Contacts of the helix formed by residues 55 - 70 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52B ASP* 3.1 29.2 + - + +
54B ASN* 1.3 78.3 - - - +
56B LYS* 1.3 59.9 + - - +
57B ARG* 3.0 32.8 + - - +
58B VAL* 3.1 20.7 + - + +
59B LYS* 2.9 30.2 + - - +
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Residues in contact with LYS 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B ASN 3.7 4.7 + - - +
55B ASN* 1.3 75.7 - - - +
57B ARG* 1.3 59.1 + - + +
59B LYS* 3.2 13.6 + - + +
60B ASN* 2.9 39.6 + - - +
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Residues in contact with ARG 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B GLY 5.5 2.2 - - - -
18B ALA* 3.7 33.1 - - - +
19B ILE* 6.0 1.7 - - + +
55B ASN* 3.0 14.7 + - - +
56B LYS* 1.3 79.3 - - + +
58B VAL* 1.3 58.0 + - + +
60B ASN* 3.4 10.0 + - - +
61B ALA* 3.0 27.7 + - - +
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Residues in contact with VAL 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ILE* 3.7 33.7 - - + -
41B PHE* 3.7 16.3 - - + -
51B SER* 3.7 20.0 - - - -
52B ASP* 3.3 30.5 - - + +
53B PRO* 4.5 2.2 - - + -
55B ASN* 3.1 18.4 + - + +
57B ARG* 1.3 74.5 - - + +
59B LYS* 1.3 65.9 + - + +
61B ALA* 3.2 4.6 + - - +
62B VAL* 3.1 21.7 + - - +
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Residues in contact with LYS 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ILE* 6.5 0.2 - - + -
53B PRO 3.3 25.8 - - - +
54B ASN* 4.1 20.4 + - - +
55B ASN 2.9 18.1 + - - +
56B LYS* 3.2 14.2 + - + +
58B VAL* 1.3 78.6 - - + +
60B ASN* 1.3 57.8 + - - +
62B VAL* 3.4 7.4 + - - +
63B LYS* 3.0 48.4 + - - +
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Residues in contact with ASN 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B LEU* 5.0 3.2 - - + +
56B LYS* 2.9 30.6 + - - +
57B ARG* 3.7 9.0 - - - +
58B VAL 3.3 0.2 - - - -
59B LYS* 1.3 75.5 - - - +
61B ALA* 1.3 56.6 + - - +
63B LYS* 3.4 21.1 + - - +
64B TYR* 3.0 27.4 + - - +
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Residues in contact with ALA 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ILE* 5.1 7.4 - - + -
21B LEU* 4.1 15.4 - - + +
24B LEU* 3.7 20.2 - - + -
41B PHE* 3.6 27.1 - - + -
57B ARG 3.0 14.7 + - - +
58B VAL* 3.2 0.4 + - - -
60B ASN* 1.3 72.6 - - - +
62B VAL* 1.3 65.2 + - - +
64B TYR* 3.3 4.5 + - - +
65B LEU* 3.0 26.3 + - - +
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Residues in contact with VAL 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B TRP* 3.7 36.3 - - + -
39B ILE* 3.6 39.5 - - + -
41B PHE* 3.9 7.4 - - + -
58B VAL 3.1 14.7 + - - +
59B LYS* 3.6 9.2 - - - +
61B ALA* 1.3 73.8 - - - +
63B LYS* 1.3 59.3 + - + +
65B LEU* 3.1 6.5 + - - +
66B GLN* 2.9 41.1 + - - +
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Residues in contact with LYS 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B LYS* 3.0 34.9 + - - +
60B ASN* 3.7 21.6 + - - +
61B ALA 3.3 0.2 - - - -
62B VAL* 1.3 76.6 - - + +
64B TYR* 1.3 62.9 + - - +
66B GLN* 3.4 16.6 + - - +
67B SER* 3.0 31.0 + - - +
70B ARG* 4.7 1.0 + - - +
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Residues in contact with TYR 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B LEU* 3.8 62.8 + - + +
22B ARG* 5.2 2.8 + - - -
24B LEU* 4.7 3.6 + - + -
60B ASN 3.0 14.2 + - - +
61B ALA 3.4 10.1 - - - +
62B VAL 3.3 0.2 - - - -
63B LYS* 1.3 74.6 - - - +
65B LEU* 1.3 83.5 + - + +
67B SER* 3.2 6.3 + - - -
68B LEU* 3.0 53.6 + - + +
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Residues in contact with LEU 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B LEU* 4.0 17.7 - - + +
25B LYS 3.7 25.6 - - - +
26B THR* 3.8 28.0 - - - +
27B TRP* 3.8 22.7 - - + -
41B PHE* 4.0 13.7 - - + -
61B ALA 3.0 17.8 + - - +
62B VAL 3.1 6.0 + - - +
64B TYR* 1.3 95.3 - - + +
66B GLN* 1.3 62.7 + - - +
68B LEU* 3.4 14.1 + - + +
69B GLU* 3.2 29.0 + - - +
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Residues in contact with GLN 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B TRP* 3.7 29.0 - - + +
62B VAL* 2.9 33.6 + - - +
63B LYS* 3.7 19.7 - - - +
65B LEU* 1.3 78.3 - - - +
67B SER* 1.3 60.0 + - - +
69B GLU* 3.4 27.5 + - - +
70B ARG* 3.5 36.9 + - - +
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Residues in contact with SER 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B LYS* 3.0 19.6 + - - +
64B TYR* 3.7 5.8 - - - -
66B GLN* 1.3 75.1 - - - +
68B LEU* 1.3 63.0 + - - +
69B GLU 3.5 0.2 + - - -
70B ARG* 3.4 34.0 + - - +
71B SER* 3.5 14.4 + - - -
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Residues in contact with LEU 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B LEU 5.6 2.0 - - - +
25B LYS 5.6 2.5 - - - +
64B TYR* 3.0 54.3 + - + +
65B LEU* 3.5 17.5 - - + +
67B SER* 1.3 75.5 - - - +
69B GLU* 1.3 62.9 + - - +
70B ARG 3.4 0.3 + - - -
71B SER* 3.5 16.1 + - - +
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Residues in contact with GLU 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A LYS* 4.2 18.0 + - - +
26B THR* 4.5 4.9 + - - -
27B TRP* 4.4 14.3 + - - -
65B LEU* 3.2 17.3 + - - +
66B GLN* 3.5 20.7 - - - +
68B LEU* 1.3 81.0 - - - +
70B ARG* 1.3 58.5 + - + +
71B SER 3.6 5.4 + - - -
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Residues in contact with ARG 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B LYS* 4.7 1.2 + - - +
66B GLN* 3.5 41.7 + - - +
67B SER* 3.4 30.8 + - - +
68B LEU 3.3 0.6 - - - -
69B GLU* 1.3 76.7 - - + +
71B SER* 1.3 63.4 + - - +
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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