Contacts of the helix formed by residues 45 - 64 (chain B) in PDB entry 1NUA
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 45 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B ASP* 1.3 70.6 - - - +
46B ASN* 1.3 67.1 + - - +
48B GLY 3.7 0.5 - - - -
49B SER* 2.8 32.8 + - - -
76B ASN* 3.7 29.1 + - + +
77B ARG 3.2 11.2 + - - +
78B PRO* 4.8 2.2 - - + -
79B PRO* 3.2 21.8 - - + +
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Residues in contact with ASN 46 (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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44B ASP* 2.9 9.9 + - - +
45B THR* 1.3 81.2 + - - +
47B ILE* 1.3 65.3 + - + +
49B SER* 2.8 24.3 + - - -
50B ILE* 3.3 17.2 - - + +
79B PRO* 3.0 32.3 - - - +
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Residues in contact with ILE 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B THR* 3.2 20.6 - - + -
44B ASP* 2.9 24.9 + - - +
46B ASN* 1.3 81.9 - - + +
48B GLY* 1.3 56.1 + - - +
50B ILE* 3.6 3.5 + - - -
51B TYR* 3.2 49.9 + - + +
112B LEU* 4.2 8.6 - - + +
113B GLY* 3.7 22.0 - - - -
114B GLY 4.4 4.7 - - - +
117B ILE* 4.8 2.2 - - + -
139B THR* 3.9 27.1 - - + +
140B THR* 6.1 1.1 - - + -
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Residues in contact with GLY 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B THR* 3.5 6.3 - - - +
44B ASP 2.9 15.9 + - - -
45B THR 3.7 0.9 - - - -
47B ILE* 1.3 75.5 - - - +
49B SER* 1.3 58.5 + - - +
50B ILE 3.0 5.4 - - - -
52B THR* 2.8 49.6 + - - -
53B PRO* 3.0 2.6 - - - +
76B ASN* 3.8 11.0 - - - -
112B LEU* 5.4 0.4 - - - -
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Residues in contact with SER 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B THR 2.8 18.8 + - - -
46B ASN* 2.8 21.1 + - - -
48B GLY* 1.3 71.6 - - - +
50B ILE* 1.3 64.0 + - - +
53B PRO* 3.8 14.7 - - - +
76B ASN* 4.7 0.6 - - - +
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Residues in contact with ILE 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ASN* 3.3 22.2 + - + +
47B ILE* 3.9 7.6 - - - +
48B GLY 3.0 0.4 - - - -
49B SER* 1.3 87.1 - - - +
51B TYR* 1.3 91.6 + - + +
53B PRO* 3.9 7.4 - - - +
54B SER* 5.0 3.3 + - - -
182B THR* 6.3 2.9 - - + -
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Residues in contact with TYR 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B TRP* 3.2 28.2 + + - +
47B ILE* 3.2 43.8 + - + +
50B ILE* 1.3 103.7 - - + +
52B THR* 1.3 68.7 + - - +
53B PRO* 3.3 2.9 - - - -
54B SER* 3.1 22.4 + - - -
55B PHE 3.4 0.5 + - - -
112B LEU* 4.3 6.7 - - + -
139B THR* 4.7 8.2 - - + +
178B GLU 5.9 0.4 - - - -
179B PHE* 3.7 41.2 + + + +
182B THR* 2.5 33.7 + - + -
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Residues in contact with THR 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B TRP* 5.0 0.4 - - - +
41B LEU* 4.1 17.7 - - + +
43B THR* 4.8 2.1 + - - -
48B GLY* 2.8 35.8 + - - -
51B TYR* 1.3 73.2 - - - +
53B PRO* 1.3 57.8 - - + +
55B PHE* 2.8 28.8 + - - +
56B GLU* 3.0 20.9 + - + +
74B ILE* 3.4 37.7 - - + +
76B ASN* 4.6 5.4 + - - +
112B LEU* 4.7 6.0 - - - +
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Residues in contact with PRO 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B GLY 3.0 13.5 - - - +
49B SER* 3.8 16.6 - - - +
50B ILE 3.9 9.6 - - - +
51B TYR 3.3 4.0 - - - -
52B THR* 1.3 91.4 - - + +
54B SER* 1.3 61.9 + - - +
55B PHE 3.1 0.9 + - - -
56B GLU* 3.3 26.2 + - - +
57B GLU* 3.5 10.7 + - - +
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Residues in contact with SER 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B TRP* 4.1 14.6 + - - +
23B ARG* 4.7 17.5 - - - +
50B ILE 5.0 1.9 + - - -
51B TYR* 3.1 18.0 + - - +
53B PRO* 1.3 80.1 - - - +
55B PHE* 1.3 56.2 + - - +
57B GLU* 3.8 7.1 - - - +
58B ALA* 3.2 24.1 + - - +
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Residues in contact with PHE 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B TRP* 3.3 57.7 - + + -
26B VAL* 3.5 22.7 - - + -
27B ALA* 3.4 42.2 - - + -
30B LEU* 4.4 11.4 - - + -
41B LEU* 4.7 11.0 - - + -
51B TYR 3.9 0.2 - - - +
52B THR* 2.8 13.1 + - - +
54B SER* 1.3 78.8 + - - +
56B GLU* 1.3 67.7 + - - +
57B GLU 3.0 1.8 - - - -
58B ALA* 2.8 5.2 + - + -
59B PHE* 2.7 33.1 + + - +
72B LEU* 4.4 24.9 - - + -
110B ILE* 5.5 4.5 - - + -
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Residues in contact with GLU 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B THR* 3.0 22.6 + - + +
53B PRO* 3.7 17.7 - - - +
55B PHE* 1.3 78.2 - - + +
57B GLU* 1.3 61.8 + - - +
59B PHE* 3.2 19.9 + - - +
60B ARG* 3.2 14.5 + - - +
72B LEU* 4.2 10.0 - - + +
74B ILE* 3.8 30.1 - - + +
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Residues in contact with GLU 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B PRO 3.5 7.6 + - - +
54B SER* 3.8 10.5 - - - +
55B PHE 3.0 0.6 - - - -
56B GLU* 1.3 76.7 - - - +
58B ALA* 1.3 63.7 + - - +
59B PHE 2.9 6.0 + - - -
60B ARG* 3.4 27.4 + - - +
61B LYS* 3.2 35.2 + - + +
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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
----------------------------------------------------------
22B TRP 4.8 0.7 - - - +
23B ARG* 3.7 24.2 - - - +
27B ALA* 3.3 23.5 - - + +
54B SER 3.2 12.7 + - - +
55B PHE* 2.8 18.1 + - + +
57B GLU* 1.3 76.2 - - - +
59B PHE* 1.3 60.4 + - - +
61B LYS* 3.7 7.1 - - - +
62B ARG* 3.6 17.2 + - - +
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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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27B ALA* 4.0 13.0 - - + -
30B LEU* 5.7 1.6 - - + -
31B ILE* 3.6 28.9 - - + +
39B TYR* 4.0 20.6 - + + -
55B PHE* 2.7 21.3 + + + +
56B GLU 3.2 11.9 - - - +
57B GLU 2.9 1.4 - - - -
58B ALA* 1.3 74.6 - - - +
60B ARG* 1.3 58.1 + - - +
61B LYS 3.1 1.4 + - - -
62B ARG* 3.2 3.5 + - - +
63B ALA* 2.6 44.1 + - + +
70B PRO* 3.7 15.3 - - + -
71B ARG 3.5 18.6 - - - -
72B LEU* 3.0 50.5 - - + -
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Residues in contact with ARG 60 (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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56B GLU 3.2 10.7 + - - +
57B GLU* 3.5 33.7 + - - +
59B PHE* 1.3 81.6 - - + +
61B LYS* 1.3 60.7 + - - +
63B ALA* 3.9 7.2 - - - -
64B ALA* 2.6 38.5 + - + +
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Residues in contact with LYS 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 GLU* 3.2 26.9 + - + +
58B ALA* 3.7 10.3 - - - +
60B ARG* 1.3 86.5 - - - +
62B ARG* 1.3 67.8 + - + +
64B ALA* 3.4 9.7 + - - +
65B GLU* 3.6 15.4 - - - +
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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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27B ALA* 4.7 2.7 - - + +
28B LYS* 3.7 51.3 - - + +
31B ILE* 4.5 17.0 - - + +
58B ALA 3.6 13.7 + - - +
59B PHE 3.2 2.9 + - - +
61B LYS* 1.3 85.4 - - + +
63B ALA* 1.3 58.8 + - - +
64B ALA 3.4 0.2 - - - -
65B GLU* 3.0 45.3 + - - +
66B ILE* 4.5 4.0 - - - +
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Residues in contact with ALA 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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31B ILE* 4.6 4.0 - - + -
59B PHE* 2.6 38.5 + - + +
60B ARG* 3.9 5.4 - - - +
62B ARG* 1.3 71.4 - - - +
64B ALA* 1.3 63.5 + - - +
65B GLU 3.2 2.8 + - - -
66B ILE* 3.3 9.1 + - - +
69B SER* 3.0 25.7 - - - -
70B PRO* 3.9 34.0 - - + +
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Residues in contact with ALA 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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60B ARG* 2.6 23.0 + - + +
61B LYS* 3.7 6.1 - - - +
62B ARG 3.4 0.2 - - - -
63B ALA* 1.3 73.9 - - - +
65B GLU* 1.3 55.9 + - + +
66B ILE 3.2 11.1 + - - +
67B THR* 5.0 2.8 + - - -
69B SER* 4.4 7.2 - - - -
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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