Contacts of the helix formed by residues 104 - 115 (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 104 (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* 4.6 10.8 + - - -
99C PRO* 3.5 26.0 - - - +
82D GLN* 5.2 2.1 - - - +
83D MET* 3.6 23.5 - - + +
102D PHE* 3.3 28.1 - - + -
103D LYS* 1.3 81.5 - - - +
105D TYR* 1.3 64.0 + - - +
106D THR 3.3 2.9 - - - -
107D LEU* 3.2 24.1 + - + +
108D LEU 3.0 17.5 + - - -
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Residues in contact with TYR 105 (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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100C ASP* 4.8 13.0 + - - +
98D ILE* 5.7 0.2 - - + -
102D PHE* 3.6 11.2 - + + +
103D LYS 3.4 4.6 + - - -
104D ASP* 1.3 75.9 - - - +
106D THR* 1.3 72.5 + - + +
108D LEU 3.2 1.4 + - - -
109D TYR* 2.8 62.7 + + + +
124D MET* 3.3 55.4 + - + +
125D GLU* 3.5 13.2 + - - -
127D TRP* 3.9 28.9 - + + -
128D LYS* 3.7 33.2 + - + +
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Residues in contact with THR 106 (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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96C LEU 5.6 0.4 - - - -
97C LEU* 3.6 24.9 - - - +
98C ILE 3.5 27.8 + - - +
100C ASP* 5.0 8.5 + - - +
105D TYR* 1.3 89.8 - - + +
107D LEU* 1.3 67.3 + - - +
109D TYR* 3.8 4.5 - - - +
110D GLU* 3.2 17.2 + - - +
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Residues in contact with LEU 107 (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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85C ARG* 4.1 30.7 - - - +
86C TYR* 4.8 8.3 - - + -
89C ASN* 4.1 15.0 + - + +
97C LEU* 3.4 46.9 - - + +
98C ILE* 3.8 14.1 - - - +
99C PRO* 4.0 3.4 - - + -
80D ASP* 4.8 3.8 - - + +
83D MET* 4.2 13.7 - - + -
104D ASP* 3.2 26.5 + - + +
106D THR* 1.3 87.1 + - - +
108D LEU* 1.3 61.8 + - - +
110D GLU* 3.4 4.7 + - - +
111D GLU* 3.2 26.2 + - - +
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Residues in contact with LEU 108 (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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83D MET* 3.8 39.4 - - + +
86D TYR* 3.8 15.5 - - + -
87D ILE* 4.1 8.7 - - + -
96D LEU* 4.4 1.6 - - + -
98D ILE* 3.8 30.3 - - + -
102D PHE* 3.8 15.3 - - + -
104D ASP 3.0 15.5 + - - +
105D TYR 3.7 3.4 - - - +
107D LEU* 1.3 73.3 - - - +
109D TYR* 1.3 65.8 + - - +
111D GLU* 3.1 2.6 + - + -
112D ALA* 2.9 21.1 + - - +
120D MET* 3.9 16.8 - - + -
124D MET* 3.7 19.7 - - + -
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Residues in contact with TYR 109 (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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105D TYR* 2.8 52.2 + + + +
106D THR* 3.8 7.2 - - - +
107D LEU 3.3 0.2 - - - -
108D LEU* 1.3 76.9 - - - +
110D GLU* 1.3 59.2 + - - +
112D ALA 3.3 1.2 + - - -
113D LYS* 2.9 42.1 + - + +
121D LEU* 3.5 50.7 + - + +
124D MET* 3.5 15.6 - - + +
125D GLU* 4.3 12.7 + - - -
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Residues in contact with GLU 110 (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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93C THR* 3.7 26.9 - - + +
95C LYS* 2.7 42.9 + - - +
97C LEU* 3.6 34.1 - - + -
79D ARG* 4.1 4.8 + - - +
106D THR 3.2 8.3 + - - +
107D LEU 3.7 2.2 - - - +
109D TYR* 1.3 80.8 - - - +
111D GLU* 1.3 53.3 + - - +
113D LYS* 3.2 13.2 + - - +
114D TYR* 2.8 38.5 + - - +
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Residues in contact with GLU 111 (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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89C ASN* 4.3 9.2 + - - +
93C THR* 4.1 9.2 - - - +
79D ARG* 2.7 54.1 + - - +
80D ASP* 4.0 12.3 + - + +
83D MET* 3.8 24.0 - - + -
84D PHE 5.7 0.2 - - - +
87D ILE* 4.0 16.2 - - + -
107D LEU 3.2 15.7 + - - +
108D LEU* 3.1 10.0 + - - +
110D GLU* 1.3 78.2 - - - +
112D ALA* 1.3 57.1 + - - +
114D TYR* 3.3 0.7 + - - +
115D PHE* 2.9 45.9 + - + -
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Residues in contact with ALA 112 (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 ILE* 3.7 9.8 - - + +
108D LEU 2.9 12.5 + - - +
109D TYR 3.7 2.9 - - - +
111D GLU* 1.3 76.3 - - - +
113D LYS* 1.3 57.6 + - - +
115D PHE* 3.6 2.0 + - - -
116D GLN 3.0 6.6 + - - -
117D LEU* 2.9 31.6 + - + +
120D MET* 3.9 32.3 - - + -
121D LEU* 3.6 22.9 - - + -
124D MET* 4.5 4.5 - - - -
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Residues in contact with LYS 113 (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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95C LYS* 3.8 17.8 - - - +
109D TYR* 2.9 32.4 + - + +
110D GLU* 3.5 21.1 - - - +
112D ALA* 1.3 75.8 - - - +
114D TYR* 1.3 65.3 + - - +
116D GLN* 3.1 18.6 + - - +
121D LEU* 3.8 21.5 - - + +
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Residues in contact with TYR 114 (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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55D ARG* 3.1 66.0 + - - -
59D LEU* 5.6 2.2 - - + +
77D ILE* 5.7 0.9 - - + -
79D ARG* 3.4 55.9 - - + +
110D GLU* 2.8 25.9 + - - +
111D GLU 3.7 2.0 - - - +
113D LYS* 1.3 75.6 - - - +
115D PHE* 1.3 81.6 + + - +
116D GLN* 3.0 9.2 + - - +
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Residues in contact with PHE 115 (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 SER* 3.3 7.6 - - - -
55D ARG* 3.1 25.9 + - - -
56D ILE* 3.8 35.0 + - + -
59D LEU* 4.6 5.2 - - + -
77D ILE* 4.3 9.2 - - + -
79D ARG* 3.8 23.1 - - + -
84D PHE* 3.9 31.6 - + - -
87D ILE* 3.9 21.1 - - + -
111D GLU* 2.9 40.8 + - + +
112D ALA 4.2 2.7 - - - +
114D TYR* 1.3 93.3 - + - +
116D GLN* 1.3 66.7 + - - +
117D LEU* 3.4 15.6 + - + +
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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