALA 2.9 21.5 + - - +
59A ALA* 3.7 5.4 - - - +
61A LEU* 1.3 70.4 - - - +
63A GLU* 1.3 64.5 + - - +
65A TYR* 3.1 9.6 - - + +
66A GLU* 2.9 60.5 + - + +
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Residues in contact with GLU 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 ALA 2.9 12.8 + - - +
60A LYS* 3.3 22.9 - - - +
62A LYS* 1.3 79.4 - - - +
64A LYS* 1.3 63.5 + - - +
66A GLU* 3.2 8.6 + - - +
67A LYS* 2.9 49.4 + - + +
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Residues in contact with LYS 64 (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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60A LYS* 3.0 14.9 + - + +
61A LEU* 2.9 20.7 + - + +
63A GLU* 1.3 75.0 - - - +
65A TYR* 1.3 63.5 + - - +
67A LYS* 2.9 8.1 + - - +
68A ASP* 2.7 51.9 + - - +
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Residues in contact with TYR 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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5A PRO* 2.9 33.7 + - + -
6A LYS* 3.1 26.1 - - - +
7A ARG* 3.8 27.1 + - + +
8A PRO* 3.9 16.8 - - + -
61A LEU 2.9 10.0 + - - +
62A LYS* 3.1 14.6 - - + +
64A LYS* 1.3 76.6 - - - +
66A GLU* 1.3 72.4 + - + +
67A LYS 2.8 0.7 + - - -
68A ASP* 2.7 30.2 + - - +
69A ILE* 2.7 37.2 + - + +
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Residues in contact with GLU 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ARG* 5.1 1.2 + - - -
62A LYS* 3.0 45.1 + - + +
63A GLU* 3.4 9.9 - - - +
65A TYR* 1.3 105.0 + - + +
67A LYS* 1.3 69.0 + - + +
69A ILE* 3.0 23.2 - - - +
70A ALA* 3.1 14.6 - - - +
73A ARG* 4.9 0.3 + - - -
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Residues in contact with LYS 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A GLU* 2.9 51.3 + - + +
64A LYS* 2.9 10.0 + - - +
65A TYR 2.8 1.0 + - - -
66A GLU* 1.3 83.0 - - - +
68A ASP* 1.3 63.4 + - - +
69A ILE 3.1 1.6 - - - -
70A ALA* 3.6 7.8 - - + +
71A ALA* 2.9 28.8 + - - +
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Residues in contact with ASP 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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5A PRO* 3.5 15.8 - - + +
64A LYS* 2.7 51.5 + - - +
65A TYR* 2.7 12.1 + - - +
67A LYS* 1.3 81.1 - - - +
69A ILE* 1.3 58.9 + - - +
71A ALA* 3.7 5.5 - - - +
72A TYR* 2.8 25.7 + - - +
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Residues in contact with ILE 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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4A ALA* 5.2 2.2 - - + -
5A PRO* 3.9 13.0 - - + +
65A TYR* 2.7 39.2 + - + +
66A GLU* 3.0 34.3 - - - +
68A ASP* 1.3 76.6 - - - +
70A ALA* 1.3 63.1 + - - +
71A ALA 2.9 4.5 - - - -
72A TYR* 3.2 26.9 - - + +
73A ARG* 2.9 60.6 + - + +
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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 GLU 3.1 17.0 - - - +
67A LYS* 3.6 10.1 - - + +
69A ILE* 1.3 83.2 - - - +
71A ALA* 1.3 57.6 + - - +
73A ARG* 3.6 16.8 - - - +
74A ALA* 3.0 24.0 + - - +
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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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67A LYS 2.9 18.1 + - - +
68A ASP* 3.7 8.3 - - - +
69A ILE 2.9 0.2 - - - -
70A ALA* 1.3 76.6 - - - +
72A TYR* 1.3 66.1 + - - +
73A ARG 3.0 2.0 - - - -
74A ALA* 2.9 19.4 + - + +
75A LYS 3.0 11.6 + - - -
76A GLY* 3.2 8.1 + - - -
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Residues in contact with TYR 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 ASN* 3.0 30.3 + - - +
4A ALA* 3.1 27.9 - - + +
5A PRO* 3.5 13.2 - - + -
68A ASP 2.8 20.7 + - - +
69A ILE* 3.2 28.0 - - + +
71A ALA* 1.3 76.4 - - - +
73A ARG* 1.3 63.1 + - + +
76A GLY* 2.9 24.9 + - - -
77A LYS* 3.0 60.1 + - + +
78A PRO* 4.0 6.0 - - + +
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Residues in contact with ARG 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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66A GLU 4.9 0.2 + - - -
69A ILE* 2.9 51.9 + - + +
70A ALA* 3.6 22.6 - - - +
72A TYR* 1.3 80.4 - - + +
74A ALA* 1.3 69.5 + - - +
75A LYS* 2.9 5.9 + - - -
77A LYS* 5.1 9.2 - - + +
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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