Contacts of the helix formed by residues 80 - 94 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85C ARG* 2.9 47.8 + - - +
89C ASN* 3.9 22.0 - - - +
92C ARG* 3.7 15.5 + - - +
36D VAL* 4.0 0.9 - - - +
79D ARG* 1.3 72.7 - - - +
81D GLY* 1.3 65.4 + - - +
82D GLN* 3.3 3.5 + - - -
83D MET* 3.0 39.5 + - + +
84D PHE* 3.3 19.9 + - - +
107D LEU* 4.8 3.2 - - - +
111D GLU* 4.0 12.8 + - - +
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Residues in contact with GLY 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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92C ARG* 4.9 0.4 - - - +
36D VAL* 3.0 29.3 + - - -
37D GLY* 4.7 2.8 + - - -
39D HIS* 3.6 20.9 + - - -
41D TYR* 2.5 35.5 + - - -
79D ARG 3.1 4.8 + - - -
80D ASP* 1.3 71.1 + - - +
82D GLN* 1.3 57.8 + - - +
84D PHE* 3.4 3.6 + - - +
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Residues in contact with GLN 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C ARG* 3.5 42.9 + - - +
39D HIS* 3.3 30.6 + - + +
41D TYR* 4.2 2.2 - - - -
80D ASP* 3.3 7.9 + - - +
81D GLY* 1.3 76.1 - - - +
83D MET* 1.3 69.4 + - + +
84D PHE 3.4 0.2 + - - -
85D ARG* 3.5 17.5 + - - +
86D TYR* 3.8 9.6 - - + -
104D ASP* 5.2 1.9 - - - +
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Residues in contact with MET 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C ARG* 3.9 13.2 - - - +
80D ASP* 3.0 24.2 + - + +
81D GLY 3.3 0.2 - - - -
82D GLN* 1.3 84.0 - - + +
84D PHE* 1.3 64.8 + - - +
86D TYR* 3.1 28.2 + - + +
87D ILE* 3.4 12.3 + - - +
102D PHE* 3.8 15.7 - - + -
104D ASP* 3.6 30.5 - - + +
107D LEU* 4.2 14.4 - - + -
108D LEU* 3.8 35.0 - - + +
111D GLU* 3.8 24.7 - - + -
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Residues in contact with PHE 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D ILE* 4.5 9.4 - - + -
36D VAL* 3.6 46.2 - - + -
41D TYR* 3.8 16.6 - + + -
48D LEU* 4.6 10.5 - - + -
56D ILE* 4.0 29.2 - - + -
77D ILE* 4.3 7.0 - - + -
79D ARG* 5.9 0.2 - - + -
80D ASP 3.3 4.6 + - - +
81D GLY 3.6 11.9 - - - +
82D GLN 3.2 0.6 - - - -
83D MET* 1.3 79.2 - - - +
85D ARG* 1.3 56.2 + - - +
87D ILE* 3.2 14.8 + - + -
88D LEU* 2.8 53.0 + - + +
91D LEU* 5.6 0.4 - - + -
111D GLU* 5.7 0.4 - - - +
115D PHE* 3.9 27.4 - + - -
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Residues in contact with ARG 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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41D TYR* 3.2 34.6 + - + +
82D GLN 3.7 9.6 - - - +
83D MET 3.1 0.4 - - - -
84D PHE* 1.3 77.1 - - - +
86D TYR* 1.3 83.8 + - + +
88D LEU* 3.5 4.3 + - - +
89D ASN* 3.0 33.2 + - - +
92D ARG* 5.2 0.8 + - - +
99D PRO* 5.7 2.0 - - - +
80E ASP* 2.9 39.4 + - - +
82E GLN* 2.8 47.4 + - - +
83E MET* 3.6 10.9 - - - +
104E ASP* 5.0 8.5 + - - -
107E LEU* 3.5 18.8 - - - +
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Residues in contact with TYR 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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82D GLN* 3.8 15.0 - - + -
83D MET* 3.1 24.8 + - + +
85D ARG* 1.3 105.8 + - + +
87D ILE* 1.3 66.2 + - - +
89D ASN* 3.5 7.2 + - - +
90D PHE* 3.0 22.5 + - - +
95D LYS 5.2 0.5 - - - +
96D LEU* 5.8 0.7 - - - +
97D LEU 3.8 14.6 + - - +
98D ILE* 3.6 18.8 - - + -
99D PRO* 3.8 29.5 - - + +
102D PHE* 3.6 26.7 - + - -
108D LEU* 3.8 27.4 - - + -
120D MET* 3.7 7.3 - - + +
107E LEU* 5.9 0.9 - - + -
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Residues in contact with ILE 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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56D ILE* 5.4 1.6 - - + -
83D MET 3.7 11.7 - - - +
84D PHE* 3.2 23.7 + - + +
86D TYR* 1.3 76.9 - - - +
88D LEU* 1.3 64.3 + - - +
90D PHE* 3.1 6.1 + - - +
91D LEU* 3.0 30.0 + - + +
108D LEU* 4.1 7.2 - - + -
111D GLU* 4.0 7.9 - - + -
112D ALA* 3.7 34.3 - - - +
115D PHE* 3.9 26.5 - - + -
117D LEU* 3.8 17.0 - - + -
120D MET* 3.9 21.3 - - + -
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Residues in contact with LEU 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D ILE* 5.8 0.2 - - + -
41D TYR* 3.9 35.4 - - + -
43D SER* 3.6 27.1 - - - +
47D THR* 3.9 10.5 - - + -
48D LEU* 3.9 17.0 - - + -
84D PHE* 2.8 32.5 + - + +
85D ARG 3.7 5.2 - - - +
87D ILE* 1.3 75.0 - - - +
89D ASN* 1.3 57.1 + - - +
91D LEU* 3.2 10.6 + - + +
92D ARG* 3.0 65.2 + - - +
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Residues in contact with ASN 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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85D ARG* 3.0 25.3 + - - +
86D TYR* 4.0 8.3 - - - +
87D ILE 3.3 0.2 - - - -
88D LEU* 1.3 73.0 - - - +
90D PHE* 1.3 60.5 + - - +
92D ARG* 3.0 31.3 + - - +
93D THR* 2.8 37.7 + - + +
95D LYS 4.3 2.0 - - - +
97D LEU* 5.0 11.4 + - + +
80E ASP* 2.9 35.9 + - - +
107E LEU* 3.7 26.9 - - + +
111E GLU* 5.0 1.8 - - - +
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Residues in contact with PHE 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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51D TYR* 3.7 36.2 - + - -
86D TYR 3.0 14.6 + - - +
87D ILE 3.1 8.3 + - - +
89D ASN* 1.3 76.3 - - - +
91D LEU* 1.3 61.5 + - - +
94D SER* 2.6 49.0 + - - -
95D LYS* 3.5 29.8 + - - +
96D LEU* 4.1 1.3 - - - -
117D LEU* 4.1 26.0 - - + -
119D PRO* 3.8 14.6 - - + -
120D MET* 3.5 58.1 - - + -
123D GLU* 5.0 3.8 - - + -
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Residues in contact with LEU 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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47D THR* 3.5 26.8 - - + +
48D LEU* 4.2 10.1 - - + +
50D LYS* 2.8 33.8 + - - +
51D TYR* 3.7 31.2 - - + +
56D ILE* 4.0 33.9 - - + -
84D PHE* 5.6 0.9 - - + -
87D ILE* 3.0 23.6 + - + +
88D LEU* 3.2 19.9 + - + +
90D PHE* 1.3 77.7 - - + +
92D ARG* 1.3 56.6 + - - +
94D SER 4.4 0.2 + - - -
117D LEU* 3.8 22.9 - - + -
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Residues in contact with ARG 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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41D TYR* 5.9 1.0 - - - -
42D THR 3.2 19.6 + - - -
43D SER* 4.4 0.2 + - - -
47D THR* 3.6 20.9 - - + +
50D LYS* 2.9 18.8 + - - +
85D ARG* 5.2 1.2 + - - +
88D LEU* 3.0 44.9 + - - +
89D ASN* 3.0 32.9 + - - +
90D PHE 3.2 0.4 - - - -
91D LEU* 1.3 77.9 - - - +
93D THR* 1.3 66.1 + - + +
37E GLY* 3.6 15.2 + - - -
78E ASP* 2.9 38.7 + - - +
79E ARG* 3.6 29.6 + - - +
80E ASP* 3.6 15.1 + - - +
81E GLY 5.0 0.4 - - - +
111E GLU* 5.9 0.4 - - - -
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Residues in contact with THR 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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50D LYS* 5.4 0.2 - - - -
89D ASN* 2.8 23.0 + - + +
92D ARG* 1.3 84.9 - - + +
94D SER* 1.3 70.6 + - - +
95D LYS* 3.0 31.2 + - - +
97D LEU* 3.6 9.6 - - + +
79E ARG* 3.6 30.1 - - - +
110E GLU* 3.6 29.5 - - + +
111E GLU* 4.6 2.2 - - - +
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Residues in contact with SER 94 (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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50D LYS* 4.4 10.2 + - - +
51D TYR* 2.7 30.1 + - - -
90D PHE* 2.6 36.8 + - - -
92D ARG 3.8 0.6 - - - -
93D THR* 1.3 74.4 - - - +
95D LYS* 1.3 61.0 + - - +
123D GLU* 5.3 4.9 - - - +
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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