Contacts of the helix formed by residues 56 - 74 (chain B) in PDB entry 5WC9
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 SER 56 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B LEU* 1.3 83.4 - - - +
57B PHE* 1.3 59.6 + - - +
58B LYS* 3.9 4.3 + - - +
59B ASN* 3.2 14.4 + - - +
60B ALA* 2.9 24.9 + - - +
147B LYS* 3.4 23.5 + - - -
173D A 5.6 1.6 - - - -
174D A 2.5 29.7 + - - -
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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
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3B SER* 5.3 0.2 - - - -
5B GLU* 3.7 37.9 - - + -
6B ILE* 4.4 18.2 - - + -
9B LEU* 3.9 20.0 - - + -
56B SER* 1.3 73.6 - - - +
58B LYS* 1.3 67.3 + - + +
60B ALA* 3.2 2.4 + - - +
61B CYS* 3.1 47.4 + - - -
147B LYS 4.3 2.6 + - - -
148B ARG 5.3 0.2 - - - -
149B VAL* 3.7 16.4 - - + +
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Residues in contact with LYS 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B SER* 3.3 4.5 + - - +
57B PHE* 1.3 86.0 - - + +
59B ASN* 1.3 62.5 + - - +
61B CYS* 3.5 5.5 + - - +
62B LYS* 3.3 20.4 + - - +
173D A 4.4 8.1 + - - +
174D A 3.2 25.6 + - - +
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Residues in contact with ASN 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B THR* 5.8 2.0 - - - +
55B LEU* 3.6 27.4 - - + +
56B SER* 3.2 25.1 + - - +
58B LYS* 1.3 79.5 - - - +
60B ALA* 1.3 57.0 + - - +
62B LYS* 3.3 5.8 + - - +
63B LEU* 3.0 44.6 + - - +
174D A 3.8 29.2 + - - +
175D T 3.3 27.0 + - - +
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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
----------------------------------------------------------
9B LEU* 3.6 27.8 - - + -
50B PHE* 3.5 10.2 - - + -
53B LEU* 4.4 5.8 - - + -
55B LEU* 3.4 19.7 - - + +
56B SER 2.9 17.5 + - - +
57B PHE* 3.2 6.7 + - - +
59B ASN* 1.3 77.0 - - - +
61B CYS* 1.3 57.4 + - - +
63B LEU 3.4 0.2 + - - -
64B LYS* 2.9 32.4 + - - +
149B VAL* 4.4 3.1 - - + -
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Residues in contact with CYS 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B GLU* 5.8 0.9 - - - -
9B LEU* 4.6 10.8 - - - -
57B PHE* 3.1 53.7 + - - +
58B LYS* 3.5 5.8 + - - +
60B ALA* 1.3 76.5 - - - +
62B LYS* 1.3 62.7 + - - +
64B LYS* 3.9 15.0 + - - +
65B ALA* 3.2 21.5 + - - +
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Residues in contact with LYS 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B LYS 3.3 11.2 + - - +
59B ASN* 3.6 11.4 - - - +
60B ALA 3.3 0.4 - - - -
61B CYS* 1.3 78.7 - - - +
63B LEU* 1.3 70.2 + - + +
65B ALA* 3.1 16.1 + - - +
66B ILE* 3.1 22.8 + - + +
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Residues in contact with LEU 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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42B PHE* 4.3 21.1 - - + -
46B THR* 3.7 30.1 - - + -
47B ILE* 5.7 2.7 - - + -
50B PHE* 3.8 24.2 - - + -
55B LEU* 3.8 22.7 - - + -
59B ASN* 3.0 34.9 + - - +
62B LYS* 1.3 79.0 - - + +
64B LYS* 1.3 56.4 + - - +
66B ILE* 3.1 9.9 + - + +
67B LEU* 2.7 46.0 + - + +
175D T 4.1 10.3 - - - +
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Residues in contact with LYS 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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8B GLU* 4.7 12.3 - - - +
9B LEU* 3.6 26.2 - - + +
12B PHE* 3.6 35.5 - - + -
50B PHE* 3.5 18.5 - - + -
60B ALA 2.9 19.0 + - - +
61B CYS* 3.9 15.7 + - - +
63B LEU* 1.3 76.0 - - - +
65B ALA* 1.3 58.9 + - - +
68B SER* 2.8 34.9 + - - +
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Residues in contact with ALA 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 CYS 3.2 10.9 + - - +
62B LYS* 3.1 12.8 + - - +
64B LYS* 1.3 78.4 - - - +
66B ILE* 1.3 65.5 + - + +
68B SER* 3.1 18.4 + - - -
69B LYS* 3.3 18.5 - - + +
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Residues in contact with ILE 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B LEU* 4.1 20.4 - - + -
37B VAL* 4.5 12.5 - - + +
38B HIS* 3.3 52.7 - - + +
42B PHE* 4.3 13.2 - - + -
62B LYS* 3.1 19.9 + - + +
63B LEU* 3.1 15.7 + - + +
65B ALA* 1.3 77.1 - - + +
67B LEU* 1.3 62.3 + - + +
69B LYS* 3.7 5.1 + - - +
70B TRP* 3.3 20.4 + - - +
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Residues in contact with LEU 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B PHE* 4.1 12.1 - - + -
16B PHE* 3.7 31.9 - - + -
30B VAL* 4.9 1.6 - - + -
34B LEU* 3.7 34.5 - - + -
47B ILE* 4.5 16.2 - - + -
50B PHE* 3.6 39.5 - - + -
63B LEU* 2.7 30.0 + - + +
64B LYS 4.1 1.6 - - - +
66B ILE* 1.3 72.4 - - + +
68B SER* 1.3 60.0 + - - +
70B TRP* 3.3 5.7 + - + +
71B LEU* 2.8 31.4 + - - +
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Residues in contact with SER 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B PHE* 3.6 25.5 - - - -
64B LYS* 2.8 22.9 + - - -
65B ALA* 3.1 10.9 + - - -
67B LEU* 1.3 78.0 - - - +
69B LYS* 1.3 67.3 + - - +
71B LEU* 3.5 3.8 + - - +
72B GLU* 3.3 22.5 + - - +
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Residues in contact with LYS 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B VAL* 3.9 21.8 - - + -
65B ALA* 3.3 18.5 + - + +
66B ILE* 4.1 1.3 - - - +
67B LEU 3.4 0.2 - - - -
68B SER* 1.3 86.0 + - - +
70B TRP* 1.3 61.4 + - - +
72B GLU* 3.8 5.5 + - - +
73B GLU* 3.2 22.3 + - - +
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Residues in contact with TRP 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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16B PHE* 3.9 24.2 - + - -
20B ARG* 5.5 2.0 - - + -
23B LEU* 5.8 0.4 - - + -
25B TYR* 3.8 32.1 - + + -
30B VAL* 3.7 26.7 - - + -
33B ALA* 2.8 38.6 + - + +
34B LEU* 3.5 23.1 - - + -
36B ALA* 5.7 0.7 - - + -
37B VAL* 4.0 24.8 - - + +
66B ILE 3.3 15.7 + - - +
67B LEU* 3.8 6.7 - - + +
68B SER 3.2 0.6 - - - -
69B LYS* 1.3 78.5 - - - +
71B LEU* 1.3 85.5 + - + +
73B GLU* 2.8 9.4 + - + +
74B ALA* 2.7 57.1 + - + +
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Residues in contact with LEU 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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12B PHE* 4.8 12.1 - - + -
15B GLU* 4.9 0.9 - - + +
16B PHE* 4.0 33.2 - - + +
19B ARG* 3.9 51.8 - - + +
20B ARG* 4.8 1.8 - - - +
23B LEU* 4.1 21.1 - - + -
67B LEU 2.8 22.1 + - - +
68B SER 3.9 4.5 - - - +
69B LYS 3.5 0.2 - - - -
70B TRP* 1.3 89.9 - - + +
72B GLU* 1.3 61.8 + - - +
74B ALA 3.1 11.8 + - - -
75B GLU* 3.2 15.3 - - - +
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Residues in contact with GLU 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ARG* 5.0 4.2 - - - +
68B SER 3.3 14.4 + - - +
69B LYS* 3.9 6.1 - - - +
70B TRP 3.3 0.4 - - - -
71B LEU* 1.3 77.4 - - - +
73B GLU* 1.3 62.5 + - - +
74B ALA 3.2 0.9 + - - -
75B GLU* 3.2 26.1 + - - +
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Residues in contact with GLU 73 (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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36B ALA* 4.0 16.2 - - - +
37B VAL* 3.4 30.1 - - + +
69B LYS 3.2 12.0 + - - +
70B TRP* 2.8 19.2 + - + +
72B GLU* 1.3 75.2 - - - +
74B ALA* 1.3 56.0 + - - +
75B GLU 3.3 0.7 - - - -
76B GLN* 3.1 22.2 + - - +
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Residues in contact with ALA 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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23B LEU* 3.3 24.3 - - + +
25B TYR* 4.0 17.9 + - + +
70B TRP* 2.7 52.6 + - + +
71B LEU* 3.1 9.1 + - - +
73B GLU* 1.3 72.8 - - - +
75B GLU* 1.3 57.0 + - - +
76B GLN* 3.6 12.7 + - - +
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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