Contacts of the helix formed by residues 61 - 75 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59C ASN 3.7 3.0 + - - -
60C LEU* 1.3 77.2 - - - +
62C GLU* 1.3 62.2 + - - +
63C GLU* 3.2 9.8 + - - +
64C GLN* 2.8 48.2 + - - +
65C ARG* 3.4 17.2 + - - +
93C GLN* 4.4 2.8 + - - +
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Residues in contact with GLU 62 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61C ASN* 1.3 73.9 - - - +
63C GLU* 1.3 54.1 + - - +
65C ARG* 3.8 21.1 + - - +
66C ASN* 2.7 51.8 + - - +
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Residues in contact with GLU 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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61C ASN* 3.2 9.8 + - - +
62C GLU* 1.3 78.6 - - - +
64C GLN* 1.3 58.2 + - + +
66C ASN* 3.7 8.4 + - + +
67C ALA* 3.1 26.5 + - - +
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Residues in contact with GLN 64 (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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60C LEU* 3.5 12.8 - - + +
61C ASN* 2.8 43.5 + - - +
63C GLU* 1.3 76.9 - - + +
65C ARG* 1.3 65.5 + - - +
67C ALA* 3.2 6.7 + - - +
68C PHE* 3.0 37.2 + - + -
89C LEU* 3.3 24.8 - - + +
93C GLN* 2.7 42.3 + - - -
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Residues in contact with ARG 65 (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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54C ILE* 3.7 20.6 + - + +
55C LEU* 3.1 31.7 + - - +
56C HIS* 5.2 2.0 - - - +
57C LEU 3.5 17.0 + - - -
58C PRO* 4.6 5.1 + - - +
60C LEU* 3.4 35.6 + - + +
61C ASN 3.4 12.1 + - - +
62C GLU* 3.9 29.6 - - - +
64C GLN* 1.3 76.5 - - - +
66C ASN* 1.3 62.8 + - - +
68C PHE* 3.5 1.3 + - - +
69C ILE* 3.0 48.8 + - + +
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Residues in contact with ASN 66 (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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62C GLU* 2.7 44.2 + - - +
63C GLU* 3.8 8.2 - - + +
64C GLN 3.2 0.2 - - - -
65C ARG* 1.3 80.6 - - - +
67C ALA* 1.3 56.4 + - - +
69C ILE* 3.8 9.0 - - - +
70C GLN* 2.7 38.8 + - - +
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Residues in contact with ALA 67 (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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63C GLU* 3.1 17.5 + - - +
64C GLN* 3.2 9.6 + - - +
66C ASN* 1.3 74.9 - - - +
68C PHE* 1.3 65.1 - - + +
70C GLN* 3.6 6.3 - - - +
71C SER* 2.9 31.7 + - - -
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Residues in contact with PHE 68 (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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54C ILE* 4.2 19.4 - - + +
60C LEU* 3.9 26.0 - - + -
64C GLN* 3.0 24.6 + - + +
65C ARG* 3.9 3.1 - - - +
67C ALA* 1.3 79.0 - - + +
69C ILE* 1.3 61.2 + - - +
71C SER* 3.3 6.5 + - - -
72C LEU* 2.8 29.9 + - - +
82C LEU* 4.0 19.0 - - + +
85C GLU* 4.0 24.7 - - + -
86C ALA* 3.4 36.8 - - + -
89C LEU* 3.9 21.5 - - + -
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Residues in contact with ILE 69 (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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51C PHE* 3.4 34.4 - - + -
54C ILE* 3.9 16.6 - - + -
55C LEU* 4.5 22.4 - - + +
65C ARG* 3.0 40.4 + - + +
66C ASN* 3.8 9.2 - - - +
68C PHE* 1.3 74.2 - - - +
70C GLN* 1.3 63.5 + - - +
72C LEU* 3.2 3.9 + - - +
73C LYS* 2.9 33.3 + - + +
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Residues in contact with GLN 70 (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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66C ASN 2.7 23.0 + - - +
67C ALA* 3.6 7.4 - - - +
69C ILE* 1.3 76.2 - - - +
71C SER* 1.3 60.9 + - - +
73C LYS* 3.2 28.2 + - - +
74C ASP* 3.1 46.1 + - - +
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Residues in contact with SER 71 (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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67C ALA 2.9 21.2 + - - -
68C PHE* 3.7 5.8 - - - -
70C GLN* 1.3 73.7 - - - +
72C LEU* 1.3 57.7 + - - +
74C ASP* 3.9 5.3 - - - +
75C ASP* 3.0 29.8 + - - +
82C LEU* 3.6 24.5 - - - +
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Residues in contact with LEU 72 (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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47C GLN* 4.2 15.5 - - + +
50C ALA* 3.9 11.9 - - + +
51C PHE* 3.1 54.1 - - + +
54C ILE* 4.2 12.3 - - + -
68C PHE 2.8 16.9 + - - +
69C ILE 3.4 5.8 - - - +
70C GLN 3.2 0.2 - - - -
71C SER* 1.3 77.5 - - - +
73C LYS* 1.3 65.0 + - - +
75C ASP 3.5 17.6 + - - +
76C PRO* 3.6 9.0 - - + +
78C GLN 4.5 8.7 - - - +
79C SER* 5.0 9.9 - - - +
82C LEU* 3.4 21.3 - - + +
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Residues in contact with LYS 73 (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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47C GLN* 4.6 4.3 - - - +
51C PHE* 4.2 22.9 - - + -
69C ILE* 2.9 19.8 + - + +
70C GLN* 3.2 31.9 + - - +
72C LEU* 1.3 76.9 - - - +
74C ASP* 1.3 65.0 + - - +
75C ASP 3.6 0.2 + - - -
76C PRO* 4.2 8.5 - - - +
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Residues in contact with ASP 74 (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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70C GLN* 3.1 40.0 + - - +
71C SER* 4.0 6.0 - - - +
73C LYS* 1.3 83.3 + - - +
75C ASP* 1.3 59.5 + - + +
76C PRO* 3.8 5.0 - - - +
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Residues in contact with ASP 75 (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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71C SER 3.0 16.2 + - - +
72C LEU* 3.6 7.3 - - - +
73C LYS 3.4 0.2 - - - -
74C ASP* 1.3 82.3 - - + +
76C PRO* 1.4 64.2 - - - +
77C SER* 2.0 36.4 + - - -
78C GLN* 4.0 18.3 + - - +
82C LEU* 4.4 4.6 - - + +
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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