Contacts of the helix formed by residues 79 - 93 (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 SER 79 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43C ARG* 5.7 0.5 - - - +
46C GLU* 3.7 39.9 + - - +
47C GLN* 5.3 3.8 - - - -
50C ALA* 4.1 12.3 - - - +
72C LEU* 5.0 10.0 - - - +
76C PRO 4.0 10.8 + - - -
77C SER 3.2 8.0 + - - -
78C GLN* 1.3 74.5 - - - +
80C ALA* 1.3 65.3 + - - +
82C LEU* 4.2 1.8 - - - +
83C LEU* 3.3 23.6 + - - +
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Residues in contact with ALA 80 (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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79C SER* 1.3 78.8 + - - +
81C ASN* 1.3 58.1 + - - +
83C LEU* 3.2 6.4 + - - +
84C ALA* 2.7 38.7 + - - +
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Residues in contact with ASN 81 (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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78C GLN* 3.5 43.3 + - + +
79C SER 3.5 1.2 - - - +
80C ALA* 1.3 80.2 - - - +
82C LEU* 1.3 57.2 + - - +
84C ALA* 3.3 6.6 + - - +
85C GLU* 2.9 31.8 + - - +
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Residues in contact with LEU 82 (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* 4.4 8.5 - - + +
68C PHE* 4.0 18.6 - - + +
71C SER* 3.6 22.0 - - - +
72C LEU* 3.4 52.0 - - + +
75C ASP* 4.4 4.0 - - + +
78C GLN* 3.4 24.4 + - + +
79C SER 4.3 2.0 - - - +
80C ALA 3.3 0.4 - - - -
81C ASN* 1.3 78.1 - - - +
83C LEU* 1.3 62.5 + - - +
85C GLU* 3.5 7.2 + - + +
86C ALA* 3.2 23.7 + - - +
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Residues in contact with LEU 83 (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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49C ASN 5.1 0.7 - - - +
50C ALA* 3.6 27.4 - - + +
53C GLU* 3.8 33.7 - - + +
54C ILE* 3.9 27.3 - - + +
57C LEU* 5.1 1.6 - - + -
79C SER 3.3 16.6 + - - +
80C ALA* 3.2 7.3 + - - +
82C LEU* 1.3 77.0 - - - +
84C ALA* 1.3 60.3 + - - +
86C ALA* 3.4 1.9 + - - +
87C LYS* 2.9 52.0 + - + +
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Residues in contact with ALA 84 (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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80C ALA* 2.7 21.7 + - + +
81C ASN* 3.7 8.1 - - - +
83C LEU* 1.3 74.4 - - - +
85C GLU* 1.3 51.1 + - - +
87C LYS* 3.0 9.5 + - - +
88C LYS* 2.6 38.3 + - - +
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Residues in contact with GLU 85 (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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68C PHE* 4.0 22.6 - - + -
81C ASN 2.9 18.1 + - - +
82C LEU* 3.8 9.9 - - + +
84C ALA* 1.3 76.2 - - - +
86C ALA* 1.3 57.7 + - - +
88C LYS* 3.0 36.6 + - - +
89C LEU* 3.0 38.1 + - - +
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Residues in contact with ALA 86 (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* 4.1 20.4 - - + -
57C LEU* 3.8 11.3 - - + +
60C LEU* 4.3 5.0 - - + +
68C PHE* 3.4 34.5 - - + -
82C LEU 3.2 17.0 + - - +
83C LEU 3.8 3.8 - - - +
85C GLU* 1.3 77.1 - - - +
87C LYS* 1.3 57.9 + - - +
89C LEU* 3.8 1.4 + - - +
90C ASN* 3.0 28.8 + - - +
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Residues in contact with LYS 87 (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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53C GLU* 3.2 25.0 + - - -
57C LEU* 4.3 19.1 - - + -
83C LEU* 2.9 43.9 + - + +
84C ALA* 3.0 7.2 + - - +
86C ALA* 1.3 77.0 - - - +
88C LYS* 1.3 59.5 + - - +
90C ASN* 3.6 5.5 - - - +
91C ASP* 2.8 47.1 + - - +
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Residues in contact with LYS 88 (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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84C ALA 2.6 21.1 + - - +
85C GLU* 3.0 37.5 + - - +
87C LYS* 1.3 72.4 - - - +
89C LEU* 1.3 72.3 + - - +
90C ASN 3.2 0.9 + - - -
91C ASP* 3.9 6.5 - - - +
92C ALA* 3.2 26.9 + - + +
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Residues in contact with LEU 89 (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* 4.5 2.5 - - + -
64C GLN* 3.3 38.6 - - + +
68C PHE* 3.9 24.9 - - + -
85C GLU* 3.0 28.5 + - - +
86C ALA 3.9 3.4 - - - +
88C LYS* 1.3 82.7 - - - +
90C ASN* 1.3 60.2 + - - +
92C ALA* 4.2 7.0 - - + +
93C GLN* 3.3 30.8 + - - +
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Residues in contact with ASN 90 (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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57C LEU* 3.5 32.5 - - + +
58C PRO* 4.1 5.7 - - - +
59C ASN* 3.0 55.9 + - - +
60C LEU* 3.2 18.5 + - + +
86C ALA 3.0 20.7 + - - +
87C LYS* 3.6 7.4 - - - +
88C LYS 3.1 0.6 - - - -
89C LEU* 1.3 77.6 - - - +
91C ASP* 1.3 73.1 + - - +
93C GLN* 3.1 10.9 + - - -
94C ALA 3.5 0.2 + - - -
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Residues in contact with ASP 91 (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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57C LEU* 6.1 0.3 - - - +
59C ASN* 5.2 0.2 - - - -
87C LYS* 2.8 35.2 + - - +
88C LYS* 3.9 5.4 + - - +
90C ASN* 1.3 83.6 + - - +
92C ALA* 1.3 60.9 + - - +
94C ALA* 3.1 24.1 + - - +
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Residues in contact with ALA 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C LYS* 3.2 16.8 + - + +
89C LEU* 4.2 8.5 - - + +
91C ASP* 1.3 77.6 - - - +
93C GLN* 1.3 55.3 + - - +
94C ALA 3.3 5.5 + - - +
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Residues in contact with GLN 93 (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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59C ASN* 3.1 35.3 + - - +
60C LEU* 3.8 8.1 - - - +
61C ASN* 5.1 3.1 + - - -
64C GLN* 2.7 43.5 + - - +
89C LEU* 3.3 24.4 + - - +
90C ASN 3.1 8.7 + - - +
92C ALA* 1.3 75.5 - - - +
94C ALA* 1.3 64.2 + - - +
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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
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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