Contacts of the helix formed by residues 52 - 76 (chain A) in PDB entry 2LY4
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 SER 52 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A MET* 1.3 76.0 - - - +
53A ALA* 1.3 66.0 + - - +
54A LYS* 3.2 10.1 - - - -
55A GLU* 2.7 25.2 + - - +
56A LYS* 3.0 26.3 + - - +
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Residues in contact with ALA 53 (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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52A SER* 1.3 70.7 - - - +
54A LYS* 1.3 57.7 + - - +
56A LYS* 3.9 10.7 - - - +
57A GLY* 2.7 33.1 + - - -
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Residues in contact with LYS 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A SER* 4.2 7.1 - - - -
53A ALA* 1.3 78.6 - - - +
55A GLU* 1.3 64.3 + - + +
57A GLY* 3.9 1.1 - - - -
58A LYS* 3.1 26.2 + - - +
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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
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51A MET* 3.2 33.2 - - + +
52A SER* 2.7 40.9 + - - +
54A LYS* 1.3 80.4 - - + +
56A LYS* 1.3 67.6 + - - +
58A LYS* 3.1 27.9 + - - +
59A PHE* 3.0 22.3 - - + -
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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
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14A SER* 3.9 0.6 - - - -
48A TRP* 3.1 69.3 - - + +
49A LYS* 3.0 22.4 + - - +
51A MET* 3.1 21.4 + - + -
52A SER 3.0 19.1 + - - +
53A ALA* 3.9 7.4 - - - +
55A GLU* 1.3 77.0 - - - +
57A GLY* 1.3 55.1 + - - +
59A PHE* 3.2 5.4 + - - +
60A GLU* 2.9 27.6 + - - +
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Residues in contact with GLY 57 (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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53A ALA 2.7 22.3 + - - -
54A LYS* 3.9 2.0 - - - -
56A LYS* 1.3 70.5 - - - +
58A LYS* 1.3 56.0 + - - +
60A GLU* 3.4 9.7 - - - +
61A ASP* 2.8 35.4 + - - +
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Residues in contact with LYS 58 (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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54A LYS 3.1 14.3 + - - +
55A GLU* 3.1 24.8 - - - +
57A GLY* 1.3 76.9 - - - +
59A PHE* 1.3 87.6 + - - +
61A ASP* 3.3 6.8 + - - +
62A MET* 3.1 39.6 + - + +
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Residues in contact with PHE 59 (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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14A SER* 3.5 21.0 - - - +
17A PHE* 4.1 6.1 - - + +
18A PHE* 3.4 43.5 - + - -
21A THR* 3.6 25.8 - - + -
48A TRP* 3.5 15.9 - + + -
51A MET* 3.8 12.8 - - + -
55A GLU* 3.0 25.8 + - + -
56A LYS 3.2 6.1 + - - +
58A LYS* 1.3 93.8 - - - +
60A GLU* 1.3 60.5 + - - +
62A MET* 3.3 24.9 + - + +
63A ALA* 2.9 29.1 + - - +
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Residues in contact with GLU 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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13A SER* 4.7 4.2 - - - -
14A SER* 3.3 30.5 + - - -
56A LYS 2.9 14.7 + - - +
57A GLY* 3.4 13.9 - - - +
59A PHE* 1.3 75.9 - - - +
61A ASP* 1.3 57.1 + - - +
63A ALA* 3.1 8.9 + - - +
64A LYS* 2.9 42.9 + - + +
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Residues in contact with ASP 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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57A GLY 2.8 20.6 + - - +
58A LYS* 3.6 7.9 - - - +
59A PHE 3.3 0.2 - - - -
60A GLU* 1.3 74.3 - - - +
62A MET* 1.3 67.8 + - - +
64A LYS* 3.1 40.7 + - - +
65A ALA* 3.2 11.3 + - - +
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Residues in contact with MET 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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17A PHE* 4.0 14.4 - - + -
21A THR* 4.9 11.9 - - + +
58A LYS* 3.1 21.6 + - + +
59A PHE* 3.4 46.9 - - + +
61A ASP* 1.3 79.7 - - - +
63A ALA* 1.3 62.7 + - - +
65A ALA* 3.2 9.2 + - - +
66A ASP* 3.1 22.0 + - - +
69A ARG* 5.5 0.2 + - - -
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Residues in contact with ALA 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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11A LYS* 5.9 0.2 - - - -
12A MET 3.8 22.7 - - - +
13A SER* 5.0 0.2 - - - -
14A SER 4.2 10.5 - - - +
17A PHE* 3.6 22.3 - - + -
59A PHE 2.9 14.5 + - - +
60A GLU* 3.1 15.0 + - - +
62A MET* 1.3 76.4 - - - +
64A LYS* 1.3 52.2 + - - +
66A ASP* 3.7 0.9 - - - +
67A LYS* 2.7 37.2 + - - +
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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 GLU* 2.9 29.6 + - + +
61A ASP* 3.1 38.4 + - - +
63A ALA* 1.3 76.6 - - + +
65A ALA* 1.3 61.6 + - - +
67A LYS* 3.4 10.9 + - - +
68A ALA* 3.1 23.9 + - - +
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Residues in contact with ALA 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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61A ASP* 3.2 8.5 + - - +
62A MET* 3.2 13.1 + - - +
64A LYS* 1.3 79.2 - - - +
66A ASP* 1.3 61.2 + - - +
68A ALA* 3.6 6.0 + - - +
69A ARG* 3.2 34.8 + - - +
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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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8A PRO* 5.9 0.5 - - - +
9A ARG* 3.2 36.7 + - - +
10A GLY 4.0 6.1 + - - +
17A PHE* 3.4 37.0 - - + -
20A GLN* 5.0 0.7 + - - -
62A MET 3.1 7.0 + - - +
63A ALA 3.8 0.2 - - - +
65A ALA* 1.3 75.1 - - - +
67A LYS* 1.3 56.7 + - - +
69A ARG* 2.7 34.3 + - - +
70A TYR* 2.7 37.2 + - - +
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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
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10A GLY 4.5 6.0 + - - -
11A LYS* 3.7 41.3 - - + +
63A ALA 2.7 18.9 + - - +
64A LYS* 3.5 10.1 - - - +
66A ASP* 1.3 76.7 - - - +
68A ALA* 1.3 60.9 + - + +
70A TYR* 3.2 9.5 - - - +
71A GLU* 2.6 64.7 + - - +
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Residues in contact with ALA 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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64A LYS 3.1 15.7 + - - +
65A ALA* 3.9 6.3 - - - +
67A LYS* 1.3 75.5 - - + +
69A ARG* 1.3 66.3 + - - +
71A GLU* 3.2 17.6 + - - +
72A ARG* 3.1 26.8 + - - +
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Residues in contact with ARG 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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9A ARG* 5.8 0.2 - - - +
65A ALA* 3.2 27.8 + - - +
66A ASP* 2.7 45.5 + - - +
68A ALA* 1.3 74.6 - - - +
70A TYR* 1.3 65.2 + - - +
72A ARG* 3.3 34.5 + - - +
73A GLU* 3.3 21.3 + - - +
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Residues in contact with TYR 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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7A LYS* 3.4 31.5 + - + +
8A PRO* 3.6 39.4 - - + +
10A GLY* 3.5 37.7 - - - +
11A LYS* 3.4 33.9 - - + -
66A ASP* 2.7 14.4 + - - +
67A LYS* 3.2 10.3 - - - +
69A ARG* 1.3 76.7 - - - +
71A GLU* 1.3 54.4 + - + +
73A GLU* 3.1 3.5 + - - +
74A MET* 2.7 72.3 + - + +
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Residues in contact with GLU 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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11A LYS* 4.8 10.7 + - + -
67A LYS* 2.6 56.5 + - + +
68A ALA* 3.2 14.1 + - - +
70A TYR* 1.3 78.3 - - + +
72A ARG* 1.3 62.6 + - - +
74A MET* 3.3 15.1 + - + +
75A LYS* 3.3 39.0 + - - +
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Residues in contact with ARG 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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68A ALA* 3.1 15.0 + - - +
69A ARG* 3.3 39.4 - - - +
71A GLU* 1.3 79.0 - - - +
73A GLU* 1.3 61.7 + - + +
75A LYS* 3.7 14.4 + - - +
76A THR* 3.8 10.4 + - - +
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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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6A LYS 5.2 2.3 - - - +
8A PRO* 3.3 34.9 - - + +
69A ARG 3.3 7.9 + - - +
70A TYR 3.1 6.5 + - - +
72A ARG* 1.3 78.0 - - + +
74A MET* 1.3 65.4 + - - +
75A LYS 3.1 2.5 - - - -
76A THR* 2.8 28.8 + - - +
77A TYR* 2.9 21.4 + - + +
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Residues in contact with MET 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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4A ASP* 5.4 1.3 - - - +
7A LYS* 5.3 7.6 - - + -
8A PRO* 5.4 2.7 - - + +
70A TYR* 2.7 58.9 + - + +
71A GLU* 3.3 13.4 + - + +
73A GLU* 1.3 72.9 - - - +
75A LYS* 1.3 69.0 + - + +
77A TYR* 3.2 47.5 + - + +
79A PRO* 6.5 0.2 - - + -
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Residues in contact with LYS 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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71A GLU* 3.3 40.4 + - - +
72A ARG* 3.9 9.2 - - - +
73A GLU 3.1 0.6 - - - -
74A MET* 1.3 85.1 - - + +
76A THR* 1.3 62.5 + - + +
77A TYR 3.2 6.5 + - - +
78A ILE* 5.6 0.7 - - - +
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Residues in contact with THR 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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72A ARG 4.2 8.1 - - - +
73A GLU* 2.8 32.9 + - - +
75A LYS* 1.3 78.9 - - + +
77A TYR* 1.3 57.4 + - - +
78A ILE* 3.5 16.9 - - - +
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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
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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