Contacts of the helix formed by residues 52 - 74 (chain B) in PDB entry 2NP5
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 52 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B PHE* 3.9 8.6 - - - +
51B SER* 1.3 88.9 - - - +
53B LYS* 1.3 64.3 + - - +
54B ASP* 3.7 10.3 + - - +
55B GLU* 3.0 25.6 + - - +
56B MSE 3.1 17.3 + - - +
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Residues in contact with LYS 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B GLU 5.7 2.8 + - - -
29B GLY 5.9 0.2 - - - -
30B ALA 3.3 26.1 + - - -
31B SER* 4.1 6.3 - - - +
32B VAL* 3.9 34.5 - - + +
52B THR* 1.3 71.9 - - - +
54B ASP* 1.3 64.0 + - - +
56B MSE 3.1 7.8 + - + +
57B PHE* 3.0 47.4 + - + -
112B ARG* 4.5 15.1 - - - +
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Residues in contact with ASP 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B THR* 3.3 9.9 + - - +
53B LYS* 1.3 78.1 - - - +
55B GLU* 1.3 56.6 + - - +
57B PHE* 3.3 6.8 + - - +
58B ALA* 2.9 27.7 + - - +
112B ARG* 5.9 0.3 + - - -
116B SER* 2.8 28.6 + - - -
117B PRO* 6.0 1.5 - - - +
118B SER* 2.8 26.1 + - - -
119B LEU* 4.4 4.3 - - - +
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Residues in contact with GLU 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B HIS 3.4 17.2 - - - +
50B PHE* 3.6 11.8 - - + -
51B SER* 2.7 41.3 + - - -
52B THR* 3.0 21.6 + - - +
54B ASP* 1.3 73.6 + - - +
56B MSE 1.3 66.9 + - - +
58B ALA* 3.4 6.4 + - + +
59B PHE* 3.0 24.1 + - + +
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Residues in contact with MSE 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B LEU* 5.0 8.3 - - + +
15B ALA* 5.8 1.0 - - - -
18B LEU* 4.1 13.5 - - + -
32B VAL* 4.0 26.2 - - + +
35B VAL* 4.2 30.7 - - + -
46B VAL* 4.0 25.1 - - - -
50B PHE* 3.8 33.9 - - + -
52B THR 3.1 7.4 + - - +
53B LYS* 3.1 12.2 + - + +
55B GLU* 1.3 80.0 - - - +
57B PHE* 1.3 90.2 + - + +
59B PHE* 3.3 4.7 + - - +
60B ALA* 3.0 21.0 + - + +
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Residues in contact with PHE 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B LEU* 3.6 18.6 - - + -
27B LEU* 3.6 28.3 - - + -
30B ALA* 3.7 22.2 - - + -
35B VAL* 5.6 0.4 - - + -
53B LYS* 3.0 39.2 + - + +
54B ASP* 3.6 10.3 - - - +
56B MSE 1.3 100.8 - - + +
58B ALA* 1.3 57.0 + - - +
60B ALA* 3.2 1.9 + - - +
61B LEU* 2.9 25.1 + - - +
109B PHE* 3.5 24.2 - + + -
112B ARG* 3.3 44.9 - - - +
119B LEU* 3.9 9.4 - - + -
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Residues in contact with ALA 58 (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 ASP 2.9 17.4 + - - +
55B GLU* 3.7 8.7 - - - +
57B PHE* 1.3 75.3 - - - +
59B PHE* 1.3 58.6 + - - +
61B LEU 3.2 0.7 + - - -
62B ARG* 2.9 38.1 + - - +
118B SER* 3.8 18.6 - - - +
119B LEU* 3.6 11.4 - - - +
122B ILE* 3.5 18.9 - - + +
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Residues in contact with PHE 59 (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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11B PRO* 3.4 40.6 - - + -
12B GLU* 3.8 26.2 - - + -
15B ALA* 3.8 9.0 - - + -
50B PHE* 3.6 26.0 - + + -
55B GLU* 3.0 17.0 + - + +
56B MSE 3.6 2.9 - - - +
57B PHE 3.3 0.2 - - - -
58B ALA* 1.3 78.6 - - - +
60B ALA* 1.3 61.1 + - - +
62B ARG* 3.3 27.5 + - + +
63B THR* 3.0 42.2 + - - -
603B NDS 3.5 25.4 - - - -
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Residues in contact with ALA 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ALA* 3.8 28.2 - - - +
18B LEU* 3.8 34.3 - - + -
19B PHE* 6.1 0.4 - - + -
56B MSE 3.0 13.8 + - + +
57B PHE 3.5 7.4 - - - +
59B PHE* 1.3 75.5 - - - +
61B LEU* 1.3 62.7 + - - +
63B THR* 3.2 3.6 + - - -
64B LEU* 3.1 22.2 + - - +
109B PHE* 4.2 3.4 - - + -
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Residues in contact with LEU 61 (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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57B PHE 2.9 16.9 + - - +
58B ALA 3.2 4.5 + - - +
60B ALA* 1.3 76.1 - - - +
62B ARG* 1.3 57.7 + - - +
64B LEU* 3.2 4.7 + - + +
65B VAL* 2.9 41.9 + - + +
106B MSE 3.8 18.8 - - + -
109B PHE* 3.8 37.4 - - + -
119B LEU* 3.9 29.8 - - + +
122B ILE* 3.7 28.9 - - + -
123B ARG* 4.2 13.7 - - + -
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Residues in contact with ARG 62 (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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58B ALA* 2.9 25.1 + - - +
59B PHE* 3.5 25.6 - - + +
61B LEU* 1.3 74.5 - - - +
63B THR* 1.3 63.0 + - - +
65B VAL* 3.3 10.6 - - - +
66B ASP* 3.0 26.7 + - - +
122B ILE* 3.6 28.7 - - + -
204B LMT 2.7 46.0 + - - +
603B NDS 2.7 45.7 + - - +
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Residues in contact with THR 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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12B GLU* 5.5 8.2 - - + +
15B ALA* 3.7 17.9 - - + +
16B ALA* 5.6 1.6 - - + +
59B PHE* 3.0 36.9 + - - -
60B ALA 3.5 8.7 - - - -
61B LEU 3.2 0.2 - - - -
62B ARG* 1.3 80.2 - - - +
64B LEU* 1.3 61.5 + - - +
66B ASP* 3.4 6.7 + - - +
67B LYS* 3.2 49.7 + - - +
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Residues in contact with LEU 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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19B PHE* 3.8 28.9 - - + -
60B ALA 3.1 13.0 + - - +
61B LEU* 3.5 11.4 - - + +
63B THR* 1.3 75.3 - - - +
65B VAL* 1.3 66.8 + - - +
67B LYS* 3.0 17.9 + - + +
68B LEU* 3.0 32.9 + - + +
102B GLU* 4.1 18.2 - - + +
105B VAL* 3.8 29.4 - - + -
106B MSE 3.7 34.8 - - + +
109B PHE* 4.9 1.6 - - + -
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Residues in contact with VAL 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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61B LEU* 2.9 41.8 + - + +
62B ARG* 3.3 18.6 - - - +
64B LEU* 1.3 72.5 - - - +
66B ASP* 1.3 59.9 + - - +
68B LEU* 3.3 8.5 + - - +
69B LEU* 2.8 40.1 + - + +
106B MSE 4.0 20.0 - - + -
122B ILE* 4.1 9.0 - - + -
123B ARG* 6.0 1.6 - - + -
126B THR* 3.6 33.2 - - + +
204B LMT 4.7 11.0 - - - +
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Residues in contact with ASP 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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62B ARG 3.0 19.6 + - - +
63B THR* 3.5 8.6 - - - +
64B LEU 3.2 0.2 - - - -
65B VAL* 1.3 77.9 - - + +
67B LYS* 1.3 63.1 + - - +
69B LEU* 3.5 7.7 + - - +
70B ALA* 2.9 32.2 + - - +
204B LMT 5.9 4.2 - - - +
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Residues in contact with LYS 67 (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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16B ALA* 6.6 0.2 - - - -
63B THR* 3.2 35.0 + - - +
64B LEU* 3.0 18.2 + - + +
66B ASP* 1.3 84.0 + - - +
68B LEU* 1.3 62.5 + - + +
70B ALA* 3.3 7.7 + - - +
71B ARG* 3.1 34.8 + - - +
102B GLU* 5.3 3.8 - - - +
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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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64B LEU* 3.0 18.6 + - + +
65B VAL* 3.3 8.3 + - - +
67B LYS* 1.3 75.2 - - + +
69B LEU* 1.3 65.1 + - + +
71B ARG* 3.0 23.4 + - - +
72B LEU* 3.0 27.7 + - + +
91B GLN* 4.7 5.0 - - - +
92B LEU* 4.4 21.7 - - + +
102B GLU* 3.3 36.1 - - + +
106B MSE 3.9 43.3 - - + -
126B THR* 6.2 1.8 - - + -
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Residues in contact with LEU 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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65B VAL* 2.8 29.7 + - + +
66B ASP* 3.9 6.3 - - - +
68B LEU* 1.3 70.0 - - + +
70B ALA* 1.3 60.8 + - - +
72B LEU* 3.3 7.6 + - + -
73B SER* 2.9 32.7 + - - -
126B THR* 4.6 15.0 - - + +
129B THR* 4.2 6.7 - - + -
130B ILE* 3.8 32.5 - - + -
204B LMT 3.4 70.8 - - + +
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Residues in contact with ALA 70 (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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66B ASP* 2.9 23.0 + - - +
67B LYS* 3.4 9.2 - - - +
68B LEU 3.2 0.2 - - - -
69B LEU* 1.3 75.3 - - - +
71B ARG* 1.3 63.0 + - + +
73B SER* 3.2 19.1 + - - -
74B GLU* 3.2 17.8 + - - +
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Residues in contact with ARG 71 (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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67B LYS* 3.1 17.3 + - - +
68B LEU* 3.0 24.9 + - - +
70B ALA* 1.3 78.6 - - + +
72B LEU* 1.3 61.8 + - - +
74B GLU* 3.1 37.8 + - - +
75B VAL* 3.6 10.2 + - - +
91B GLN* 2.6 59.1 + - + +
99B ARG* 3.8 7.3 - - - +
102B GLU* 2.7 43.0 + - - -
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Residues in contact with LEU 72 (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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68B LEU* 3.0 14.6 + - + +
69B LEU* 3.6 14.8 - - + +
71B ARG* 1.3 75.3 - - - +
73B SER* 1.3 61.9 + - - +
74B GLU 3.3 0.5 + - - -
75B VAL* 3.3 20.3 + - - +
77B ARG* 5.6 3.1 + - - -
88B ALA* 3.3 41.5 - - + +
89B MSE 4.5 4.3 - - + -
91B GLN* 4.2 9.6 - - + -
92B LEU* 4.5 14.8 - - + -
130B ILE* 3.8 37.9 - - + -
204B LMT 3.8 32.9 - - + +
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Residues in contact with SER 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B LEU 2.9 11.7 + - - -
70B ALA* 3.3 13.0 - - - -
71B ARG 3.2 0.2 - - - -
72B LEU* 1.3 76.1 - - - +
74B GLU* 1.3 58.9 + - - +
75B VAL 3.2 6.2 + - - +
204B LMT 2.5 36.6 - - - +
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Residues in contact with GLU 74 (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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70B ALA* 3.2 7.4 + - - +
71B ARG* 3.1 42.6 + - - +
73B SER* 1.3 77.1 - - - +
75B VAL* 1.3 65.6 + - + +
76B GLU* 3.3 4.7 + - - +
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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
------------------------------------------------------------
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