Contacts of the helix formed by residues 100 - 113 (chain D) in PDB entry 5BZZ
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 LEU 100 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233B ARG* 3.8 15.8 - - + +
234B ARG 3.1 30.5 - - - +
235B GLU* 4.5 2.9 - - + -
88D TYR* 3.7 32.3 - - + +
89D PRO 4.1 3.8 - - - +
90D PHE* 3.4 35.2 - - + -
96D PRO* 3.9 7.9 - - + -
97D GLN* 3.1 32.8 + - - +
99D GLU* 1.3 77.5 - - - +
101D ILE* 1.3 65.7 + - - +
103D PRO* 3.4 13.6 - - - +
104D PHE* 3.5 9.6 + - + +
134D MET* 4.8 3.1 - - - -
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Residues in contact with ILE 101 (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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96D PRO* 3.5 31.9 - - + -
97D GLN 3.9 1.1 - - - +
98D LEU* 3.3 30.2 + - + +
100D LEU* 1.3 79.3 - - - +
102D LYS* 1.3 58.6 + - - +
104D PHE* 3.2 6.2 + - - +
105D CYS* 3.0 26.2 + - - -
133D VAL* 5.0 2.5 - - + -
134D MET* 3.6 14.8 - - + -
137D ALA* 3.7 21.5 - - + -
174D TYR* 3.9 26.0 - - + +
178D TYR* 3.5 33.4 - - + -
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Residues in contact with LYS 102 (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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98D LEU 4.6 2.1 + - - +
99D GLU* 4.3 2.4 + - - +
101D ILE* 1.3 77.0 - - - +
103D PRO* 1.3 69.0 - - + +
105D CYS* 3.3 1.9 + - - +
106D GLU* 2.9 61.8 + - + +
141D HIS* 5.4 3.2 - - + -
178D TYR* 3.6 31.4 + - + +
187D ASP* 5.2 10.5 + - - -
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Residues in contact with PRO 103 (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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235B GLU* 3.5 34.8 - - + +
88D TYR* 3.5 9.0 + - + +
99D GLU 3.1 24.7 - - - +
100D LEU* 3.4 10.1 - - - +
102D LYS* 1.3 91.6 - - + +
104D PHE* 1.3 57.5 + - - +
106D GLU* 4.0 10.4 - - + +
107D ASP* 2.9 30.5 + - - +
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Residues in contact with PHE 104 (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 TYR* 3.6 31.4 - + + -
70D LEU* 4.2 11.7 - - + -
88D TYR* 3.6 38.5 - + + -
100D LEU* 3.5 9.8 + - + +
101D ILE* 3.2 10.9 + - - +
102D LYS 3.2 0.6 - - - -
103D PRO* 1.3 77.6 - - - +
105D CYS* 1.3 67.0 + - - +
107D ASP* 3.2 3.1 + - - +
108D LEU* 2.8 52.6 + - + +
122D ILE* 4.0 21.5 - - + -
134D MET* 3.6 51.6 - - + -
138D TYR* 4.6 0.4 - - + -
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Residues in contact with CYS 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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101D ILE* 3.0 18.7 + - - -
102D LYS 3.5 7.4 - - - +
104D PHE* 1.3 87.0 - - - +
106D GLU* 1.3 51.6 + - - +
108D LEU* 3.2 2.8 + - - +
109D ASP* 2.7 37.5 + - - +
137D ALA* 3.9 4.9 - - - -
138D TYR* 3.6 40.1 - - + -
141D HIS* 3.6 31.4 - - + +
178D TYR* 3.9 12.3 - - - +
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Residues in contact with GLU 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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102D LYS* 2.9 52.3 + - + +
103D PRO* 4.0 9.9 - - + +
105D CYS* 1.3 71.5 - - - +
107D ASP* 1.3 63.7 + - - +
109D ASP* 3.7 7.4 - - - +
110D GLN* 3.1 24.3 + - - +
141D HIS* 4.1 16.8 - - + +
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Residues in contact with ASP 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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236B ASP* 3.9 10.9 - - - +
66D LYS* 2.8 21.8 + - - -
68D TYR* 2.7 32.4 + - + -
86D ALA* 4.1 1.0 - - - +
88D TYR* 2.6 37.5 + - + +
103D PRO 2.9 11.7 + - - +
104D PHE 3.3 4.5 - - - +
106D GLU* 1.3 75.3 - - - +
108D LEU* 1.3 62.2 + - - +
110D GLN* 3.3 7.2 + - - +
111D TRP* 3.2 17.7 + - - +
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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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32D ILE* 5.3 3.6 - - + -
68D TYR* 3.3 20.2 + - + +
104D PHE* 2.8 38.9 + - + +
105D CYS* 3.5 4.5 - - - +
107D ASP* 1.3 72.7 - - - +
109D ASP* 1.3 64.9 + - - +
111D TRP* 3.3 2.5 + - + +
112D LEU* 3.1 36.1 + - + +
120D ALA* 3.3 34.5 - - + -
122D ILE* 4.5 9.6 - - + -
135D ILE* 5.8 1.8 - - - -
138D TYR* 3.4 39.3 - - + -
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Residues in contact with ASP 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 CYS 2.7 21.1 + - - +
106D GLU* 3.7 9.4 - - - +
108D LEU* 1.3 74.0 - - - +
110D GLN* 1.3 56.6 + - - +
112D LEU* 3.4 0.9 + - - +
113D SER* 2.8 39.8 + - - -
138D TYR* 2.7 34.4 + - + -
141D HIS* 4.1 15.6 + - - +
142D ARG* 4.0 12.8 + - - +
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Residues in contact with GLN 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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106D GLU 3.1 15.4 + - - +
107D ASP* 3.3 6.3 + - - +
109D ASP* 1.3 80.0 - - - +
111D TRP* 1.3 63.4 + - - +
113D SER* 3.5 5.7 + - - -
114D GLU* 3.3 51.7 + - - +
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Residues in contact with TRP 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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63D ASN 4.9 4.0 - - - -
64D HIS* 3.6 16.4 - - - -
65D TYR 3.3 29.8 - - - -
66D LYS* 3.3 26.4 - - + +
68D TYR* 3.6 20.2 - - - +
83D CYS* 6.0 0.2 - - + -
84D ARG* 3.8 26.5 - - - +
107D ASP 3.2 4.3 + - - +
108D LEU 3.7 2.5 - - - +
110D GLN* 1.3 80.7 - - - +
112D LEU* 1.3 75.1 + - + +
114D GLU* 3.4 15.0 + - - +
118D HIS* 2.7 66.4 + + - -
119D VAL 2.7 28.4 + - - +
120D ALA* 4.2 6.5 - - + -
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Residues in contact with LEU 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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31D ASN* 3.7 33.8 + - + +
32D ILE* 4.0 15.9 - - + -
108D LEU* 3.1 36.0 + - + +
109D ASP 4.0 2.2 - - - +
111D TRP* 1.3 85.0 - - + +
113D SER* 1.3 56.8 + - - +
114D GLU 3.3 0.9 - - - -
115D ASP 3.2 19.6 - - - +
116D ASP* 5.3 0.3 - - - -
118D HIS* 3.5 27.2 - - - +
120D ALA* 3.8 12.8 - - + +
138D TYR* 3.8 28.0 - - + +
142D ARG* 5.4 3.4 - - - +
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Residues in contact with SER 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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109D ASP* 2.8 28.0 + - - -
110D GLN* 3.9 7.2 - - - -
111D TRP 3.3 0.4 - - - -
112D LEU* 1.3 75.1 - - - +
114D GLU* 1.3 61.6 + - - +
115D ASP 3.6 0.9 - - - -
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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