Contacts of the helix formed by residues 78 - 93 (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 GLN 78 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75B ASP* 3.5 26.9 + - + +
76B PRO 3.3 0.4 - - - -
77B SER* 1.3 86.4 + - - +
79B SER* 1.3 61.5 + - - +
80B ALA* 3.3 3.1 - - - +
81B ASN* 3.4 34.7 - - + +
82B LEU* 3.1 30.6 + - + +
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Residues in contact with SER 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B GLU* 4.7 6.8 + - - +
47B GLN* 3.6 18.3 + - - +
50B ALA* 4.4 12.3 - - - +
72B LEU* 3.5 29.3 - - - +
76B PRO 2.7 19.1 + - - -
77B SER 3.3 2.7 + - - -
78B GLN* 1.3 75.3 - - - +
80B ALA* 1.3 58.7 + - - +
82B LEU* 3.5 1.4 + - - +
83B LEU* 3.1 30.9 + - - +
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Residues in contact with ALA 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B SER 4.8 2.8 + - - +
78B GLN* 3.3 0.6 - - - -
79B SER* 1.3 77.3 + - - +
81B ASN* 1.3 68.1 + - - +
83B LEU* 3.5 6.7 + - - +
84B ALA* 3.1 25.3 + - - +
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Residues in contact with ASN 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B GLN* 3.4 47.0 + - + +
79B SER 3.4 0.4 - - - -
80B ALA* 1.3 80.7 - - - +
82B LEU* 1.3 58.3 + - + +
84B ALA* 3.7 5.3 - - - +
85B GLU* 3.1 27.5 + - - +
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Residues in contact with LEU 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B ILE* 4.6 9.9 - - + +
68B PHE* 4.0 22.8 - - + +
71B SER* 3.6 24.2 - - - +
72B LEU* 3.5 43.3 - - + +
75B ASP* 4.5 3.1 - - + +
78B GLN* 3.1 27.7 + - + +
79B SER* 4.0 3.6 - - - +
80B ALA 3.2 0.2 - - - -
81B ASN* 1.3 77.3 - - + +
83B LEU* 1.3 60.7 + - - +
84B ALA 3.2 0.4 - - - -
85B GLU* 3.9 6.6 - - + +
86B ALA* 2.9 32.4 + - - +
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Residues in contact with LEU 83 (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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50B ALA* 4.1 25.1 - - + +
53B GLU* 3.8 42.0 - - + +
54B ILE* 4.3 18.1 - - + +
57B LEU* 5.4 1.6 - - + -
79B SER 3.1 17.6 + - - +
80B ALA* 3.9 6.3 - - - +
82B LEU* 1.3 73.7 - - - +
84B ALA* 1.3 64.8 + - - +
86B ALA* 4.0 2.8 - - - -
87B LYS* 3.1 48.2 + - + +
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Residues in contact with ALA 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ALA 3.1 18.4 + - - +
81B ASN* 3.7 6.3 - - - +
83B LEU* 1.3 77.0 - - - +
85B GLU* 1.3 57.5 + - - +
87B LYS* 3.2 8.1 + - - +
88B LYS* 2.9 31.3 + - - +
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Residues in contact with GLU 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B PHE* 4.0 21.2 - - + -
81B ASN 3.1 15.9 + - - +
82B LEU* 3.9 10.8 - - + +
83B LEU 3.4 0.2 - - - -
84B ALA* 1.3 78.9 - - - +
86B ALA* 1.3 57.6 + - - +
88B LYS* 2.9 36.2 + - - +
89B LEU* 3.0 36.7 + - - +
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Residues in contact with ALA 86 (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* 4.1 19.3 - - + -
57B LEU* 3.8 10.9 - - + +
60B LEU* 4.3 5.1 - - + +
68B PHE* 3.3 33.8 - - + -
82B LEU 2.9 19.7 + - - +
83B LEU 4.0 3.4 - - - +
85B GLU* 1.3 77.7 - - - +
87B LYS* 1.3 57.1 + - - +
89B LEU* 3.9 1.2 - - - +
90B ASN* 3.0 28.4 + - - +
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Residues in contact with LYS 87 (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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53B GLU* 3.2 23.7 + - - -
57B LEU* 4.4 19.3 - - + -
83B LEU* 3.1 39.5 + - + +
84B ALA* 3.7 6.1 - - - +
86B ALA* 1.3 76.4 - - - +
88B LYS* 1.3 59.0 + - - +
90B ASN* 3.6 5.1 - - - +
91B ASP* 2.8 46.4 + - - +
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Residues in contact with LYS 88 (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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84B ALA 2.9 17.1 + - - +
85B GLU* 2.9 39.6 + - - +
87B LYS* 1.3 75.9 - - - +
89B LEU* 1.3 71.1 + - - +
90B ASN 3.2 0.7 + - - -
91B ASP* 3.9 6.0 - - - +
92B ALA* 3.2 27.2 + - + +
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Residues in contact with LEU 89 (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* 4.5 1.8 - - + -
64B GLN* 3.3 37.0 - - + +
68B PHE* 3.9 24.0 - - + -
85B GLU* 3.0 27.7 + - - +
86B ALA 4.3 2.7 - - - +
88B LYS* 1.3 82.0 - - - +
90B ASN* 1.3 60.1 + - - +
92B ALA* 4.2 7.4 - - + +
93B GLN* 3.3 30.3 + - - +
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Residues in contact with ASN 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B LEU* 3.5 32.8 - - + +
58B PRO* 4.2 5.3 - - - +
59B ASN* 3.0 54.1 + - - +
60B LEU* 3.2 18.2 + - + +
86B ALA 3.0 20.9 + - - +
87B LYS* 3.6 7.2 - - - +
88B LYS 3.1 0.2 - - - -
89B LEU* 1.3 77.6 - - - +
91B ASP* 1.3 73.1 + - - +
93B GLN* 3.1 11.1 + - - -
94B ALA 3.6 0.2 + - - -
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Residues in contact with ASP 91 (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 LEU* 6.1 0.3 - - - +
59B ASN* 5.2 0.2 - - - -
87B LYS* 2.8 34.3 + - - +
88B LYS* 3.9 5.0 + - - +
90B ASN* 1.3 84.6 + - - +
92B ALA* 1.3 60.4 + - - +
94B ALA* 3.1 24.7 + - - +
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Residues in contact with ALA 92 (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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88B LYS* 3.2 17.3 + - + +
89B LEU* 4.2 9.0 - - + +
91B ASP* 1.3 78.7 - - - +
93B GLN* 1.3 55.8 + - - +
94B ALA 3.3 5.3 + - - +
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Residues in contact with GLN 93 (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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59B ASN* 3.1 33.7 + - - +
60B LEU* 3.8 7.9 - - - +
61B ASN* 5.1 3.2 + - - -
64B GLN* 2.7 43.7 + - - -
89B LEU* 3.3 24.1 + - - +
90B ASN 3.1 9.8 + - - +
92B ALA* 1.3 76.7 - - - +
94B ALA* 1.3 63.0 + - - +
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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