Contacts of the helix formed by residues 55 - 69 (chain D) in PDB entry 1NR4
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 55 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52D ASP* 3.1 30.4 + - + +
54D ASN* 1.3 76.4 - - - +
56D LYS* 1.3 61.9 + - - +
57D ARG* 2.9 40.8 + - - +
58D VAL* 3.0 21.3 + - + +
59D LYS* 3.0 31.0 + - - +
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Residues in contact with LYS 56 (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 ASN 4.9 8.3 - - - +
55D ASN* 1.3 74.7 - - - +
57D ARG* 1.3 61.7 + - + +
59D LYS* 3.2 18.7 + - + +
60D ASN* 2.9 38.7 + - - +
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Residues in contact with ARG 57 (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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17D GLY* 3.7 25.1 + - - +
18D ALA* 3.3 34.5 - - - +
55D ASN* 2.9 21.6 + - - +
56D LYS* 1.3 73.3 - - + +
58D VAL* 1.3 63.0 - - + +
60D ASN* 3.4 9.1 + - - +
61D ALA* 3.0 24.3 + - - +
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Residues in contact with VAL 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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39D ILE* 3.8 27.8 - - + -
41D PHE* 3.7 25.2 - - + -
51D SER* 3.7 18.6 - - - -
52D ASP 3.4 29.4 - - - +
53D PRO* 4.6 2.5 - - + +
55D ASN* 3.0 18.6 + - + +
57D ARG* 1.3 74.6 - - + +
59D LYS* 1.3 67.2 + - - +
61D ALA* 3.1 3.8 + - - -
62D VAL* 3.0 21.3 + - - +
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Residues in contact with LYS 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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39D ILE* 6.5 0.4 - - + -
53D PRO 3.2 25.6 - - - +
54D ASN* 3.9 23.7 + - - +
55D ASN 3.0 19.3 + - - +
56D LYS* 3.2 19.4 + - + +
58D VAL* 1.3 79.0 - - + +
60D ASN* 1.3 63.7 + - - +
62D VAL* 3.3 10.1 + - - +
63D LYS* 3.1 36.5 + - - +
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Residues in contact with ASN 60 (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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21D LEU* 5.3 1.0 - - - +
56D LYS* 2.9 25.5 + - - +
57D ARG* 3.7 9.6 - - - +
59D LYS* 1.3 76.1 - - - +
61D ALA* 1.3 57.9 + - - +
63D LYS* 3.3 12.1 + - - +
64D TYR* 3.0 24.8 + - - +
64G TYR* 4.6 0.5 + - - -
68G LEU* 3.0 57.6 + - + +
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Residues in contact with ALA 61 (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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19D ILE* 5.6 2.2 - - + +
21D LEU* 4.0 16.6 - - + -
24D LEU* 3.7 24.7 - - + -
41D PHE* 3.8 15.3 - - + -
57D ARG 3.0 16.9 + - - +
58D VAL* 3.1 4.2 + - - +
60D ASN* 1.3 74.2 - - - +
62D VAL* 1.3 65.7 + - - +
64D TYR* 3.3 4.7 + - - +
65D LEU* 3.1 24.4 + - - +
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Residues in contact with VAL 62 (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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27D TRP* 3.7 34.3 - - + -
39D ILE* 3.8 37.2 - - + -
41D PHE* 4.0 8.7 - - + -
58D VAL 3.0 18.5 + - - +
59D LYS* 3.5 10.8 - - - +
61D ALA* 1.3 75.7 - - - +
63D LYS* 1.3 57.3 + - + +
65D LEU* 3.1 7.7 + - - +
66D GLN* 2.8 44.0 + - - +
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Residues in contact with LYS 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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59D LYS* 3.1 23.6 + - - +
60D ASN* 3.5 21.1 + - - +
61D ALA 3.3 0.4 - - - -
62D VAL* 1.3 73.7 - - + +
64D TYR* 1.3 64.3 + - - +
66D GLN* 3.2 18.5 + - - +
67D SER* 2.9 30.3 + - - +
64G TYR* 4.1 2.0 - - - -
67G SER* 2.7 54.1 + - - +
68G LEU* 4.3 6.3 + - + -
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Residues in contact with TYR 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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21D LEU* 3.6 44.6 + - + -
22D ARG* 5.1 0.5 - - - -
24D LEU* 4.6 3.0 + - + -
60D ASN 3.0 13.1 + - - +
61D ALA 3.3 8.3 - - - +
63D LYS* 1.3 75.5 - - - +
65D LEU* 1.3 78.4 + - + +
67D SER* 3.2 2.8 + - - -
68D LEU* 2.9 53.2 + - + +
21G LEU* 4.4 10.3 - - + -
22G ARG* 3.5 47.6 + - + +
64G TYR* 3.4 33.4 - + + +
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Residues in contact with LEU 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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24D LEU* 4.0 26.5 - - + +
25D LYS 3.8 21.1 - - - +
26D THR* 3.8 20.6 - - + +
27D TRP* 3.7 33.7 - - + -
41D PHE* 4.0 14.8 - - + -
61D ALA 3.1 12.5 + - - +
62D VAL 3.1 6.3 + - - +
64D TYR* 1.3 93.0 - - + +
66D GLN* 1.3 64.0 + - - +
68D LEU* 3.4 13.0 + - + +
69D GLU* 3.3 22.5 + - - +
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Residues in contact with GLN 66 (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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27D TRP* 4.1 20.6 - - + +
62D VAL* 2.8 31.7 + - + +
63D LYS* 3.6 29.5 - - - +
64D TYR 3.2 0.2 - - - -
65D LEU* 1.3 76.7 - - - +
67D SER* 1.3 62.0 + - - +
69D GLU* 3.5 23.8 + - - +
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Residues in contact with SER 67 (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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63D LYS 2.9 16.9 + - - -
64D TYR 3.8 1.1 - - - -
66D GLN* 1.3 75.9 - - - +
68D LEU* 1.3 66.3 + - - +
69D GLU 3.2 3.9 - - - -
21G LEU* 3.6 19.5 - - - +
60G ASN* 2.9 36.4 + - - +
64G TYR* 3.5 29.2 + - - +
67G SER* 5.1 1.7 + - - -
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Residues in contact with LEU 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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24D LEU 5.4 2.9 - - - +
25D LYS 5.8 1.1 - - - +
64D TYR* 2.9 48.7 + - + +
65D LEU* 3.6 16.6 - - + +
67D SER* 1.3 80.7 - - - +
69D GLU* 1.3 66.8 + - - +
21G LEU* 3.8 24.0 - - + +
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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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44C VAL* 5.6 1.9 - - - +
65D LEU 3.3 10.4 + - - +
66D GLN* 3.7 20.3 - - - +
67D SER 3.2 4.4 - - - -
68D LEU* 1.3 85.7 - - - +
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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