Contacts of the helix formed by residues 78 - 93 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75D ASP* 3.8 14.5 + - - +
76D PRO 3.4 0.6 - - - -
77D SER* 1.3 94.6 + - - +
79D SER* 1.3 59.9 + - - +
80D ALA* 3.1 5.2 - - - +
81D ASN* 3.3 36.8 + - + +
82D LEU* 3.1 30.5 + - + +
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Residues in contact with SER 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D GLU* 4.6 6.7 + - - +
47D GLN* 3.6 18.9 + - - +
50D ALA* 4.3 13.7 - - - +
72D LEU* 3.5 29.2 - - - -
76D PRO 2.8 18.8 + - - -
77D SER 3.4 2.7 + - - -
78D GLN* 1.3 76.4 - - - +
80D ALA* 1.3 58.5 + - - +
82D LEU* 3.4 1.8 + - - +
83D LEU* 3.0 30.6 + - - +
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Residues in contact with ALA 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77D SER 5.0 0.4 + - - -
78D GLN* 4.0 4.0 - - - +
79D SER* 1.3 79.3 + - - +
81D ASN* 1.3 65.3 + - - +
83D LEU* 3.5 7.8 + - - +
84D ALA* 3.1 26.4 + - - +
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Residues in contact with ASN 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D GLN* 3.3 43.4 + - + +
80D ALA* 1.3 78.5 - - - +
82D LEU* 1.3 61.1 + - + +
84D ALA* 3.8 5.3 - - - +
85D GLU* 3.2 28.8 + - - +
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Residues in contact with LEU 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D ILE* 4.4 10.3 - - + +
68D PHE* 4.1 20.3 - - + +
71D SER* 3.5 24.2 - - - +
72D LEU* 3.4 48.2 - - + +
75D ASP* 4.3 4.9 - - + +
78D GLN* 3.1 21.8 + - + +
79D SER* 3.9 4.5 - - - +
80D ALA 3.2 0.2 - - - -
81D ASN* 1.3 79.3 - - + +
83D LEU* 1.3 61.0 + - - +
85D GLU* 3.4 6.4 + - + +
86D ALA* 2.9 31.2 + - - +
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Residues in contact with LEU 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D ASN* 5.5 1.1 - - + -
50D ALA* 4.1 24.2 - - + +
53D GLU* 3.8 37.5 - - + +
54D ILE* 4.3 19.2 - - + +
57D LEU* 5.4 1.1 - - + -
79D SER 3.0 17.6 + - - +
80D ALA* 4.0 6.5 - - - +
82D LEU* 1.3 73.7 - - - +
84D ALA* 1.3 65.9 + - - +
86D ALA* 3.6 1.3 + - - +
87D LYS* 3.1 48.7 + - + +
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Residues in contact with ALA 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D ALA 3.1 18.6 + - - +
81D ASN* 3.8 6.1 - - - +
83D LEU* 1.3 77.5 - - - +
85D GLU* 1.3 56.8 + - - +
87D LYS* 3.2 8.2 + - - +
88D LYS* 2.9 30.8 + - - +
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Residues in contact with GLU 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D PHE* 4.0 20.9 - - + -
81D ASN* 3.2 19.5 + - - +
82D LEU* 3.9 8.7 - - + +
84D ALA* 1.3 78.6 - - - +
86D ALA* 1.3 58.4 + - - +
88D LYS* 2.9 37.0 + - - +
89D LEU* 3.0 36.2 + - - +
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Residues in contact with ALA 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D ILE* 4.1 20.0 - - + -
57D LEU* 3.8 10.0 - - + +
60D LEU* 4.3 4.8 - - + +
68D PHE* 3.3 34.7 - - + -
82D LEU 2.9 18.4 + - - +
83D LEU 4.0 3.4 - - - +
85D GLU* 1.3 78.0 - - - +
87D LYS* 1.3 59.3 + - - +
89D LEU* 3.9 1.2 - - - +
90D ASN* 3.0 27.9 + - - +
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Residues in contact with LYS 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D GLU* 3.2 25.4 + - - -
57D LEU* 4.3 19.7 - - + -
83D LEU* 3.1 43.7 + - + +
84D ALA* 3.7 5.4 - - - +
86D ALA* 1.3 76.7 - - - +
88D LYS* 1.3 60.1 + - - +
90D ASN* 3.6 5.3 - - - +
91D ASP* 2.8 45.9 + - - +
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Residues in contact with LYS 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D ALA 2.9 16.1 + - - +
85D GLU* 2.9 38.7 + - - +
87D LYS* 1.3 76.1 - - - +
89D LEU* 1.3 66.8 + - - +
90D ASN 3.2 0.9 + - - -
91D ASP* 3.9 6.4 - - - +
92D ALA* 3.2 26.2 + - + +
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Residues in contact with LEU 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D LEU* 4.4 2.9 - - + -
64D GLN* 3.3 36.6 - - + +
68D PHE* 3.9 24.7 - - + -
85D GLU* 3.0 28.6 + - - +
86D ALA 4.2 2.7 - - - +
88D LYS* 1.3 80.4 - - - +
90D ASN* 1.3 60.7 + - - +
92D ALA* 4.1 7.1 + - + +
93D GLN* 3.3 29.1 + - - +
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Residues in contact with ASN 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57D LEU* 3.5 32.1 - - + +
58D PRO* 4.2 5.5 - - - +
59D ASN* 3.0 50.2 + - - +
60D LEU* 3.2 15.9 + - + +
86D ALA 3.0 21.6 + - - +
87D LYS* 3.6 7.6 - - - +
88D LYS 3.1 0.6 - - - -
89D LEU* 1.3 77.4 - - - +
91D ASP* 1.3 73.4 + - - +
93D GLN* 3.1 16.5 + - - +
94D ALA 3.5 1.4 + - - -
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Residues in contact with ASP 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87D LYS* 2.8 32.6 + - - +
88D LYS* 3.9 7.1 + - - +
90D ASN* 1.3 84.7 + - - +
92D ALA* 1.3 61.1 + - - +
94D ALA* 3.1 24.5 + - - +
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Residues in contact with ALA 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88D LYS* 3.2 16.8 + - + +
89D LEU* 4.2 8.5 - - + +
91D ASP* 1.3 79.1 - - - +
93D GLN* 1.3 55.2 + - - +
94D ALA 3.2 6.5 + - - +
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Residues in contact with GLN 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D ASN* 3.1 32.2 + - - +
60D LEU* 3.8 8.1 - - - +
61D ASN* 5.1 0.9 - - - -
64D GLN* 2.7 43.6 + - - +
89D LEU* 3.3 23.6 + - - +
90D ASN 3.1 10.0 + - - +
92D ALA* 1.3 75.4 - - - +
94D 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