Contacts of the helix formed by residues 63 - 76 (chain A) in PDB entry 1NOY
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 MET 63 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A LEU* 4.1 18.2 - - + -
62A SER* 1.3 70.7 - - - +
64A LYS* 1.3 63.8 + - - +
65A ASP 3.2 0.2 - - - -
66A ALA* 3.6 9.7 - - + +
67A ARG* 3.0 62.0 + - - +
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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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62A SER* 3.1 12.2 + - - +
63A MET* 1.3 78.5 - - - +
65A ASP* 1.3 60.2 + - - +
67A ARG* 3.4 13.5 + - + +
68A ASP* 3.0 61.7 + - - +
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Residues in contact with ASP 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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60A PHE* 3.8 18.4 - - + -
61A PRO* 3.0 31.3 - - + +
62A SER* 3.1 23.0 + - - +
64A LYS* 1.3 78.1 - - - +
66A ALA* 1.3 63.8 - - - +
68A ASP* 3.0 14.8 + - - +
69A TRP* 2.9 24.3 + - - +
72A ARG* 4.3 2.2 + - - +
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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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34A LEU* 3.9 23.0 - - + +
35A PRO* 3.8 23.3 - - + +
60A PHE* 3.7 21.4 - - + -
62A SER 3.4 2.2 + - - +
63A MET* 3.4 16.3 + - + +
65A ASP* 1.3 77.5 - - - +
67A ARG* 1.3 58.8 + - - +
69A TRP* 3.4 3.6 + - - +
70A MET* 2.9 31.2 + - - +
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Residues in contact with ARG 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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34A LEU* 3.6 25.5 - - + +
63A MET* 3.0 45.1 + - - +
64A LYS* 3.5 15.7 - - + +
66A ALA* 1.3 74.5 - - - +
68A ASP* 1.3 67.2 - - - +
70A MET* 3.8 7.0 - - - +
71A LYS* 3.0 25.5 + - - +
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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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64A LYS* 3.0 51.9 + - - +
65A ASP* 3.0 16.5 + - - +
67A ARG* 1.3 78.8 - - - +
69A TRP* 1.3 62.6 + - - +
71A LYS* 3.2 7.9 + - - +
72A ARG* 3.0 38.9 + - - +
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Residues in contact with TRP 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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35A PRO* 3.7 20.4 - - + -
37A MET 5.3 0.9 - - - -
38A PHE* 3.8 31.5 - + + +
39A ARG 4.7 5.4 + - - -
42A LYS* 5.9 0.6 - - + +
43A GLU* 3.2 32.1 + - - +
60A PHE* 3.5 23.1 - + + -
65A ASP 2.9 7.6 + - - +
66A ALA 3.6 3.1 - - - +
68A ASP* 1.3 76.1 - - - +
70A MET* 1.3 94.9 + - + +
72A ARG* 2.8 39.6 + - - +
73A MET* 3.0 35.5 + - + +
82A GLY* 3.5 43.1 - - - -
83A MET* 5.7 0.2 - - + -
85A ASP* 5.0 4.9 - - + -
86A PHE* 4.4 11.9 - + + -
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Residues in contact with MET 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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13A ASN* 3.4 42.7 + - + +
33A TYR 4.4 1.3 - - - +
34A LEU* 4.2 12.6 - - + -
35A PRO* 3.1 36.3 - - + -
66A ALA 2.9 15.3 + - - +
67A ARG* 3.8 8.7 - - - +
69A TRP* 1.3 94.7 - - + +
71A LYS* 1.3 57.0 + - - +
73A MET* 3.3 19.2 - - - +
74A GLU* 4.1 3.3 + - - +
83A MET* 4.8 7.4 - - - -
86A PHE* 3.4 30.1 - - + -
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Residues in contact with LYS 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 ARG 3.0 17.2 + - - +
68A ASP* 3.6 5.6 - - - +
69A TRP 3.0 0.2 - - - -
70A MET* 1.3 74.5 - - - +
72A ARG* 1.3 65.7 + - - +
73A MET 3.1 2.0 + - - -
74A GLU* 3.6 7.4 + - + +
75A ASP* 3.6 15.4 + - - +
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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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38A PHE* 5.9 2.4 - - - -
43A GLU* 3.9 23.8 + - + +
60A PHE* 5.4 1.8 - - - -
65A ASP 4.3 2.2 + - - -
68A ASP* 3.0 21.3 + - - +
69A TRP* 2.8 45.9 + - + +
71A LYS* 1.3 74.8 - - - +
73A MET* 1.3 72.2 + - + +
75A ASP* 2.7 33.8 + - - +
76A ILE* 2.8 17.2 + - + +
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Residues in contact with MET 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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13A ASN* 5.3 3.6 - - - +
43A GLU* 4.2 17.5 - - + -
69A TRP* 3.0 61.3 + - + +
70A MET* 3.3 19.3 - - - +
72A ARG* 1.3 79.1 - - + +
74A GLU* 1.3 58.6 + - - +
76A ILE* 2.8 23.3 + - + +
77A GLY 2.8 29.2 + - - +
80A ALA* 4.2 13.6 - - + +
82A GLY* 4.0 18.6 - - - +
83A MET* 4.3 20.0 - - + +
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Residues in contact with GLU 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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13A ASN* 5.8 5.8 - - - +
70A MET 4.1 3.0 + - - +
71A LYS* 3.6 10.8 + - + +
72A ARG 3.3 0.6 - - - -
73A MET* 1.3 72.7 - - - +
75A ASP* 1.3 59.5 + - - +
76A ILE 2.9 4.7 - - - -
77A GLY* 2.9 32.0 + - - +
78A LEU* 4.5 4.0 + - - -
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Residues in contact with ASP 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 LYS 3.6 10.9 + - - +
72A ARG* 2.7 32.3 + - - +
74A GLU* 1.3 78.1 - - - +
76A ILE* 1.3 70.9 + - - +
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Residues in contact with ILE 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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43A GLU* 4.6 24.2 - - + +
46A LYS* 5.9 6.5 - - - -
72A ARG* 2.8 20.9 + - + +
73A MET* 2.8 24.0 + - + +
75A ASP* 1.3 97.3 - - - +
77A GLY* 1.3 54.9 + - - +
80A ALA* 3.7 24.5 - - + -
81A LEU 5.4 0.7 - - - +
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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