Contacts of the helix formed by residues 61 - 75 (chain B) in PDB entry 5XBY
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 61 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59B ASN 3.7 3.0 + - - -
60B LEU* 1.3 76.5 - - - +
62B GLU* 1.3 61.8 + - - +
63B GLU* 3.2 9.5 + - - +
64B GLN* 2.8 53.2 + - - +
65B ARG* 3.3 11.4 + - - +
93B GLN* 4.4 3.6 + - - +
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Residues in contact with GLU 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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61B ASN* 1.3 74.2 - - - +
63B GLU* 1.3 52.9 + - - +
65B ARG* 3.8 21.5 + - - +
66B ASN* 2.7 52.5 + - - +
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Residues in contact with GLU 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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61B ASN* 3.2 10.7 + - - +
62B GLU* 1.3 78.6 - - - +
64B GLN* 1.3 59.0 + - + +
66B ASN* 3.8 8.0 - - + +
67B ALA* 3.1 29.3 + - - +
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Residues in contact with GLN 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 LEU* 3.5 12.9 - - + +
61B ASN* 2.8 46.5 + - - +
63B GLU* 1.3 73.9 - - + +
65B ARG* 1.3 65.8 + - - +
66B ASN 3.2 0.2 - - - -
67B ALA* 3.1 7.0 + - - +
68B PHE* 3.0 37.6 + - + -
89B LEU* 3.3 24.1 - - + +
93B GLN* 2.7 41.9 + - - -
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Residues in contact with ARG 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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54B ILE* 3.6 20.9 + - - +
55B LEU* 3.1 34.7 + - - +
56B HIS 5.3 1.4 - - - -
57B LEU 3.5 17.4 + - - +
58B PRO* 4.6 5.3 + - - +
60B LEU* 3.4 36.3 + - + +
61B ASN 3.3 11.9 + - - +
62B GLU* 3.9 32.4 - - - +
64B GLN* 1.3 75.6 - - - +
66B ASN* 1.3 63.5 + - - +
68B PHE* 3.5 1.4 + - - +
69B ILE* 3.0 45.1 + - + +
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Residues in contact with ASN 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 GLU* 2.7 42.0 + - - +
63B GLU* 3.8 8.7 - - + +
64B GLN 3.2 0.2 - - - -
65B ARG* 1.3 81.1 - - - +
67B ALA* 1.3 55.8 + - - +
69B ILE* 3.8 8.6 - - - +
70B GLN* 2.7 39.0 + - - +
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Residues in contact with ALA 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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63B GLU* 3.1 18.2 + - - +
64B GLN* 3.1 10.5 + - - +
66B ASN* 1.3 75.7 - - - +
68B PHE* 1.3 64.6 + - + +
70B GLN* 3.6 6.4 - - - +
71B SER* 2.9 32.6 + - - -
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Residues in contact with PHE 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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54B ILE* 4.2 18.4 - - + +
60B LEU* 3.9 26.5 - - + -
64B GLN* 3.0 24.9 + - + +
65B ARG 4.0 2.9 - - - +
67B ALA* 1.3 79.0 - - + +
69B ILE* 1.3 61.9 + - - +
71B SER* 3.3 5.9 + - - -
72B LEU* 2.8 30.2 + - - +
82B LEU* 4.0 20.3 - - + +
85B GLU* 4.0 24.0 - - + -
86B ALA* 3.3 35.4 - - + -
89B LEU* 3.9 22.2 - - + -
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Residues in contact with ILE 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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51B PHE* 3.6 40.3 - - + +
54B ILE* 3.8 17.3 - - + -
55B LEU* 4.2 22.0 - - + -
65B ARG* 3.0 40.6 + - + +
66B ASN* 3.8 9.4 - - - +
68B PHE* 1.3 73.1 - - - +
70B GLN* 1.3 63.4 + - - +
72B LEU* 3.2 7.7 + - - +
73B LYS* 2.9 35.8 + - + +
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Residues in contact with GLN 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 ASN 2.7 23.0 + - - +
67B ALA* 3.6 7.6 - - - +
69B ILE* 1.3 75.4 - - - +
71B SER* 1.3 60.8 + - - +
73B LYS* 3.2 28.4 + - - +
74B ASP* 3.1 46.5 + - - +
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Residues in contact with SER 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 ALA 2.9 20.6 + - - -
68B PHE* 3.7 5.8 - - - -
70B GLN* 1.3 74.4 - - - +
72B LEU* 1.3 57.6 + - - +
74B ASP* 3.5 5.4 + - - +
75B ASP* 3.0 30.0 + - - +
82B LEU* 3.6 27.5 - - - +
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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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47B GLN* 4.4 12.3 + - + +
50B ALA* 4.0 7.9 - - + -
51B PHE* 3.4 47.8 - - + +
54B ILE* 4.2 11.2 - - + -
68B PHE 2.8 17.0 + - - +
69B ILE* 3.4 7.4 - - - +
71B SER* 1.3 77.4 - - - +
73B LYS* 1.3 64.9 + - - +
75B ASP 3.5 16.2 + - - +
76B PRO* 3.6 5.7 - - - +
79B SER* 3.5 39.0 - - - +
82B LEU* 3.5 11.0 - - + -
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Residues in contact with LYS 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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51B PHE* 6.0 6.3 - - + -
69B ILE* 2.9 23.1 + - + +
70B GLN* 3.2 33.0 + - - +
72B LEU* 1.3 77.3 - - - +
74B ASP* 1.3 64.7 + - - +
75B ASP 3.6 0.2 + - - -
76B PRO* 4.3 8.1 - - - +
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Residues in contact with ASP 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 GLN* 3.1 40.3 + - - +
71B SER* 4.0 6.4 - - - +
73B LYS* 1.3 81.9 + - - +
75B ASP* 1.3 60.8 + - + +
76B PRO* 3.8 5.0 - - - +
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Residues in contact with ASP 75 (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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71B SER 3.0 16.7 + - - +
72B LEU* 3.6 9.2 - - - +
73B LYS 3.4 0.4 - - - -
74B ASP* 1.3 81.1 - - + +
76B PRO* 1.3 63.9 - - - +
77B SER* 2.5 31.4 + - - -
78B GLN* 3.5 36.9 + - + +
79B SER 4.2 0.3 + - - -
82B LEU* 4.5 2.1 - - + +
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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