Contacts of the helix formed by residues 80 - 94 (chain B) in PDB entry 5BXD
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 ASP 80 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A ARG* 2.7 55.5 + - - +
89A ASN* 3.7 23.1 + - - +
92A ARG* 3.3 14.6 + - - +
36B VAL* 3.9 0.7 - - - +
79B ARG* 1.3 73.0 - - - +
81B GLY* 1.3 64.5 + - - +
82B GLN* 3.2 4.1 + - - +
83B MET* 2.9 34.5 + - + +
84B PHE* 3.4 19.1 + - - +
107B LEU* 4.5 4.6 - - - +
111B GLU* 4.2 11.5 + - + +
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Residues in contact with GLY 81 (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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92A ARG* 4.6 0.8 - - - +
36B VAL* 3.1 28.6 + - - -
37B GLY* 4.5 3.0 + - - -
39B HIS* 3.6 20.3 + - - -
41B TYR* 2.5 33.0 + - - -
79B ARG 3.1 4.6 + - - -
80B ASP* 1.3 71.2 - - - +
82B GLN* 1.3 57.9 + - - +
84B PHE* 3.4 5.0 + - - +
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Residues in contact with GLN 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A TYR* 5.6 4.4 + - - -
85A ARG* 3.3 47.5 + - - +
39B HIS* 3.7 25.9 + - + +
41B TYR* 4.3 2.2 - - - -
80B ASP* 3.2 7.5 + - - +
81B GLY* 1.3 76.1 - - - +
83B MET* 1.3 69.4 + - + +
84B PHE 3.4 0.3 + - - -
85B ARG* 3.5 19.6 - - - +
86B TYR* 3.9 9.6 - - + -
104B ASP* 4.5 1.9 - - - +
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Residues in contact with MET 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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85A ARG* 3.3 14.1 - - - +
80B ASP* 2.9 23.0 + - + +
81B GLY 3.3 0.2 - - - -
82B GLN* 1.3 78.7 - - + +
84B PHE* 1.3 66.5 + - - +
85B ARG 3.1 2.9 - - - -
86B TYR* 3.0 35.0 + - + +
87B ILE* 3.3 12.7 + - - +
102B PHE* 4.2 5.2 - - + -
104B ASP* 3.3 38.4 - - + +
107B LEU* 4.0 14.6 - - + +
108B LEU* 3.7 36.9 - - + +
111B GLU* 3.8 21.8 - - + -
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Residues in contact with PHE 84 (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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34B ILE* 4.5 17.0 - - + -
36B VAL* 3.7 36.6 - - + -
41B TYR* 3.8 17.5 - + + -
48B LEU* 4.8 0.4 - - + -
56B ILE* 3.9 24.0 - - + -
60B PHE* 5.2 0.2 - + - -
77B ILE* 4.4 9.0 - - + -
80B ASP 3.4 11.3 + - - +
81B GLY 3.4 11.2 + - - +
82B GLN 3.3 0.8 - - - -
83B MET* 1.3 78.1 - - - +
85B ARG* 1.3 57.6 + - - +
87B ILE* 3.3 10.2 + - + +
88B LEU* 2.8 55.3 + - + +
111B GLU* 5.5 0.8 - - - +
115B PHE* 3.8 37.2 - + - -
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Residues in contact with ARG 85 (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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41B TYR* 3.3 32.3 + - + +
82B GLN 3.5 11.0 - - - +
84B PHE* 1.3 79.4 - - - +
86B TYR* 1.3 84.4 + - + +
88B LEU* 3.4 3.9 + - - +
89B ASN* 3.0 33.4 + - - +
92B ARG* 5.3 0.6 + - - +
99B PRO* 4.9 1.0 - - - +
80C ASP* 2.9 38.9 + - - +
82C GLN* 3.3 32.8 + - - +
83C MET* 3.5 14.3 - - - +
104C ASP* 3.5 25.7 + - - -
107C LEU* 3.6 15.6 - - - +
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Residues in contact with TYR 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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82B GLN* 3.9 16.2 - - + -
83B MET* 3.0 26.3 + - + +
85B ARG* 1.3 98.2 + - + +
87B ILE* 1.3 65.7 + - - +
89B ASN* 3.9 6.9 - - - +
90B PHE* 3.0 23.9 + - - +
95B LYS 5.2 0.3 - - - +
96B LEU* 5.5 1.1 - - + -
97B LEU 3.4 21.3 - - - +
98B ILE* 4.0 4.7 - - + -
99B PRO* 3.3 40.9 - - + +
102B PHE* 3.7 22.6 - + - -
108B LEU* 3.9 24.2 - - + -
120B MET* 3.5 7.0 - - + +
107C LEU* 4.3 7.4 - - + -
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Residues in contact with ILE 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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56B ILE* 4.1 17.3 - - + -
83B MET 3.6 12.3 - - - +
84B PHE* 3.3 17.0 + - + +
86B TYR* 1.3 76.9 - - - +
88B LEU* 1.3 62.9 + - - +
90B PHE* 3.2 4.0 + - - +
91B LEU* 3.0 28.4 + - + +
108B LEU* 3.9 7.2 - - + -
111B GLU* 4.1 6.5 - - + +
112B ALA* 3.7 30.1 - - - +
115B PHE* 4.1 22.9 - - + -
117B LEU* 3.7 18.8 - - + -
120B MET* 3.7 27.6 - - + -
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Residues in contact with LEU 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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34B ILE* 5.7 0.2 - - + -
41B TYR* 3.8 36.6 - - + -
43B SER* 3.8 14.6 - - - +
47B THR* 4.3 0.9 - - + -
48B LEU* 3.7 30.1 - - + -
84B PHE* 2.8 32.4 + - + +
85B ARG* 3.6 4.9 - - - +
87B ILE* 1.3 77.7 - - - +
89B ASN* 1.3 58.0 + - - +
91B LEU* 3.2 14.0 + - + +
92B ARG* 3.0 67.6 + - - +
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Residues in contact with ASN 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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85B ARG* 3.0 29.0 + - - +
86B TYR* 3.9 9.4 - - - +
87B ILE 3.3 0.2 - - - -
88B LEU* 1.3 73.6 - - - +
90B PHE* 1.3 53.9 + - - +
92B ARG* 3.2 18.9 + - - +
93B THR* 2.7 50.3 + - + +
95B LYS 4.5 1.8 - - - +
97B LEU* 5.3 13.1 + - + +
79C ARG* 6.1 0.2 - - - -
80C ASP* 3.0 43.2 + - - +
107C LEU* 4.7 10.5 - - - +
111C GLU* 4.7 5.3 - - - +
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Residues in contact with PHE 90 (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 LYS* 4.4 1.4 + - - -
51B TYR* 3.3 40.8 - + - -
86B TYR 3.0 15.5 + - - +
87B ILE 3.4 7.6 - - - +
89B ASN* 1.3 75.3 - - - +
91B LEU* 1.3 59.2 + - + +
94B SER* 2.7 44.5 + - - -
95B LYS 3.5 28.2 + - - +
96B LEU 4.3 0.7 - - - -
117B LEU* 4.2 13.7 - - + -
119B PRO* 3.5 7.6 - - + -
120B MET* 3.3 63.0 - - + -
123B GLU* 3.9 17.7 - - - -
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Residues in contact with LEU 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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47B THR* 3.2 37.7 + - + +
48B LEU* 3.7 24.0 - - + +
50B LYS* 3.2 35.1 + - + +
51B TYR* 5.0 3.1 - - + -
56B ILE* 3.9 21.8 - - + -
87B ILE* 3.0 24.7 + - + +
88B LEU* 3.3 15.0 - - + +
90B PHE* 1.3 83.5 - - + +
92B ARG* 1.3 59.9 + - - +
94B SER* 4.5 0.7 + - - -
117B LEU* 3.6 34.5 - - + -
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Residues in contact with ARG 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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41B TYR* 5.8 0.6 - - - -
42B THR 3.2 18.8 + - - -
43B SER* 4.3 0.2 + - - -
47B THR* 3.9 19.1 - - + +
85B ARG* 5.3 0.4 + - - +
88B LEU* 3.0 50.9 + - - +
89B ASN* 3.2 20.5 + - - +
91B LEU* 1.3 79.5 - - - +
93B THR* 1.3 62.1 + - + +
94B SER* 5.0 1.3 + - - -
37C GLY* 3.5 13.3 + - - -
78C ASP* 2.7 42.5 + - - +
79C ARG* 3.3 48.4 + - - +
80C ASP* 3.5 8.5 + - - +
81C GLY 4.9 0.4 - - - +
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Residues in contact with THR 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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89B ASN* 2.7 32.6 + - + +
92B ARG* 1.3 78.4 - - + +
94B SER* 1.3 70.4 + - - +
95B LYS* 3.0 40.3 + - - +
97B LEU* 4.2 7.9 - - + +
79C ARG* 3.6 30.1 - - - +
110C GLU* 4.0 25.4 - - + +
111C GLU* 4.6 3.6 - - - +
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Residues in contact with SER 94 (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 LYS* 3.5 23.8 + - - +
51B TYR* 5.3 1.6 - - - -
90B PHE* 2.7 34.1 + - - -
91B LEU 4.9 0.5 + - - -
92B ARG 3.7 1.2 + - - -
93B THR* 1.3 75.2 - - - +
95B LYS* 1.3 60.5 + - - +
123B GLU* 3.7 14.6 - - - +
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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