Contacts of the helix formed by residues 52 - 71 (chain A) in PDB entry 4NAC
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 LYS 52 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A LYS 3.7 2.4 + - - +
51A ALA* 1.3 77.3 - - - +
53A PRO* 1.3 77.8 - - + +
54A ASN* 3.9 20.9 - - - +
55A ARG* 2.8 18.6 + - + +
56A LYS* 3.1 7.5 + - - +
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Residues in contact with PRO 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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51A ALA 3.7 1.8 - - - +
52A LYS* 1.3 88.2 - - + +
54A ASN* 1.3 58.2 + - - +
55A ARG 2.9 5.7 + - - -
56A LYS* 3.2 28.6 + - + +
57A LEU* 4.3 3.1 + - - +
95A GLU* 3.4 29.6 - - + +
96A THR* 3.6 21.5 - - + +
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Residues in contact with ASN 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ASN* 5.4 3.5 + - - -
52A LYS* 3.9 17.5 - - - +
53A PRO* 1.3 78.2 - - - +
55A ARG* 1.3 75.3 + - - +
57A LEU* 5.1 4.3 + - - +
58A THR* 4.9 1.2 + - - -
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Residues in contact with ARG 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LEU 6.0 1.1 - - - +
16A LEU* 3.5 21.1 + - - -
17A SER* 3.5 23.8 - - - +
18A ASN* 3.8 12.9 - - - +
51A ALA* 4.2 9.6 - - + -
52A LYS* 2.8 14.7 + - + +
54A ASN* 1.3 90.1 + - - +
56A LYS* 1.3 65.9 + - - +
57A LEU 3.2 2.9 - - - -
58A THR* 3.0 43.2 + - - -
59A PHE* 3.6 22.4 - - + -
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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
----------------------------------------------------------
48A LEU* 3.1 32.5 + - + +
49A ARG 3.2 10.3 + - - -
51A ALA* 2.8 27.5 + - - +
52A LYS 3.1 10.5 + - - +
53A PRO* 3.2 23.7 + - + +
55A ARG* 1.3 78.5 - - - +
57A LEU* 1.3 63.6 + - - +
59A PHE* 3.0 22.0 + - - +
60A LEU* 3.5 6.2 + - - +
91A HIS* 2.9 39.3 + - + +
92A VAL* 4.1 20.0 - - + -
95A GLU* 3.9 25.4 - - + -
96A THR* 4.9 1.1 - - + -
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Residues in contact with LEU 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ASN* 6.0 1.1 - - - +
53A PRO 4.3 2.8 + - - +
54A ASN 5.6 3.6 - - - +
55A ARG 3.2 1.2 - - - -
56A LYS* 1.3 78.4 - - - +
58A THR* 1.3 64.6 + - - +
60A LEU* 3.1 10.2 + - + +
61A TYR* 3.0 40.7 + - + +
92A VAL* 4.0 9.6 - - + -
96A THR* 5.2 5.6 - - + -
100A CYS* 4.6 17.5 - - + +
103A HIS* 3.4 44.0 - - + -
104A LEU* 3.9 36.8 - - + +
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Residues in contact with THR 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LEU* 3.6 31.0 - - + -
17A SER* 3.6 16.2 - - - +
18A ASN* 2.7 30.0 + - - +
23A VAL* 4.9 4.6 - - + +
54A ASN 4.9 0.9 + - - -
55A ARG* 3.0 40.1 + - - +
57A LEU* 1.3 80.4 - - - +
59A PHE* 1.3 55.4 + - - +
61A TYR* 3.3 5.9 + - + +
62A LEU* 3.0 27.7 + - - +
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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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13A LEU* 4.0 37.2 - - + -
16A LEU* 4.5 9.2 - - + -
44A TRP* 3.0 43.5 + + + +
47A GLU* 3.6 27.6 - - + -
48A LEU* 3.5 37.9 - - + -
51A ALA* 3.9 21.8 - - + -
55A ARG* 3.6 23.3 - - + -
56A LYS 3.0 9.9 + - - +
58A THR* 1.3 79.2 - - - +
60A LEU* 1.3 56.5 + - - +
62A LEU* 3.5 4.6 + - - +
63A ALA 3.0 21.5 + - - -
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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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44A TRP* 4.1 23.1 - - + -
48A LEU* 5.1 0.9 - - + -
56A LYS 3.5 3.1 + - - +
57A LEU* 3.1 13.2 + - + +
59A PHE* 1.3 76.2 - - + +
61A TYR* 1.3 63.9 + - + +
63A ALA* 3.6 3.5 - - + +
64A ASN* 2.8 29.5 + - - +
85A ILE* 4.3 6.3 - - + -
88A ALA* 4.4 7.6 - - + -
89A PHE* 4.0 34.8 - - + -
92A VAL* 3.8 24.9 - - + -
104A LEU* 3.2 35.2 - - + -
107A VAL* 5.0 9.8 - - + +
111A TRP* 5.2 1.7 - - + -
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Residues in contact with TYR 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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18A ASN* 3.6 31.9 - - + -
23A VAL* 4.4 13.4 - - + +
57A LEU* 3.0 37.8 + - + +
58A THR* 3.5 6.3 - - - +
60A LEU* 1.3 76.9 - - + +
62A LEU* 1.3 62.6 + - - +
64A ASN* 3.3 10.3 + - + +
65A ASP* 3.0 22.3 + - - +
103A HIS* 3.2 27.6 + - + +
106A ARG* 2.8 33.1 + - - -
107A VAL* 4.0 22.7 - - + -
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Residues in contact with LEU 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LEU* 3.8 18.6 - - + -
16A LEU* 4.0 11.4 - - + -
23A VAL* 3.9 35.1 - - + +
26A LEU* 3.6 32.3 - - + -
27A SER* 4.0 9.2 - - - +
30A LEU* 4.2 7.9 - - + -
44A TRP* 4.1 14.4 - - + +
58A THR 3.0 12.9 + - - +
59A PHE 3.5 7.6 - - - +
61A TYR* 1.3 76.7 - - - +
63A ALA* 1.3 58.5 + - - +
65A ASP* 3.0 3.3 + - - +
66A VAL* 2.8 49.9 + - + +
81A PHE* 6.5 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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44A TRP* 3.8 20.6 - - + +
59A PHE 3.0 17.9 + - - +
60A LEU* 3.3 6.7 + - - +
62A LEU* 1.3 76.4 - - - +
64A ASN* 1.3 54.4 + - - +
66A VAL* 4.5 2.0 - - - -
67A ILE* 2.7 47.1 + - + +
81A PHE* 3.9 25.8 - - + -
85A ILE* 4.7 7.0 - - + -
111A TRP* 5.2 1.6 - - + -
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Residues in contact with ASN 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 LEU 2.8 17.6 + - - +
61A TYR* 3.4 14.5 + - - +
63A ALA* 1.3 73.3 - - - +
65A ASP* 1.3 65.4 + - - +
67A ILE* 4.1 0.4 - - - +
68A GLN* 3.0 46.2 + - - +
107A VAL* 4.3 16.5 - - + +
110A ILE* 4.5 14.1 - - - +
111A TRP* 2.8 39.8 + - - +
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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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23A VAL* 4.0 20.1 - - + +
24A GLN* 4.7 12.8 - - - +
27A SER* 2.7 31.7 + - - +
61A TYR 3.0 13.2 + - - +
62A LEU 3.5 6.5 - - - +
64A ASN* 1.3 81.0 - - - +
66A VAL* 1.3 59.5 + - - +
68A GLN* 5.1 0.9 - - - -
69A ASN* 2.9 52.2 + - - +
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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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27A SER* 3.6 31.4 - - - +
30A LEU* 3.9 20.2 - - + -
31A ILE* 3.9 7.0 - - + +
62A LEU* 2.8 25.7 + - + +
63A ALA* 3.8 6.1 - - - +
65A ASP* 1.3 74.1 - - - +
67A ILE* 1.3 67.0 + - - +
70A SER* 2.9 29.1 + - - -
77A PHE* 3.6 44.6 - - + -
81A PHE* 4.1 7.9 - - + -
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Residues in contact with ILE 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 ALA* 2.7 27.2 + - + +
64A ASN* 4.1 2.7 - - - +
66A VAL* 1.3 71.8 - - - +
68A GLN* 1.3 64.3 + - + +
70A SER* 2.7 21.2 + - - -
71A LYS* 3.4 10.7 - - - +
77A PHE* 4.3 4.5 - - - +
78A THR* 3.9 15.9 + - - +
81A PHE* 3.4 37.9 - - + -
85A ILE* 4.8 1.1 - - + -
111A TRP* 4.0 24.9 - - + -
116A VAL* 3.7 26.9 - - + -
117A TYR* 3.5 25.8 - - + +
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Residues in contact with GLN 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 ASN* 3.0 42.4 + - - +
65A ASP* 4.3 1.6 - - - +
67A ILE* 1.3 80.8 - - - +
69A ASN* 1.3 67.1 + - - +
70A SER 3.3 0.7 + - - -
71A LYS* 3.4 25.9 + - - +
72A ARG 4.6 0.7 + - - -
110A ILE* 3.6 15.5 - - - +
111A TRP* 4.6 0.4 - - - +
114A ARG* 2.9 38.6 + - - +
116A VAL* 3.7 33.7 - - + +
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Residues in contact with ASN 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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27A SER* 4.8 0.2 - - - +
28A LEU* 6.6 0.2 - - + -
31A ILE* 3.6 18.4 - - + +
65A ASP* 2.9 41.4 + - - +
68A GLN* 1.3 81.7 + - - +
70A SER* 1.3 60.2 + - - +
71A LYS 3.3 0.6 + - - -
72A ARG* 3.8 21.3 + - - +
73A LYS* 4.6 2.6 + - - +
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Residues in contact with SER 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ILE* 3.6 17.5 - - - +
34A ARG* 5.7 1.5 - - - -
66A VAL 2.9 16.6 + - - -
67A ILE* 2.7 20.3 + - - -
69A ASN* 1.3 73.7 - - - +
71A LYS* 1.3 60.9 + - - +
72A ARG 3.1 3.1 - - - -
73A LYS* 2.8 21.6 + - - +
74A GLY 3.0 19.1 + - - +
76A GLU* 5.2 1.1 - - - +
77A PHE* 3.5 34.4 - - - +
78A THR* 4.3 4.5 + - - -
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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
----------------------------------------------------------
67A ILE* 3.4 15.9 - - - +
68A GLN* 3.6 18.6 - - - +
69A ASN 3.3 1.0 - - - -
70A SER* 1.3 79.1 + - - +
72A ARG* 1.3 61.8 + - - +
73A LYS 3.3 0.9 + - - -
74A GLY* 3.5 17.6 + - - +
75A PRO* 6.4 0.2 - - + -
78A THR* 3.0 29.7 + - - +
114A ARG 6.1 0.2 - - - -
115A SER 5.0 2.1 + - - -
116A VAL* 3.0 49.9 + - - +
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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
------------------------------------------------------------
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