Contacts of the helix formed by residues 55 - 70 (chain A) in PDB entry 1Y8M
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 VAL 55 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A THR 3.7 1.6 + - - -
54A ASP* 1.3 71.5 - - - +
56A ASN* 1.3 70.1 + - + +
57A ASP 3.2 1.1 - - - -
58A GLU* 3.2 7.1 + - + -
59A ARG* 3.1 25.7 + - + +
89A LYS 5.1 3.6 - - - +
90A LEU* 3.4 28.9 - - + -
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Residues in contact with ASN 56 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A ASP* 3.2 7.0 - - + +
55A VAL* 1.3 86.0 - - + +
57A ASP* 1.3 68.8 + - - +
59A ARG* 3.0 33.6 - - - +
60A LEU* 3.4 12.8 + - - +
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Residues in contact with ASP 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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22A LEU* 5.4 4.2 - - - +
49A LEU* 3.0 53.9 - - + +
52A SER* 3.3 26.6 + - - +
54A ASP* 3.7 14.4 + - - +
55A VAL 3.2 0.2 - - - -
56A ASN* 1.3 83.4 - - - +
58A GLU* 1.3 65.3 + - - +
60A LEU* 3.7 6.0 - - - +
61A GLY* 3.0 18.4 + - - -
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Residues in contact with GLU 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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49A LEU 2.4 20.0 - - - +
50A ILE* 3.4 26.4 - - + +
52A SER 2.5 23.5 - - - +
53A THR 4.1 1.9 - - - +
54A ASP 3.0 17.0 - - - +
55A VAL* 3.2 11.3 + - + +
57A ASP* 1.3 78.0 - - - +
59A ARG* 1.3 63.5 + - - +
61A GLY* 3.4 0.7 + - - -
62A VAL* 3.1 27.5 + - - +
86A GLY 4.8 3.1 - - - +
89A LYS* 3.7 33.0 - - + +
90A LEU* 3.8 19.5 - - + -
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Residues in contact with ARG 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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55A VAL* 3.1 17.2 + - + +
56A ASN* 3.0 36.2 - - - +
58A GLU* 1.3 77.7 - - - +
60A LEU* 1.3 62.1 + - + +
62A VAL* 3.9 4.3 - - - +
63A LYS* 3.5 21.3 + - - +
90A LEU* 4.2 18.8 - - + +
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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
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42A ARG* 6.0 1.3 - - - +
45A TYR* 4.7 10.8 - - + +
49A LEU* 3.8 28.7 - - + -
56A ASN* 3.7 16.8 - - - +
57A ASP* 3.4 6.9 + - - +
58A GLU 3.1 0.6 - - - -
59A ARG* 1.3 81.5 - - + +
61A GLY* 1.3 66.6 + - - +
63A LYS* 3.2 19.9 + - + +
64A ILE* 3.2 27.7 + - + +
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Residues in contact with GLY 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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46A ALA* 3.9 29.4 - - - -
49A LEU* 4.5 2.4 - - - +
50A ILE* 4.6 3.6 - - - -
57A ASP 3.0 16.0 + - - -
58A GLU 4.0 1.1 - - - -
60A LEU* 1.3 76.8 - - - +
62A VAL* 1.3 63.9 + - - +
64A ILE* 3.0 5.7 + - - +
65A LEU* 2.9 32.0 + - - +
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Residues in contact with VAL 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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50A ILE* 5.2 1.0 - - + +
58A GLU 3.1 19.7 + - - +
59A ARG* 3.9 7.9 - - - +
60A LEU 3.2 0.2 - - - -
61A GLY* 1.3 76.6 - - - +
63A LYS* 1.3 59.3 + - - +
65A LEU* 3.3 10.0 + - + +
66A THR* 2.5 39.8 + - - +
83A LEU* 4.0 8.4 - - + +
86A GLY* 3.9 31.9 - - - +
87A CYS* 4.2 15.5 - - - -
90A LEU* 3.9 13.2 - - + -
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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 ARG 3.5 11.5 + - - +
60A LEU* 3.2 22.3 + - + +
61A GLY 3.2 0.6 - - - -
62A VAL* 1.3 81.8 - - + +
64A ILE* 1.3 61.3 + - + +
66A THR* 3.3 6.1 + - - -
67A ASP* 2.5 44.0 + - - +
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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
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42A ARG* 3.5 49.6 - - + +
45A TYR* 3.8 16.8 - - + -
46A ALA* 3.7 17.5 - - + -
49A LEU* 4.2 12.6 - - + -
60A LEU* 3.2 22.9 + - + +
61A GLY 3.0 6.8 + - - +
63A LYS* 1.3 77.6 - - + +
65A LEU* 1.3 68.0 + - - +
67A ASP* 2.8 18.8 + - + +
68A ILE* 2.9 35.1 + - + +
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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
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43A PHE* 3.8 27.8 - - + +
46A ALA* 4.1 13.5 - - + -
50A ILE* 3.7 30.3 - - + -
61A GLY 2.9 19.7 + - - +
62A VAL* 3.7 3.6 - - + +
64A ILE* 1.3 78.9 - - - +
66A THR* 1.3 56.7 + - - +
68A ILE* 4.1 5.3 - - + +
69A TYR* 3.2 25.6 + - - +
79A CYS* 4.0 13.6 - - - +
82A TYR* 3.7 40.4 - - + +
83A LEU* 3.5 23.9 - - + +
86A GLY* 5.5 0.2 - - - -
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Residues in contact with THR 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 VAL* 2.5 29.3 + - - +
63A LYS* 3.7 7.0 - - - -
64A ILE 3.0 1.0 - - - -
65A LEU* 1.3 76.0 - - - +
67A ASP* 1.3 68.1 + - - +
69A TYR* 3.6 8.9 - - + +
70A LYS* 3.1 48.5 + - + +
83A LEU* 3.8 14.5 - - + +
99A TYR* 4.6 15.0 - - + +
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Residues in contact with ASP 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 LYS* 2.5 37.9 - - - +
64A ILE* 2.8 10.6 + - - +
66A THR* 1.3 80.2 - - - +
68A ILE* 1.3 60.4 + - + +
70A LYS* 3.2 19.1 + - - +
71A GLU* 2.9 36.7 + - - +
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Residues in contact with ILE 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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39A ILE* 3.3 33.7 - - + +
42A ARG* 4.1 9.6 - - + -
43A PHE* 3.7 35.7 - - + +
64A ILE* 2.9 38.7 + - + +
65A LEU* 4.2 7.9 - - + +
67A ASP* 1.3 77.6 - - + +
69A TYR* 1.3 54.3 + - - +
71A GLU* 4.8 2.5 - - - -
72A ALA* 2.7 45.4 + - + +
75A ARG* 4.8 4.0 - - - -
79A CYS* 4.6 12.0 - - - -
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Residues in contact with TYR 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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65A LEU 3.2 20.4 + - - +
66A THR* 3.6 11.0 - - + +
67A ASP 3.1 0.6 - - - -
68A ILE* 1.3 80.9 - - - +
70A LYS* 1.3 76.9 + - + +
71A GLU 3.5 0.3 + - - -
72A ALA* 3.6 11.7 - - - +
73A GLU* 5.3 0.3 - - - -
75A ARG 5.7 0.7 - - - -
76A ARG* 3.9 47.7 + - + +
79A CYS* 4.1 26.2 - - + -
80A LEU* 4.5 19.2 - - + +
83A LEU* 5.0 6.7 - - + -
99A TYR* 5.8 8.1 - + - -
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Residues in contact with LYS 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 THR* 3.1 38.7 + - + +
67A ASP* 3.9 16.5 + - - +
69A TYR* 1.3 92.2 - - + +
71A GLU* 1.3 59.1 + - + +
72A ALA 4.5 1.3 - - - +
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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
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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