Contacts of the helix formed by residues 45 - 65 (chain A) in PDB entry 1NRX
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 45 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ASP* 1.3 70.1 - - - +
46A ASN* 1.3 72.3 + - - +
49A SER* 3.0 25.3 + - - -
76A ASN* 4.2 26.1 - - + +
77A ARG 3.2 13.4 + - - +
78A PRO* 5.1 2.2 - - + -
79A PRO* 3.3 21.1 - - - +
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Residues in contact with ASN 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ASP* 3.0 11.7 + - - +
45A THR* 1.3 88.1 + - - +
47A ILE* 1.3 64.1 + - - +
49A SER* 3.2 12.9 + - - -
50A ILE* 3.5 14.0 - - + +
79A PRO* 3.2 32.3 - - - +
400A NAD 3.2 26.6 + - - +
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Residues in contact with ILE 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A THR* 2.6 31.0 - - - +
44A ASP* 2.7 28.7 - - - +
46A ASN* 1.3 78.1 - - - +
48A GLY* 1.3 69.3 + - - +
50A ILE* 3.1 15.6 + - - +
51A TYR* 3.1 41.9 + - + +
112A LEU* 3.9 11.0 - - + +
113A GLY* 4.6 3.1 - - - -
139A THR* 3.5 38.8 - - + +
400A NAD 3.9 25.3 + - + +
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Residues in contact with GLY 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A THR* 3.4 15.0 - - - -
44A ASP 2.6 23.1 + - - -
45A THR 3.9 0.2 - - - -
47A ILE* 1.3 71.2 - - - +
49A SER* 1.3 52.6 + - - +
50A ILE 2.6 11.4 + - - -
51A TYR 2.7 1.6 + - - -
52A THR* 2.6 47.7 + - - -
76A ASN* 4.3 3.1 - - - -
112A LEU* 5.2 2.0 - - - -
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Residues in contact with SER 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A THR* 3.0 15.3 + - - -
46A ASN* 3.2 12.0 + - - -
48A GLY* 1.3 68.8 - - - -
50A ILE* 1.3 66.5 + - - +
52A THR* 3.9 1.8 + - - -
53A PRO* 3.9 18.3 - - - +
76A ASN* 4.7 4.8 - - - +
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Residues in contact with ILE 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ASN 3.5 18.6 - - - +
47A ILE 3.4 6.3 - - - +
48A GLY 2.6 6.7 + - - -
49A SER* 1.3 82.5 - - - +
51A TYR* 1.3 86.4 + - + +
53A PRO* 4.7 2.6 - - - +
54A SER* 5.6 1.6 - - - -
182A THR* 4.1 17.5 - - + -
400A NAD 4.0 24.9 - - + -
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Residues in contact with TYR 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A TRP* 3.2 38.9 + + + +
47A ILE* 3.1 35.2 + - + +
48A GLY 2.7 9.5 + - - -
50A ILE* 1.3 96.8 - - + +
52A THR* 1.3 63.8 + - - +
53A PRO* 3.5 2.8 - - - -
54A SER* 3.5 13.7 + - - -
55A PHE 3.7 0.9 + - - -
112A LEU* 4.6 8.3 - - + -
178A GLU* 3.9 8.6 + - + -
179A PHE* 3.6 44.8 + + + -
181A GLU* 4.8 3.1 + - - +
182A THR* 2.5 39.3 + - + +
400A NAD 4.2 0.4 - - - -
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Residues in contact with THR 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LEU* 4.7 10.0 - - + +
43A THR* 4.1 7.8 - - - +
48A GLY* 2.6 41.8 + - - -
49A SER* 4.7 1.1 - - - -
51A TYR* 1.3 70.8 - - - +
53A PRO* 1.4 70.1 - - - +
55A PHE* 3.1 17.5 + - - +
56A GLU* 3.2 16.6 + - - +
74A ILE* 3.7 40.6 - - + -
76A ASN* 4.4 5.5 + - - +
112A LEU* 5.1 3.4 - - - +
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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
----------------------------------------------------------
48A GLY 4.0 0.2 - - - +
49A SER* 3.9 21.3 - - - +
50A ILE 4.7 2.2 - - - +
51A TYR 3.6 3.1 - - - +
52A THR* 1.4 96.9 - - + +
54A SER* 1.3 62.3 + - - +
56A GLU* 3.3 26.7 + - - +
57A GLU* 3.3 12.6 + - - +
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Residues in contact with SER 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A TRP* 4.0 12.0 - - - -
23A ARG* 3.8 28.6 - - - +
50A ILE 5.6 1.1 + - - -
51A TYR* 3.5 15.8 + - - -
52A THR 3.3 0.4 + - - -
53A PRO* 1.3 78.7 - - - +
55A PHE* 1.3 57.6 + - - +
57A GLU* 3.2 10.1 - - - +
58A ALA* 2.9 24.4 + - - +
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Residues in contact with PHE 55 (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 TRP* 3.3 57.9 - + + -
26A VAL* 3.9 2.2 - - + -
27A ALA* 3.8 30.7 - - + -
30A LEU* 4.1 13.2 - - + -
41A LEU* 4.2 11.9 - - + -
51A TYR 3.7 1.0 + - - -
52A THR* 3.1 10.5 + - - +
54A SER* 1.3 77.0 + - - +
56A GLU* 1.3 56.4 + - + +
57A GLU 2.9 2.5 - - - -
58A ALA* 2.9 10.7 + - + -
59A PHE* 2.5 45.5 + + + +
72A LEU* 3.8 26.9 - - + -
110A ILE* 3.8 31.2 - - + -
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Residues in contact with GLU 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A THR* 3.2 15.6 + - - +
53A PRO* 3.6 24.1 - - - +
55A PHE* 1.3 76.4 - - + +
57A GLU* 1.3 56.7 + - - +
59A PHE* 3.9 1.1 - - - +
60A ARG* 3.1 30.5 + - - +
72A LEU* 4.1 14.1 - - + -
74A ILE* 3.0 35.1 - - + +
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Residues in contact with GLU 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A PRO 3.3 7.9 + - - +
54A SER* 3.2 12.0 + - - +
55A PHE 2.9 0.4 - - - -
56A GLU* 1.3 76.0 - - - +
58A ALA* 1.3 67.4 + - - +
59A PHE 3.1 1.3 - - - -
60A ARG* 2.4 48.4 + - - +
61A LYS* 2.9 23.6 + - + +
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Residues in contact with ALA 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A TRP 4.5 4.9 - - - +
23A ARG* 3.7 24.0 - - - +
24A ASN* 5.7 0.7 - - - -
27A ALA* 3.5 22.7 - - + +
54A SER 2.9 15.1 + - - +
55A PHE* 3.6 13.9 - - + +
57A GLU* 1.3 77.1 - - - +
59A PHE* 1.3 64.0 + - - +
61A LYS* 3.2 22.1 - - + +
62A ARG* 3.2 8.0 + - - +
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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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27A ALA* 3.9 11.4 - - + +
30A LEU* 6.0 1.1 - - + -
31A ILE* 3.9 22.4 - - + -
39A TYR* 4.1 20.9 - + + -
55A PHE* 2.5 41.5 + + + +
56A GLU 4.0 1.8 - - - +
58A ALA* 1.3 68.1 - - - +
60A ARG* 1.3 69.4 + - + +
61A LYS 2.7 3.0 + - - -
62A ARG* 3.0 2.8 + - - -
63A ALA* 2.5 46.4 + - + +
70A PRO* 3.7 23.8 - - + -
71A ARG* 3.4 21.3 - - - -
72A LEU* 3.3 48.7 - - + -
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Residues in contact with ARG 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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56A GLU 3.1 11.0 + - - +
57A GLU* 2.4 52.4 + - - +
59A PHE* 1.3 83.7 - - + +
61A LYS* 1.3 72.4 + - - +
63A ALA* 3.7 7.6 - - - -
64A ALA* 2.8 26.6 + - + +
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Residues in contact with LYS 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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23A ARG 6.2 0.4 - - - +
57A GLU* 2.9 26.3 + - + +
58A ALA* 3.2 14.1 - - + +
59A PHE 2.7 3.2 + - - -
60A ARG* 1.3 85.3 - - - +
62A ARG* 1.3 94.9 + - + +
64A ALA* 3.3 7.1 + - - +
65A GLU* 3.3 16.7 + - - +
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Residues in contact with ARG 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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27A ALA* 4.3 6.1 - - + +
28A LYS* 3.6 58.3 - - + +
31A ILE* 4.0 7.0 - - + +
58A ALA 3.2 11.9 + - - +
59A PHE 3.0 3.0 + - - +
61A LYS* 1.3 103.4 - - + +
63A ALA* 1.3 63.9 + - - +
65A GLU* 2.7 52.3 + - - +
66A ILE* 3.5 13.2 - - - +
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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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31A ILE* 3.5 13.4 - - + +
59A PHE* 2.5 52.7 + - + +
60A ARG* 3.4 8.5 - - - +
61A LYS 2.9 1.0 + - - -
62A ARG* 1.3 69.5 - - - +
64A ALA* 1.3 59.6 + - - +
65A GLU 2.9 9.8 + - - -
66A ILE* 3.0 17.8 + - - +
69A SER* 3.4 11.0 + - - -
70A PRO* 4.0 11.6 - - + +
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Residues in contact with ALA 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ARG* 2.8 23.9 + - + +
61A LYS 4.1 1.6 - - - +
63A ALA* 1.3 74.8 - - - +
65A GLU* 1.3 56.9 + - - +
66A ILE 2.9 13.4 + - - +
67A THR* 4.8 2.1 + - - -
69A SER* 3.2 15.0 + - - +
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Residues in contact with GLU 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LYS* 3.3 17.6 + - - +
62A ARG* 2.7 53.5 + - - +
63A ALA 2.9 1.8 + - - -
64A ALA* 1.3 74.5 - - - +
66A ILE* 1.3 73.3 + - + +
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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
------------------------------------------------------------
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