Contacts of the helix formed by residues 49 - 73 (chain D) in PDB entry 3NM9
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 49 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D TRP* 3.1 76.7 + - + +
44D ARG* 5.2 2.4 + - - +
46D MET* 3.6 25.6 + - - +
47D LYS 3.6 2.9 + - - +
48D ASP* 1.3 75.0 + - - +
50D SER* 1.3 64.7 + - - +
51D GLU 3.4 2.2 - - - -
52D TRP* 3.0 18.8 + - - +
53D GLU* 3.0 36.0 + - + +
61P ASP* 3.4 22.9 + - - +
65P ARG* 5.0 5.8 - - - +
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Residues in contact with SER 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D ASP* 3.2 20.7 + - - -
49D LYS* 1.3 75.3 - - - +
51D GLU* 1.3 68.5 + - - +
53D GLU* 3.0 12.3 + - - +
54D ALA* 2.8 27.0 + - - +
58P LYS* 5.7 12.6 - - - -
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Residues in contact with GLU 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D ASP* 4.9 1.4 + - - -
49D LYS 3.4 0.6 - - - -
50D SER* 1.3 81.7 + - - +
52D TRP* 1.3 99.7 + - + +
54D ALA* 3.4 5.7 + - - +
55D LYS* 3.1 53.3 + - + +
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Residues in contact with TRP 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D ALA* 3.4 21.0 - - - +
14D LEU* 3.6 24.2 - - + +
15D TRP* 3.5 42.7 - + + -
18D SER* 3.3 31.6 - - - -
43D TRP* 3.8 15.0 - + + -
46D MET* 4.4 12.7 - - - +
48D ASP 5.1 1.6 - - - -
49D LYS* 3.0 11.0 + - - +
51D GLU* 1.3 113.9 + - + +
53D GLU* 1.3 59.4 + - - +
55D LYS* 3.9 19.7 - - + +
56D ALA* 3.0 28.6 + - - +
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Residues in contact with GLU 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D ALA* 4.2 13.2 - - + -
43D TRP* 5.1 2.1 - - + -
49D LYS* 3.0 32.4 + - + +
50D SER* 3.6 7.8 + - - +
52D TRP* 1.3 77.3 - - - +
54D ALA* 1.3 60.2 + - - +
56D ALA* 3.5 7.5 + - - +
57D ALA* 2.9 28.9 + - - +
53P GLU 5.2 1.9 - - - +
54P ALA* 5.3 5.3 - - - +
57P ALA* 3.8 34.4 - - + +
58P LYS* 4.4 3.8 + - - -
61P ASP* 2.9 39.2 - - - +
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Residues in contact with ALA 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D SER 2.8 16.8 + - - +
51D GLU* 3.6 7.6 - - - +
53D GLU* 1.3 73.4 - - - +
55D LYS* 1.3 66.6 + - + +
57D ALA* 3.1 7.2 + - - +
58D LYS* 3.1 23.7 + - - +
54P ALA* 5.3 15.6 - - + +
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Residues in contact with LYS 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D LEU* 3.8 21.2 - - + +
51D GLU* 3.1 38.9 + - + +
52D TRP* 4.1 20.7 - - + +
54D ALA* 1.3 77.5 - - + +
56D ALA* 1.3 57.7 + - - +
58D LYS* 3.5 6.1 + - - +
59D ALA* 3.0 29.1 + - - +
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Residues in contact with ALA 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D PRO* 5.5 0.5 - - - +
9D LEU 4.3 5.5 - - - +
10D SER* 4.2 1.3 - - - -
11D ALA* 3.5 29.6 - - + +
14D LEU* 3.6 8.6 - - - +
52D TRP 3.0 21.4 + - - +
53D GLU* 3.5 6.7 - - - +
55D LYS* 1.3 77.9 - - - +
57D ALA* 1.3 60.4 + - - +
59D ALA* 3.3 6.8 - - - +
60D LYS* 3.1 20.8 + - - +
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Residues in contact with ALA 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D GLU 2.9 17.4 + - - +
54D ALA* 3.1 8.2 + - - +
56D ALA* 1.3 72.5 - - - +
58D LYS* 1.3 61.3 + - - +
59D ALA 3.0 1.6 - - - -
60D LYS* 2.8 22.0 + - - +
61D ASP* 3.0 16.3 + - - +
49P LYS 5.0 2.0 - - - +
50P SER* 5.3 4.3 - - - +
53P GLU* 3.7 41.6 - - + +
54P ALA 5.0 0.9 - - - +
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Residues in contact with LYS 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D ALA 3.1 12.1 + - - +
55D LYS* 4.0 5.8 - - - +
57D ALA* 1.3 77.9 - - - +
59D ALA* 1.3 62.2 + - - +
61D ASP* 4.3 15.5 - - + -
62D ASP* 3.1 45.0 + - - +
65D ARG* 5.9 2.2 - - - +
47P LYS 6.0 0.4 - - - -
48P ASP* 3.9 27.4 + - - +
50P SER* 4.7 9.5 + - - +
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Residues in contact with ALA 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D PRO* 3.7 9.9 - - + +
9D LEU* 4.3 16.6 - - + +
14D LEU* 4.8 4.9 - - + -
55D LYS 3.0 19.5 + - - +
56D ALA* 3.3 11.4 - - - +
57D ALA 3.0 0.2 - - - -
58D LYS* 1.3 77.8 - - - +
60D LYS* 1.3 55.8 + - - +
62D ASP* 3.6 8.7 - - - +
63D TYR* 3.1 27.5 + - - +
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Residues in contact with LYS 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D PRO* 3.9 19.5 - - + +
56D ALA 3.1 11.2 + - - +
57D ALA* 2.8 10.5 + - - +
59D ALA* 1.3 76.1 - - - +
61D ASP* 1.3 68.3 + - - +
63D TYR* 3.8 6.5 - - + -
64D ASP* 2.8 57.1 + - - +
1L G 3.6 28.3 + - - +
53P GLU* 5.3 9.4 - - - +
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Residues in contact with ASP 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57D ALA 3.0 9.3 + - - +
58D LYS* 3.6 22.6 - - + +
60D LYS* 1.3 72.6 - - - +
62D ASP* 1.3 68.2 + - - +
64D ASP* 2.9 17.0 + - - +
65D ARG* 3.0 19.9 + - - +
47P LYS 3.5 14.8 - - - +
48P ASP* 4.0 3.8 - - - +
49P LYS* 3.2 41.0 + - - +
53P GLU* 3.3 28.0 - - - +
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Residues in contact with ASP 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58D LYS* 3.1 38.5 + - - +
59D ALA* 3.6 8.3 - - - +
61D ASP* 1.3 76.0 - - - +
63D TYR* 1.3 57.4 + - - +
65D ARG* 3.2 26.7 + - - +
66D ALA* 2.9 29.7 + - - +
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Residues in contact with TYR 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D PRO* 4.1 10.6 + - + -
6D LYS 3.2 30.1 - - - -
7D ARG* 3.8 7.3 - - - +
8D PRO* 3.5 35.4 - - + -
59D ALA 3.1 17.4 + - - +
60D LYS* 3.8 6.3 - - - +
61D ASP 3.0 0.2 + - - -
62D ASP* 1.3 79.7 - - - +
64D ASP* 1.3 82.4 + - - +
66D ALA* 3.3 7.3 + - - +
67D VAL* 2.9 50.1 + - + +
1L G 4.0 31.5 + - - -
2L G 4.4 4.9 + - - -
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Residues in contact with ASP 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D LYS* 2.8 48.3 + - - +
61D ASP* 2.9 6.4 + - - +
63D TYR* 1.3 86.8 - - - +
65D ARG* 1.3 60.6 + - - +
67D VAL* 3.9 10.2 - - - +
68D LYS* 3.0 28.1 + - - +
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Residues in contact with ARG 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D LYS* 5.9 2.6 - - - +
61D ASP* 3.0 12.5 + - - +
62D ASP* 3.3 34.5 + - - +
64D ASP* 1.3 74.5 - - - +
66D ALA* 1.3 61.6 + - - +
68D LYS* 2.9 32.7 + - + +
69D GLU* 3.0 17.3 + - + +
47P LYS* 4.8 27.0 + - - +
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Residues in contact with ALA 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D PRO* 3.4 25.6 - - + +
62D ASP 2.9 13.6 + - - +
63D TYR* 3.3 10.5 + - - +
65D ARG* 1.3 78.2 - - + +
67D VAL* 1.3 56.5 + - - +
69D GLU* 3.8 7.7 + - - +
70D PHE* 3.2 21.5 + - - +
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Residues in contact with VAL 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D PRO* 3.8 17.5 - - + +
63D TYR* 2.9 53.9 + - + +
64D ASP* 3.9 13.5 - - - +
65D ARG 3.0 0.4 - - - -
66D ALA* 1.3 73.9 - - - +
68D LYS* 1.3 66.0 + - - +
70D PHE* 3.3 4.5 + - + +
71D GLU* 2.9 50.7 + - + +
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Residues in contact with LYS 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D ASP 3.0 12.0 + - - +
65D ARG* 2.9 18.4 + - + +
67D VAL* 1.3 75.6 - - - +
69D GLU* 1.3 57.3 + - + +
70D PHE 3.1 0.5 + - - -
71D GLU* 3.2 9.0 + - - +
72D ALA* 2.8 40.4 + - + +
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Residues in contact with GLU 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D ARG* 3.0 18.8 + - + +
66D ALA* 3.9 9.0 - - - +
68D LYS* 1.3 79.9 - - + +
70D PHE* 1.3 56.1 + - - +
72D ALA* 4.0 5.4 - - - -
73D ASN* 2.2 60.9 + - - +
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Residues in contact with PHE 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D SER 3.2 39.3 - - - -
3D ASP 3.7 11.2 - - - -
4D LYS* 3.6 32.1 - - + -
5D PRO* 3.9 11.7 - - + -
66D ALA 3.2 19.4 + - - +
67D VAL* 3.6 5.6 - - + +
68D LYS 3.2 0.4 - - - -
69D GLU* 1.3 73.0 - - - +
71D GLU* 1.3 77.4 + - - +
72D ALA 3.1 1.7 + - - -
73D ASN* 3.4 9.7 + - - +
74D GLY* 3.5 15.0 + - - -
71J GLU* 6.0 3.1 - - - -
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Residues in contact with GLU 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D VAL* 2.9 41.4 + - + +
68D LYS* 3.7 6.3 - - - +
70D PHE* 1.3 87.4 - - - +
72D ALA* 1.3 61.7 + - - +
73D ASN 3.5 0.2 + - - -
74D GLY* 4.1 5.2 + - - -
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Residues in contact with ALA 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D LYS* 2.8 24.7 + - + +
69D GLU* 3.7 7.6 - - - +
71D GLU* 1.3 79.6 - - - +
73D ASN* 1.3 73.8 + - - +
74D GLY* 3.6 1.7 + - - +
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Residues in contact with ASN 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D GLU* 2.2 51.3 + - + +
70D PHE* 3.4 4.2 + - - -
72D ALA* 1.3 93.5 - - - +
74D GLY* 1.3 62.6 + - - +
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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
------------------------------------------------------------
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