Contacts of the helix formed by residues 60 - 76 (chain A) in PDB entry 2NAQ
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 ASN 60 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A CYS* 5.9 4.0 - - - -
39A LEU* 5.5 13.6 - - - +
55A LEU 3.9 9.0 - - - +
56A MET* 3.2 19.5 + - - +
59A PHE* 1.3 92.9 - - - +
61A GLY* 1.3 60.5 + - - +
64A LYS* 3.3 52.4 + - + +
65A ALA* 4.1 16.2 - - - +
68A MET* 5.5 4.2 - - - +
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Residues in contact with GLY 61 (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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56A MET 3.0 6.0 + - - -
57A ILE* 3.2 19.4 + - - -
58A ASP 4.4 1.1 - - - -
59A PHE 3.6 1.0 - - - -
60A ASN* 1.3 79.1 - - - +
62A GLU* 1.3 61.1 + - - -
63A GLU 3.3 3.1 - - - -
65A ALA* 2.8 30.6 + - - +
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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
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4A THR* 4.6 14.5 + - - +
8A LEU* 4.7 2.4 - - - +
57A ILE* 4.0 39.4 + - + +
61A GLY* 1.3 73.2 - - - -
63A GLU* 1.3 62.5 + - - +
65A ALA* 4.4 0.9 - - - +
66A TRP* 2.5 77.8 + - + +
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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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61A GLY* 3.3 0.6 - - - -
62A GLU* 1.3 82.5 - - - +
64A LYS* 1.3 68.4 + - - +
66A TRP* 3.6 4.6 + - - +
67A ALA* 3.4 19.3 + - - +
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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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33A GLN* 5.1 13.2 - - - +
36A CYS* 5.4 11.8 - - - -
60A ASN* 3.3 47.3 + - + +
61A GLY 3.8 1.4 + - - -
63A GLU* 1.3 83.9 + - - +
65A ALA* 1.3 69.0 + - - +
67A ALA* 3.0 19.0 + - + +
68A MET* 3.1 35.6 + - + +
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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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56A MET* 3.5 38.2 - - + +
57A ILE* 4.5 4.0 - - + +
60A ASN* 4.1 6.8 - - - +
61A GLY 2.8 23.7 + - - +
62A GLU* 4.2 5.6 - - - +
64A LYS* 1.3 77.9 - - - +
66A TRP* 1.3 68.5 + - + +
68A MET* 3.1 9.2 + - - +
69A ALA* 2.9 20.7 + - - +
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Residues in contact with TRP 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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4A THR* 4.8 8.9 - - + +
8A LEU* 4.6 15.9 - - + +
62A GLU* 2.5 57.3 + - + +
63A GLU* 3.9 4.9 - - - +
64A LYS 3.2 0.6 - - - -
65A ALA* 1.3 79.8 - - + +
67A ALA* 1.3 65.3 + - - +
69A ALA* 3.0 9.7 + - + +
70A VAL* 2.9 27.6 + - - +
89A GLU* 2.7 51.5 + - + +
90A PRO* 3.5 38.4 - - + -
91A LYS 5.8 1.3 - - - -
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Residues in contact with ALA 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 GLU* 3.4 15.8 + - - +
64A LYS* 3.0 17.3 + - + +
66A TRP* 1.3 78.1 - - - +
68A MET* 1.3 63.1 + - + +
70A VAL* 3.3 9.4 - - - +
71A TRP* 3.1 26.9 + - - +
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Residues in contact with MET 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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27A LEU* 4.5 19.5 - - + -
30A TYR* 3.6 48.5 - - + -
33A GLN* 5.7 1.6 - - - -
39A LEU* 6.2 2.9 - - + -
56A MET* 4.8 10.3 - - + -
60A ASN* 5.5 4.3 - - - +
64A LYS* 3.1 38.3 + - + +
65A ALA* 3.6 10.1 - - - +
67A ALA* 1.3 76.9 - - + +
69A ALA* 1.3 65.3 + - - +
71A TRP* 4.6 8.5 - - - -
72A ILE* 3.1 41.0 + - + +
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Residues in contact with ALA 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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8A LEU* 6.5 1.1 - - + -
23A PHE* 5.3 3.8 - - + -
56A MET* 5.0 9.6 - - + +
65A ALA 2.9 13.2 + - - +
66A TRP* 3.0 14.3 + - + +
68A MET* 1.3 79.9 - - - +
70A VAL* 1.3 59.9 + - - +
72A ILE* 3.6 3.9 + - - +
73A PHE* 2.8 49.5 + - + -
89A GLU* 6.1 0.4 - - - +
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Residues in contact with VAL 70 (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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66A TRP 2.9 15.0 + - - +
67A ALA* 3.3 18.6 - - - +
69A ALA* 1.3 74.8 - - - +
71A TRP* 1.3 80.4 + - + +
72A ILE 3.3 0.7 + - - -
73A PHE* 3.3 22.0 + - + +
74A ALA* 3.5 11.6 + - - +
82A TYR* 4.1 35.3 - - + +
85A ALA* 6.2 2.0 - - + -
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Residues in contact with TRP 71 (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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26A HIS* 3.6 31.9 - + - -
30A TYR* 5.2 17.0 - + - -
31A PRO* 6.5 0.7 - - + -
67A ALA 3.1 16.9 + - - +
68A MET* 4.3 9.0 - - - +
70A VAL* 1.3 85.0 - - + +
72A ILE* 1.3 73.2 + - + +
74A ALA* 3.7 8.8 + - + +
75A ALA* 3.5 23.7 + - + -
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Residues in contact with ILE 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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23A PHE* 3.6 50.7 - - + +
26A HIS* 4.2 24.0 - - + -
27A LEU* 4.2 23.3 - - + -
30A TYR* 6.3 1.8 - - + -
56A MET* 5.9 0.9 - - + -
68A MET* 3.1 34.3 + - + +
69A ALA 4.1 3.8 - - - +
70A VAL 3.2 0.2 - - - -
71A TRP* 1.3 91.5 - - + +
73A PHE* 1.3 67.6 + - + +
75A ALA* 2.9 19.3 + - - +
76A ILE* 3.2 14.6 + - + +
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Residues in contact with PHE 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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11A TYR* 6.2 5.2 - + + -
12A LEU* 5.7 6.3 - - + -
15A LEU* 5.6 6.7 - - + -
23A PHE* 4.2 20.4 - + - -
69A ALA* 2.8 40.8 - - + -
70A VAL* 3.3 17.6 + - + +
72A ILE* 1.3 81.1 - - + +
74A ALA* 1.3 64.4 + - - +
75A ALA 3.0 0.7 + - - -
76A ILE* 3.2 23.6 + - + +
78A ARG* 3.1 37.9 + - + +
81A LEU* 3.7 33.4 - - + -
82A TYR* 5.2 5.2 - - + +
85A ALA* 4.7 17.3 - - + -
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Residues in contact with ALA 74 (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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70A VAL 3.5 9.1 + - - +
71A TRP* 3.9 12.3 - - + +
72A ILE 3.3 0.6 - - - -
73A PHE* 1.3 78.6 - - - +
75A ALA* 1.3 62.8 + - - +
77A ASN* 3.3 14.0 + - - +
78A ARG 4.6 3.8 - - - +
79A ARG* 5.1 7.4 - - + +
82A TYR* 6.3 0.4 - - + +
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Residues in contact with ALA 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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26A HIS* 4.2 24.2 - - + +
71A TRP* 3.5 21.2 + - + +
72A ILE* 2.9 13.7 + - - +
74A ALA* 1.3 79.2 - - - +
76A ILE* 1.3 60.0 + - + +
77A ASN* 3.0 16.5 + - - -
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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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15A LEU* 4.6 8.7 - - + -
19A ASP* 3.5 35.2 - - - +
22A LYS* 5.0 19.3 - - + +
23A PHE* 5.4 5.4 - - + +
26A HIS* 5.7 6.3 - - + -
72A ILE* 3.5 20.6 - - + +
73A PHE* 3.3 22.2 - - + +
75A ALA* 1.3 77.1 - - + +
77A ASN* 1.3 74.4 + - - +
78A ARG* 3.8 16.6 - - + +
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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