Contacts of the helix formed by residues 65 - 78 (chain A) in PDB entry 2N57
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 THR 65 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A GLU* 3.1 19.9 + - - +
26A GLY* 4.2 8.7 - - - +
27A ALA 3.2 8.7 - - - -
28A SER* 3.0 27.8 - - - +
29A PHE* 3.7 6.0 - - - -
63A ILE* 4.3 0.2 - - - +
64A LEU* 1.3 77.6 + - + +
66A VAL* 1.3 66.8 + - - +
67A GLY* 4.3 0.5 - - - -
68A ASP* 2.8 46.8 + - - +
69A ALA* 3.3 4.0 + - - +
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Residues in contact with VAL 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 VAL* 4.8 3.1 - - + -
9A LYS* 4.4 11.0 - - + +
12A VAL* 5.9 0.2 - - + -
23A VAL* 3.7 27.8 - - + -
24A THR 3.2 25.6 - - - +
25A GLU* 3.8 0.9 + - - +
27A ALA* 2.9 25.0 + - + +
29A PHE* 3.2 33.8 - - + -
65A THR* 1.3 71.9 - - - +
67A GLY* 1.3 64.8 + - - +
68A ASP 3.0 0.5 + - - -
69A ALA* 3.1 2.3 + - - +
70A VAL* 2.8 46.3 + - + +
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Residues in contact with GLY 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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25A GLU* 3.4 33.2 + - - +
65A THR* 3.2 1.5 - - - -
66A VAL* 1.3 79.9 - - - +
68A ASP* 1.3 58.2 + - - +
70A VAL* 4.5 4.9 - - - -
71A LYS* 2.9 45.6 + - - +
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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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62A THR 3.8 9.7 - - - +
63A ILE* 3.7 10.1 - - + -
64A LEU* 3.2 24.0 + - - +
65A THR* 2.8 39.8 + - - +
67A GLY* 1.3 75.0 - - - +
69A ALA* 1.3 59.3 + - - +
71A LYS* 3.8 6.7 - - - +
72A PHE* 2.9 33.6 + - - +
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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 VAL* 4.8 2.9 - - + -
29A PHE* 4.4 13.0 - - + -
44A VAL* 5.8 1.1 - - + -
47A PHE* 4.7 15.5 - - + -
63A ILE* 3.3 32.8 - - + +
65A THR 3.3 3.9 + - - +
66A VAL 3.1 7.0 + - - +
68A ASP* 1.3 78.7 - - - +
70A VAL* 1.3 63.6 + - - +
72A PHE* 3.3 3.1 + - - +
73A ILE* 3.0 37.4 + - + +
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Residues in contact with VAL 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A THR* 3.5 14.5 - - + +
5A ALA* 3.4 40.4 - - + +
8A VAL* 3.4 34.3 - - + -
9A LYS* 5.1 1.1 - - + -
66A VAL* 2.8 40.3 + - + +
67A GLY* 4.0 4.5 - - - +
69A ALA* 1.3 72.2 - - - +
71A LYS* 1.3 65.6 + - + +
72A PHE 3.2 0.2 + - - -
73A ILE* 3.2 2.1 + - - +
74A ASP* 2.9 20.5 + - + +
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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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25A GLU* 4.6 16.8 + - - -
67A GLY* 2.9 34.3 + - - +
68A ASP* 3.8 7.6 - - - +
70A VAL* 1.3 74.6 - - + +
72A PHE* 1.3 57.3 + - - +
74A ASP* 3.5 6.9 + - - +
75A LYS* 2.9 48.5 + - - +
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Residues in contact with PHE 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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55A ILE* 3.4 32.1 - - + -
56A PRO* 4.8 7.0 - - + -
59A ALA* 3.2 31.6 - - + -
62A THR* 3.3 19.5 - - + -
63A ILE* 3.6 24.7 - - + -
68A ASP* 2.9 16.6 + - + +
69A ALA* 3.4 7.4 - - - +
70A VAL 3.1 0.2 - - - -
71A LYS* 1.3 74.2 - - - +
73A ILE* 1.3 67.7 + - + +
75A LYS* 3.0 11.2 + - + +
76A ALA* 2.9 25.2 + - + +
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Residues in contact with ILE 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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4A THR* 4.3 2.5 - - + -
8A VAL* 3.5 24.5 - - + -
47A PHE* 3.4 43.1 - - + +
48A GLU* 5.4 0.7 - - - +
51A PHE* 3.4 49.8 - - + -
53A VAL* 4.7 6.9 - - + +
55A ILE* 6.3 3.6 - - + -
63A ILE* 6.5 0.7 - - + -
69A ALA 3.0 21.3 + - - +
70A VAL 3.7 2.9 - - - +
72A PHE* 1.3 75.8 - - + +
74A ASP* 1.3 54.2 + - - +
76A ALA* 3.8 4.5 - - - +
77A SER* 2.8 35.5 + - - -
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Residues in contact with ASP 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 THR* 2.8 31.9 + - + +
70A VAL* 2.9 16.2 + - + +
71A LYS* 3.7 7.0 - - - +
73A ILE* 1.3 74.8 - - - +
75A LYS* 1.3 67.0 - - + +
77A SER* 3.4 18.8 + - - -
78A ALA* 3.6 8.0 + - - +
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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 LYS* 2.9 36.3 + - - +
72A PHE* 3.4 11.7 - - + +
74A ASP* 1.3 80.1 - - + +
76A ALA* 1.3 60.7 + - - +
78A ALA* 3.4 16.7 + - - +
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Residues in contact with ALA 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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53A VAL* 3.5 31.7 - - + +
54A GLU 5.1 3.1 - - - +
55A ILE* 4.0 22.9 - - + -
72A PHE* 2.9 16.6 + - + +
73A ILE* 4.2 1.3 - - - +
75A LYS* 1.3 72.6 - - - +
77A SER* 1.3 65.7 + - - +
78A ALA 3.1 9.7 + - - -
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Residues in contact with SER 77 (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 PHE* 4.5 19.6 - - - -
53A VAL* 3.8 11.3 - - - +
73A ILE 2.8 21.0 + - - -
74A ASP* 3.4 16.5 + - - -
75A LYS 3.2 0.2 - - - -
76A ALA* 1.3 78.1 - - - +
78A ALA* 1.3 59.7 + - - +
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Residues in contact with ALA 78 (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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74A ASP 3.6 6.2 + - - +
75A LYS* 3.4 13.8 + - - +
76A ALA 3.1 9.2 - - - -
77A SER* 1.3 83.8 - - - +
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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