Contacts of the helix formed by residues 47 - 63 (chain C) in PDB entry 2NS8
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 47 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27C THR* 3.5 14.1 - - - -
45C VAL* 3.4 7.8 - - - +
46C LYS* 1.3 96.0 - - + +
48C LYS* 1.3 63.2 + - - +
49C ARG* 3.9 12.1 - - - +
50C ALA* 3.1 29.1 + - - +
51C LEU 3.3 8.3 + - - -
157D GLU* 5.1 10.9 + - - +
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Residues in contact with LYS 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C ILE* 2.4 34.2 + - - -
23C GLU* 3.7 12.3 + - - +
25C LEU* 2.6 32.7 + - + +
26C THR* 4.9 6.9 - - + +
27C THR* 3.7 14.0 - - + +
47C ASN* 1.3 72.3 - - - +
49C ARG* 1.3 60.1 + - - +
51C LEU* 3.2 6.0 + - + +
52C LEU* 2.9 53.2 + - + +
23D GLU* 4.9 8.3 + - - +
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Residues in contact with ARG 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C ASN* 3.3 12.0 + - - +
48C LYS* 1.3 76.0 - - - +
50C ALA* 1.3 68.1 + - - +
52C LEU* 3.4 28.1 + - - +
53C ASP* 3.3 46.2 + - - +
99C VAL 4.5 2.8 + - - -
101C LEU 3.3 23.8 + - - -
102C GLY* 4.4 0.8 - - - -
103C THR 4.7 0.4 - - - +
150D GLU* 4.0 19.0 + - - +
153D VAL* 6.3 0.8 - - - +
154D ALA* 3.8 27.7 - - - +
157D GLU* 3.2 48.2 - - + +
158D ARG* 3.7 20.0 - - + +
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Residues in contact with ALA 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206B GLN* 4.6 8.5 - - - +
207B ILE* 4.8 14.6 - - + +
45C VAL* 4.5 4.5 - - + -
46C LYS* 4.5 11.2 - - + +
47C ASN* 3.1 26.8 + - - +
49C ARG* 1.3 76.2 - - - +
51C LEU* 1.3 65.4 + - - +
53C ASP* 3.1 16.9 + - - +
54C ALA* 3.2 13.0 + - - +
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Residues in contact with LEU 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B ILE* 5.1 5.8 - - + -
9C VAL* 5.3 6.3 - - + -
10C ILE* 5.5 1.3 - - + -
13C ALA* 3.8 11.7 - - + -
25C LEU* 3.9 28.7 - - + -
26C THR 4.9 2.9 - - - +
27C THR* 4.6 13.7 - - + +
30C LEU* 3.8 30.1 - - + -
45C VAL* 4.0 15.2 - - + +
47C ASN 3.3 9.0 + - - +
48C LYS* 3.2 11.7 + - + +
50C ALA* 1.3 77.8 - - - +
52C LEU* 1.3 62.1 + - - +
53C ASP 3.1 0.7 + - - -
54C ALA* 3.2 6.6 + - + +
55C LEU* 2.9 56.9 + - + +
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Residues in contact with LEU 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C ILE* 3.9 32.5 - - + -
25C LEU* 3.7 27.4 - - + -
48C LYS* 2.9 40.1 + - + +
49C ARG* 3.9 29.8 - - - +
51C LEU* 1.3 75.8 - - - +
53C ASP* 1.3 57.7 + - - +
55C LEU* 3.8 5.6 - - + -
56C ALA* 3.1 27.5 + - - +
98C LYS 5.4 0.7 - - - +
99C VAL* 3.6 26.2 - - + +
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Residues in contact with ASP 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C ARG* 3.3 30.9 + - - +
50C ALA* 3.1 10.3 + - - +
51C LEU 3.1 0.8 - - - -
52C LEU* 1.3 74.5 - - - +
54C ALA* 1.3 67.0 + - - +
56C ALA* 3.3 5.6 + - - +
57C ILE* 3.0 33.2 + - + +
103C THR* 4.5 9.4 + - - -
104C ARG 5.3 5.8 - - - +
158D ARG* 3.3 40.2 + - - -
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Residues in contact with ALA 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B ILE* 3.7 28.5 - - + -
6C LYS* 5.0 6.3 - - - +
10C ILE* 3.5 25.2 - - + +
50C ALA 3.2 4.2 + - - +
51C LEU 3.2 6.8 + - - +
53C ASP* 1.3 79.3 - - - +
55C LEU* 1.3 57.7 + - + +
57C ILE* 3.3 14.7 + - - +
58C GLU* 2.9 30.1 + - - +
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Residues in contact with LEU 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C ILE* 4.2 13.2 - - + -
13C ALA* 3.7 20.0 - - + +
14C LEU* 3.5 27.5 - - + +
17C LEU* 4.8 7.2 - - + -
25C LEU* 3.8 29.2 - - + -
51C LEU* 2.9 41.9 + - + +
52C LEU* 3.7 14.4 - - + +
53C ASP 3.2 0.2 - - - -
54C ALA* 1.3 75.6 - - - +
56C ALA* 1.3 65.3 + - - +
58C GLU* 3.2 5.9 + - - +
59C MET* 2.9 28.6 + - - +
99C VAL* 3.8 11.7 - - + -
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Residues in contact with ALA 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C LEU 3.1 15.4 + - - +
53C ASP* 3.6 7.2 - - - +
55C LEU* 1.3 79.7 - - - +
57C ILE* 1.3 61.8 + - + +
59C MET 3.4 0.3 + - - -
60C LEU* 3.3 12.8 + - + +
99C VAL* 3.7 12.1 - - + +
100C HIS* 3.0 40.0 - - + +
103C THR* 3.5 28.0 - - + +
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Residues in contact with ILE 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C LYS* 5.9 6.1 - - - +
53C ASP* 3.0 24.5 + - + +
54C ALA* 3.5 14.1 - - - +
56C ALA* 1.3 73.2 - - + +
58C GLU* 1.3 70.5 + - + +
60C LEU* 3.0 12.3 + - - +
61C ASP* 2.9 28.3 + - - +
103C THR* 6.3 2.7 - - + -
104C ARG 6.1 0.4 - - - +
106C THR* 4.3 19.1 - - + -
108C LYS* 3.4 28.3 - - - +
109C GLN* 3.9 20.4 - - - +
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Residues in contact with GLU 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C ILE* 3.4 40.2 - - + -
11C ASN* 5.0 0.2 - - - +
14C LEU* 4.5 5.4 - - + -
54C ALA 2.9 12.5 + - - +
55C LEU 3.2 3.8 + - - +
57C ILE* 1.3 80.5 - - + +
59C MET* 1.3 62.8 + - - +
61C ASP* 3.2 15.6 + - - +
62C ARG* 2.8 68.5 + - - +
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Residues in contact with MET 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C LEU* 4.8 11.4 - - + -
17C LEU* 5.0 2.0 - - - -
55C LEU 2.9 18.9 + - - +
57C ILE 3.2 0.2 - - - -
58C GLU* 1.3 76.0 - - - +
60C LEU* 1.3 58.6 + - - +
62C ARG* 4.8 2.2 - - - +
63C HIS* 3.0 38.8 + - - +
64C HIS 4.0 0.2 + - - -
89C ALA* 3.2 27.6 - - - +
90C LEU* 4.0 2.0 - - - +
92C SER* 3.9 6.1 - - - +
93C HIS* 3.4 38.1 - - + +
96C GLY* 3.6 31.0 - - - -
99C VAL* 4.6 10.5 - - - -
100C HIS* 3.5 28.7 - - + +
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Residues in contact with LEU 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C ALA 3.3 13.4 + - - +
57C ILE* 3.0 7.0 + - - +
59C MET* 1.3 74.5 - - - +
61C ASP* 1.3 68.3 + - - +
62C ARG 3.1 1.6 - - - -
63C HIS 3.3 0.2 + - - -
64C HIS* 3.0 54.6 + - + +
65C THR* 5.5 0.2 - - - +
86C PHE* 4.0 14.8 - - + -
89C ALA* 4.0 12.1 - - + -
100C HIS* 3.3 26.2 - - + +
103C THR* 5.9 2.5 - - + -
109C GLN* 4.7 11.7 - - - +
0F ACE 3.3 38.1 - - + +
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Residues in contact with ASP 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C ILE* 2.9 23.3 + - - +
58C GLU* 3.8 18.2 - - - +
60C LEU* 1.3 81.1 - - - +
62C ARG* 1.3 60.9 + - - +
65C THR* 5.4 3.1 - - - +
108C LYS* 3.1 29.7 + - - -
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Residues in contact with ARG 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C ASN* 2.7 30.3 + - - +
14C LEU* 3.8 26.2 - - - +
58C GLU* 2.8 39.7 + - - +
59C MET* 5.1 1.1 - - - +
61C ASP* 1.3 79.5 - - - +
63C HIS* 1.3 90.2 + - + +
65C THR* 4.0 11.1 - - - +
93C HIS* 4.4 12.9 + - - -
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Residues in contact with HIS 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C MET* 3.0 26.1 + - - +
60C LEU 3.3 0.2 + - - -
62C ARG* 1.3 103.7 + - + +
64C HIS* 1.3 56.6 + - - +
65C THR* 2.6 31.1 + - - +
85C SER* 4.0 4.6 + - - +
88C ASN* 4.1 18.5 + - - +
89C ALA* 3.7 17.3 - - - -
92C SER* 3.3 35.7 + - - -
93C HIS* 4.1 8.9 - + - -
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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