Contacts of the helix formed by residues 107 - 124 (chain D) in PDB entry 6BCH
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 107 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106D THR* 1.3 70.8 - - - +
108D LYS* 1.3 55.9 + - - +
109D ARG 3.1 5.6 - - - -
110D ALA* 2.9 28.7 + - + +
111D ASP* 4.5 0.2 - - - -
163D ARG* 3.7 22.4 + - - +
164D LEU 5.4 1.7 + - - -
165D LEU* 4.9 5.5 - - - +
166D VAL* 3.4 36.3 + - + +
214D ARG* 3.7 35.8 + - + +
215D ASP* 3.2 23.3 + - - +
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Residues in contact with LYS 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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26D ALA 5.5 2.7 - - - +
27D ASP* 4.6 9.6 - - - +
30D SER* 5.6 6.3 - - - +
32D PHE* 4.3 9.6 - - + -
104D LEU* 4.2 11.7 - - + +
106D THR* 3.1 14.6 + - - +
107D GLN* 1.3 74.4 - - - +
109D ARG* 1.3 54.5 + - - +
110D ALA 3.1 0.2 - - - -
111D ASP* 3.0 19.6 + - + +
112D TYR* 2.7 34.0 + - - +
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Residues in contact with ARG 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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104D LEU* 4.0 31.3 - - + +
105D ILE* 5.2 0.4 - - - -
106D THR 3.2 16.9 + - - +
108D LYS* 1.3 77.6 - - - +
110D ALA* 1.3 55.3 + - - +
112D TYR* 3.0 14.1 + - + +
113D LEU* 2.8 35.7 + - + +
164D LEU* 6.0 2.9 - - + -
166D VAL* 5.2 9.4 - - + -
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Residues in contact with ALA 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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107D GLN* 2.9 15.1 + - + +
109D ARG* 1.3 74.8 - - - +
111D ASP* 1.3 67.3 + - - +
113D LEU* 3.0 22.0 + - - +
114D LEU* 3.0 17.0 + - - +
163D ARG* 4.1 21.8 - - + +
164D LEU* 3.4 36.1 - - + +
166D VAL* 5.6 3.9 - - + +
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Residues in contact with ASP 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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32D PHE* 4.7 9.6 - - + -
107D GLN 3.7 0.4 + - - -
108D LYS* 3.0 22.5 + - + +
110D ALA* 1.3 75.1 - - - +
112D TYR* 1.3 53.4 + - - +
114D LEU* 3.0 6.1 + - - +
115D PHE* 2.8 35.8 + - - +
143D LEU* 3.5 17.6 - - + +
144D ASN* 3.2 33.4 + - - +
163D ARG* 2.4 40.9 + - - +
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Residues in contact with TYR 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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32D PHE* 3.3 32.5 - + + -
95D VAL* 5.0 0.7 - - + -
96D ILE* 3.0 52.4 + - + +
99D PHE* 3.6 31.5 - + + +
100D ASP* 3.0 18.5 + - - -
104D LEU* 3.9 11.9 - - + -
108D LYS 2.7 12.3 + - - +
109D ARG* 3.1 17.5 - - + +
111D ASP* 1.3 77.1 - - - +
113D LEU* 1.3 66.4 + - + +
115D PHE* 3.0 11.0 + + - +
116D LYS* 2.6 41.7 + - + +
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Residues in contact with LEU 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 ARG* 2.8 19.4 + - + +
110D ALA* 3.0 7.6 + - - +
112D TYR* 1.3 91.6 - - + +
114D LEU* 1.3 64.7 + - + +
116D LYS* 3.0 7.7 + - + +
117D LYS* 3.0 22.7 + - - +
164D LEU* 3.7 35.7 - - + -
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Residues in contact with LEU 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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34D LEU* 5.5 1.6 - - + -
110D ALA 3.0 14.2 + - - +
111D ASP* 3.4 5.2 - - - +
113D LEU* 1.3 76.5 - - + +
115D PHE* 1.3 63.5 + - - +
117D LYS* 3.0 6.9 + - - +
118D ALA* 3.0 22.4 + - - +
139D LEU* 3.7 43.4 - - + +
142D SER* 3.4 41.1 - - - +
143D LEU* 3.7 9.4 - - + +
161D ALA* 4.1 14.1 - - + -
162D GLU 4.2 13.2 - - - +
163D ARG* 3.8 19.1 - - + +
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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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32D PHE* 3.7 37.7 - + + -
33D MET 3.7 12.6 - - - -
34D LEU* 4.5 10.3 - - + -
50D PRO* 3.5 28.3 - - + -
51D ARG 3.3 23.8 - - - -
52D PHE* 5.0 0.4 - - + -
92D LEU* 3.6 32.1 - - + -
95D VAL* 5.6 2.0 - - + -
96D ILE* 4.2 20.2 - - + -
111D ASP 2.8 12.6 + - - +
112D TYR* 3.2 13.2 - + - +
114D LEU* 1.3 75.3 - - - +
116D LYS* 1.3 61.4 + - - +
118D ALA* 3.0 8.2 + - - +
119D PHE* 2.8 30.5 + - + +
143D LEU* 4.8 4.2 - - + +
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Residues in contact with LYS 116 (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 ILE* 4.8 17.3 - - + -
112D TYR* 2.6 29.7 + - + +
113D LEU* 3.0 12.1 + - + +
115D PHE* 1.3 76.3 - - - +
117D LYS* 1.3 64.9 + - - +
119D PHE* 3.0 7.8 + - - +
120D TYR* 2.9 37.8 + - + -
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Residues in contact with LYS 117 (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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113D LEU 3.0 11.5 + - - +
114D LEU* 3.5 7.4 - - - +
116D LYS* 1.3 74.6 - - - +
118D ALA* 1.3 63.8 + - - +
120D TYR* 3.0 9.0 + - - +
121D LEU* 3.0 26.2 + - + +
139D LEU* 3.8 22.2 - - + -
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Residues in contact with ALA 118 (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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34D LEU* 3.6 39.7 - - + -
114D LEU 3.0 7.3 + - - +
115D PHE 3.0 6.9 + - - +
117D LYS* 1.3 75.9 - - - +
119D PHE* 1.3 54.2 + - - +
121D LEU* 3.0 8.5 + - - +
122D ILE* 2.7 42.9 + - + +
136D ILE* 4.7 7.0 - - + -
139D LEU* 3.4 17.7 - - + +
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Residues in contact with PHE 119 (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 PRO* 4.5 6.0 - - + +
89D LEU* 3.6 50.3 - - + -
92D LEU* 3.9 25.6 - - + -
93D GLU* 4.2 15.7 - - + -
96D ILE* 3.5 22.9 - - + -
115D PHE* 2.8 20.3 + + + +
116D LYS* 3.3 9.4 - - - +
118D ALA* 1.3 77.1 - - - +
120D TYR* 1.3 73.1 + + - +
122D ILE* 3.0 11.3 + - - +
123D LYS* 2.5 55.4 + - + +
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Residues in contact with TYR 120 (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 ILE* 4.8 17.7 - - + +
100D ASP* 5.5 1.4 + - - -
116D LYS* 2.9 29.2 + - + +
117D LYS* 3.5 10.1 - - - +
119D PHE* 1.3 94.1 - + - +
121D LEU* 1.3 65.4 + - + +
123D LYS* 3.0 32.5 + - + +
124D ASN* 2.8 37.0 + - - +
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Residues in contact with LEU 121 (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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117D LYS* 3.0 13.2 + - + +
118D ALA 3.3 6.1 - - - +
120D TYR* 1.3 75.6 - - - +
122D ILE* 1.3 60.4 + - - +
124D ASN* 3.5 2.7 + - - +
125D LYS 3.2 2.6 + - - -
126D GLU* 3.0 61.1 + - + +
127D HIS 3.6 3.6 + - - +
132D GLY* 4.5 4.9 - - - +
135D GLN* 4.0 33.7 - - + +
136D ILE* 3.9 22.7 - - + -
139D LEU* 3.9 28.9 - - + -
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Residues in contact with ILE 122 (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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34D LEU* 4.3 6.3 - - + -
48D VAL* 3.9 23.8 - - + +
50D PRO* 3.7 38.8 - - + -
89D LEU* 4.3 20.5 - - + +
118D ALA 2.7 29.3 + - - +
119D PHE* 3.4 6.1 - - - +
121D LEU* 1.3 72.4 - - - +
123D LYS* 1.3 65.5 + - - +
125D LYS* 2.9 17.0 + - - +
127D HIS* 3.6 26.6 + - + +
136D ILE* 3.9 16.2 - - + -
4F A 4.8 3.6 + - - +
5F T 6.0 0.4 - - - +
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Residues in contact with LYS 123 (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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89D LEU* 4.7 17.0 - - + +
119D PHE* 2.5 40.9 + - + +
120D TYR* 3.4 40.8 - - + +
122D ILE* 1.3 73.4 - - - +
124D ASN* 1.3 87.5 + - - +
125D LYS* 3.2 6.6 + - - +
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Residues in contact with ASN 124 (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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120D TYR* 2.8 25.3 + - - +
121D LEU* 5.3 0.4 - - - +
123D LYS* 1.3 110.6 + - - +
125D LYS* 1.3 68.1 + - - +
126D GLU* 3.1 31.7 + - + +
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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