Contacts of the helix formed by residues 99 - 116 (chain A) in PDB entry 2CT8
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 99 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A LYS* 6.0 1.4 - - - -
94A PHE 4.4 2.1 - - - +
95A ILE* 3.3 13.8 - - + +
96A ARG* 2.7 50.9 + - - +
98A THR* 1.3 78.1 + - - +
100A PRO* 1.3 75.2 - - + +
101A TYR* 4.6 9.6 - - + +
102A HIS* 3.0 22.2 + - + +
103A VAL* 3.2 10.2 - - - +
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Residues in contact with PRO 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A THR 3.2 7.8 - - - +
99A ASP* 1.3 82.8 - - + +
101A TYR* 1.3 87.1 + - + +
102A HIS 2.9 1.6 + - - -
103A VAL* 3.0 13.6 + - + +
104A LYS* 3.0 42.7 + - - +
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Residues in contact with TYR 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A ASP* 4.4 8.7 - - + -
100A PRO* 1.3 95.8 - - + +
102A HIS* 1.3 61.3 + - - +
104A LYS* 3.6 16.6 + - - +
105A PHE* 3.2 21.1 + - - +
239A SER* 4.9 3.7 - - - +
242A GLU* 3.6 41.3 - - + +
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Residues in contact with HIS 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A ILE* 4.0 10.9 - - + +
96A ARG 4.2 9.0 - - - +
97A THR* 3.5 29.0 - - + +
99A ASP* 3.0 13.6 + - + +
100A PRO 2.9 0.6 + - - -
101A TYR* 1.3 77.2 - - - +
103A VAL* 1.3 58.4 - - - +
105A PHE* 2.7 24.6 + - - +
106A VAL* 2.9 26.8 + - + +
217A ILE* 4.3 0.7 - - + -
232A ASP* 2.7 45.0 + - - -
235A PHE 4.1 1.8 - - - -
236A ASN* 3.7 21.8 - - + -
239A SER* 2.8 34.0 + - - +
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Residues in contact with VAL 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A HIS* 4.8 3.4 - - + +
97A THR 3.9 15.7 - - - +
98A THR* 4.2 7.0 - - - +
99A ASP 3.2 20.6 - - - +
100A PRO* 3.6 10.3 - - + +
102A HIS* 1.3 73.5 - - - +
104A LYS* 1.3 72.0 + - + +
106A VAL* 3.4 1.7 + - - +
107A GLN* 3.2 38.1 + - - +
217A ILE* 3.5 30.0 - - + +
218A PRO* 6.0 2.5 - - + -
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Residues in contact with LYS 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A PRO* 3.0 40.0 + - - +
101A TYR* 3.8 13.6 - - - +
103A VAL* 1.3 83.8 - - + +
105A PHE* 1.3 63.2 + - - +
107A GLN* 3.3 11.0 + - - +
108A LYS* 3.0 44.0 + - - +
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Residues in contact with PHE 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A TYR 3.2 11.0 + - - +
102A HIS 2.7 14.8 + - - +
104A LYS* 1.3 75.3 - - - +
106A VAL* 1.3 58.1 + - + +
108A LYS* 3.8 10.7 - - + +
109A VAL* 2.9 54.3 + - + +
235A PHE* 3.7 26.0 - + + -
238A ILE* 3.7 29.6 - - + -
239A SER* 3.7 29.2 - - - -
245A VAL* 5.9 2.0 - - + -
277A TYR* 4.7 9.2 - + - -
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Residues in contact with VAL 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A HIS* 2.9 50.1 + - + +
103A VAL 3.8 0.9 - - - +
104A LYS 3.3 0.2 - - - -
105A PHE* 1.3 79.9 - - + +
107A GLN* 1.3 57.8 + - - +
109A VAL* 3.8 4.4 - - - +
110A PHE* 2.8 29.5 + - - +
217A ILE* 3.8 20.6 - - + -
227A ILE* 3.8 20.2 - - + -
231A PHE* 3.9 22.7 - - + +
232A ASP* 3.9 17.0 - - + +
235A PHE* 4.7 7.4 - - + -
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Residues in contact with GLN 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A VAL* 3.2 24.2 + - - +
104A LYS* 3.7 11.2 - - - +
106A VAL* 1.3 75.9 - - - +
108A LYS* 1.3 66.2 + - + +
110A PHE* 3.0 5.2 + - - +
111A GLU* 2.9 22.0 + - - +
217A ILE* 3.6 15.7 - - + -
218A PRO* 2.4 41.5 + - - +
220A PRO* 3.1 36.4 - - + +
227A ILE* 4.6 0.7 - - + -
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Residues in contact with LYS 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A LYS* 3.0 33.7 + - - +
105A PHE* 3.8 9.6 - - + +
107A GLN* 1.3 77.3 - - + +
109A VAL* 1.3 65.5 + - + +
111A GLU* 3.3 5.5 + - - +
112A GLU* 3.1 22.6 + - - +
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Residues in contact with VAL 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A PHE* 2.9 50.4 + - + +
106A VAL* 3.9 3.4 - - - +
108A LYS* 1.3 78.3 - - + +
110A PHE* 1.3 65.5 + - - +
112A GLU* 3.3 8.0 + - - +
113A CYS* 3.2 22.4 + - - -
231A PHE* 4.0 9.0 - - + -
235A PHE* 3.4 37.2 - - + -
275A LEU* 3.5 20.9 - - + -
277A TYR* 3.9 11.4 - - - +
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Residues in contact with PHE 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A VAL 2.8 20.9 + - - +
107A GLN* 3.0 9.8 + - - +
109A VAL* 1.3 78.0 - - - +
111A GLU* 1.3 62.0 + - - +
113A CYS* 3.5 4.7 + - - +
114A TYR* 3.2 16.3 + - + +
119A ILE* 4.0 24.0 - - + +
162A TYR* 4.5 13.7 - + + -
206A VAL* 3.7 28.7 - - + -
207A THR* 5.0 1.6 - - - -
219A VAL* 3.4 41.5 - - + -
220A PRO* 4.0 7.6 - - + -
221A PHE* 4.3 13.9 - + - -
227A ILE* 3.9 20.4 - - + -
231A PHE* 3.7 26.9 - + + -
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Residues in contact with GLU 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A GLN 2.9 14.6 + - - +
108A LYS* 3.8 5.6 - - - +
110A PHE* 1.3 75.7 - - - +
112A GLU* 1.3 55.0 + - - +
114A TYR* 2.8 14.0 + - + +
115A LYS* 2.6 61.0 + - + +
220A PRO* 4.5 9.6 - - + +
221A PHE* 3.3 38.4 - - + +
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Residues in contact with GLU 112 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A LYS 3.1 14.2 + - - +
109A VAL* 3.3 10.3 + - - +
111A GLU* 1.3 76.5 - - - +
113A CYS* 1.3 60.0 + - - +
115A LYS* 3.6 17.3 + - - +
116A ARG* 2.6 73.0 + - - +
275A LEU* 3.4 24.2 - - + -
277A TYR* 5.6 1.1 - - - +
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Residues in contact with CYS 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A VAL* 3.2 12.8 + - - -
110A PHE* 3.8 6.1 - - - +
111A GLU 3.1 0.6 - - - -
112A GLU* 1.3 78.7 - - - +
114A TYR* 1.3 61.5 + - - +
116A ARG* 3.2 8.3 + - - +
117A GLY 3.2 3.8 + - - -
118A ASP* 2.9 31.6 + - + -
119A ILE* 3.6 21.8 - - + -
164A PHE* 4.9 5.4 - - - -
231A PHE* 5.0 10.3 - - + -
235A PHE* 5.6 0.2 - - - -
271A PHE* 4.7 3.4 - - - -
274A SER* 3.2 26.7 - - - +
275A LEU* 3.6 24.5 - - - -
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Residues in contact with TYR 114 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A PHE 3.2 11.8 + - - +
111A GLU* 2.8 16.4 + - + +
113A CYS* 1.3 75.5 - - - +
115A LYS* 1.3 65.3 + - + +
117A GLY* 2.7 26.3 + - - -
119A ILE* 2.9 45.3 - - + +
120A TYR* 4.8 3.8 - - - -
121A LEU* 5.2 0.9 - - + -
162A TYR* 4.5 13.4 - + - -
221A PHE* 3.4 42.5 - + + -
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Residues in contact with LYS 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A GLU* 2.6 44.5 + - + +
112A GLU* 3.9 19.6 + - - +
114A TYR* 1.3 77.9 - - + +
116A ARG* 1.3 62.5 + - + +
117A GLY* 3.2 1.2 + - - -
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Residues in contact with ARG 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A GLU* 2.6 50.3 + - - +
113A CYS* 3.5 9.0 - - - +
114A TYR 3.0 1.4 - - - -
115A LYS* 1.3 76.3 - - + +
117A GLY* 1.3 61.0 + - - +
118A ASP* 3.3 11.7 + - - +
274A SER 2.7 37.3 + - - -
275A LEU* 3.3 24.9 + - - +
276A GLY* 3.7 4.6 - - - +
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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