Contacts of the helix formed by residues 99 - 116 (chain B) in PDB entry 2CSX
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93B LYS* 4.7 8.4 + - - +
94B PHE 4.8 1.4 - - - +
95B ILE* 3.9 7.4 - - + +
96B ARG* 2.8 50.3 + - - +
98B THR* 1.3 81.3 + - - +
100B PRO* 1.3 78.0 - - + +
101B TYR* 4.7 5.6 - - + +
102B HIS* 3.1 18.4 + - + +
103B VAL* 3.2 10.4 + - - +
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Residues in contact with PRO 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B THR 3.4 5.4 - - - +
99B ASP* 1.3 86.9 - - + +
101B TYR* 1.3 77.4 + - + +
102B HIS 2.7 0.5 + - - -
103B VAL* 2.7 34.0 + - + +
104B LYS* 2.9 8.7 + - - +
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Residues in contact with TYR 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B ASP* 3.5 5.5 - - + -
100B PRO* 1.3 88.2 - - + +
102B HIS* 1.3 56.9 + - - +
104B LYS* 3.7 9.5 + - + +
105B PHE* 2.9 30.4 + - - +
239B SER* 5.2 7.0 - - - +
242B GLU* 3.2 50.7 + - + +
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Residues in contact with HIS 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B ILE* 4.6 8.1 - - + -
96B ARG 4.3 9.2 - - - +
97B THR* 3.4 32.3 - - + +
99B ASP* 3.1 13.2 + - + +
100B PRO 2.7 4.9 + - - -
101B TYR* 1.3 73.8 - - - +
103B VAL* 1.3 56.0 + - - +
105B PHE* 3.0 2.3 + - - +
106B VAL* 2.7 53.9 + - + +
217B ILE* 4.5 0.7 - - + -
232B ASP* 2.8 48.9 + - - -
235B PHE 3.8 2.0 - - - -
236B ASN* 3.5 24.0 - - - -
239B SER* 2.8 27.1 + - - +
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Residues in contact with VAL 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B HIS* 4.1 5.6 - - + +
97B THR 3.6 21.3 - - - +
98B THR 4.5 6.1 - - - +
99B ASP 3.2 4.0 + - - +
100B PRO* 2.7 38.6 + - + +
102B HIS* 1.3 73.4 - - - +
104B LYS* 1.3 59.8 + - + +
106B VAL* 3.1 2.1 + - - +
107B GLN* 2.8 47.1 + - - +
216B GLY 5.7 0.9 - - - +
217B ILE* 3.7 31.6 - - + +
218B PRO* 6.2 0.4 - - + -
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Residues in contact with LYS 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B PRO 3.6 12.1 - - - +
101B TYR* 3.7 9.2 - - + +
103B VAL* 1.3 84.2 - - + +
105B PHE* 1.3 55.9 + - - +
107B GLN* 3.3 12.0 + - - +
108B LYS* 3.0 68.3 + - - +
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Residues in contact with PHE 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B TYR 2.9 20.9 + - - +
102B HIS 3.5 3.4 - - - +
104B LYS* 1.3 72.9 - - - +
106B VAL* 1.3 62.8 + - + +
108B LYS* 3.3 11.3 + - + +
109B VAL* 2.9 62.8 + - + +
235B PHE* 3.4 37.9 - + + -
238B ILE* 3.6 28.7 - - + -
239B SER* 3.4 27.8 - - - -
245B VAL* 5.9 1.3 - - + -
277B TYR* 4.9 8.1 - + - -
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Residues in contact with VAL 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B HIS* 2.7 57.0 + - + +
103B VAL 3.5 4.5 - - - +
105B PHE* 1.3 74.8 - - + +
107B GLN* 1.3 57.2 + - - +
109B VAL* 3.7 3.8 - - - +
110B PHE* 2.8 28.4 + - - +
217B ILE* 3.8 17.5 - - + -
227B ILE* 3.6 23.1 - - + -
231B PHE* 3.5 34.2 - - + +
232B ASP 4.0 0.4 - - - +
235B PHE* 4.5 4.5 - - + -
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Residues in contact with GLN 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B VAL* 2.8 25.0 + - - +
104B LYS* 3.5 12.0 - - - +
105B PHE 3.2 0.2 - - - -
106B VAL* 1.3 76.0 - - - +
108B LYS* 1.3 60.1 + - + +
110B PHE* 3.6 1.7 - - - +
111B GLU* 2.8 31.0 + - - +
217B ILE* 3.7 11.7 - - + +
218B PRO* 3.0 46.2 + - - +
220B PRO* 3.2 36.0 - - + +
227B ILE* 4.3 1.1 - - + -
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Residues in contact with LYS 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B LYS* 3.0 56.7 + - - +
105B PHE* 3.8 10.3 - - + +
107B GLN* 1.3 75.9 - - + +
109B VAL* 1.3 60.3 + - + +
111B GLU* 3.2 8.3 + - - +
112B GLU* 2.8 33.3 + - - +
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Residues in contact with VAL 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B PHE* 2.9 54.2 + - + +
106B VAL* 3.9 4.9 - - - +
108B LYS* 1.3 77.6 - - + +
110B PHE* 1.3 62.7 + - - +
112B GLU* 3.9 5.4 - - - +
113B CYS* 3.1 23.4 + - - +
231B PHE* 4.4 3.4 - - + -
235B PHE* 3.3 35.7 - - + -
275B LEU* 3.5 20.8 - - + +
277B TYR* 4.7 8.3 - - - +
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Residues in contact with PHE 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B VAL 2.8 18.9 + - - +
107B GLN 3.6 2.9 - - - +
109B VAL* 1.3 77.4 - - - +
111B GLU* 1.3 67.6 + - - +
113B CYS* 3.4 2.4 + - - +
114B TYR* 3.1 17.3 + - - +
119B ILE* 3.6 30.9 - - + +
162B TYR* 4.2 14.4 - + + -
206B VAL* 3.3 29.6 - - + -
207B THR* 4.7 1.1 - - - -
219B VAL* 3.2 44.0 - - + -
220B PRO* 4.4 1.8 - - + -
221B PHE* 3.7 15.7 - + - -
227B ILE* 3.6 27.1 - - + -
231B PHE* 4.0 20.4 - + + -
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Residues in contact with GLU 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B GLN 2.8 18.5 + - - +
108B LYS* 3.3 8.5 - - - +
110B PHE* 1.3 76.3 - - - +
112B GLU* 1.3 64.9 + - - +
114B TYR* 3.0 24.4 + - - +
115B LYS* 3.1 34.3 + - - +
220B PRO* 3.7 16.6 - - + +
221B PHE* 3.5 37.0 - - - +
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Residues in contact with GLU 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B LYS 2.8 20.6 + - - +
109B VAL* 3.9 5.6 - - - +
111B GLU* 1.3 72.3 - - + +
113B CYS* 1.3 67.3 + - - +
115B LYS* 3.1 27.7 + - - +
116B ARG* 2.7 54.7 + - - +
275B LEU* 3.8 17.5 - - + +
277B TYR* 5.5 4.3 - - + +
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Residues in contact with CYS 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B VAL 3.1 19.4 + - - +
112B GLU* 1.3 76.4 - - - +
114B TYR* 1.3 63.2 + - - +
116B ARG* 3.1 20.0 + - - +
117B GLY 3.4 4.5 + - - -
118B ASP* 3.5 20.6 + - - -
119B ILE* 3.7 30.5 - - + -
164B PHE* 4.0 10.8 - - - -
231B PHE* 4.0 11.7 - - + -
271B PHE 5.3 0.2 - - - -
274B SER* 3.3 24.2 - - - -
275B LEU* 4.0 12.8 - - + +
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Residues in contact with TYR 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B PHE 3.1 12.0 + - - +
111B GLU* 3.0 19.2 + - - +
113B CYS* 1.3 73.5 - - - +
115B LYS* 1.3 71.6 + - + +
117B GLY* 2.9 16.6 + - - -
119B ILE* 2.8 43.6 - - + +
120B TYR* 4.9 4.5 - - - -
121B LEU* 6.3 0.7 - - + -
162B TYR* 4.9 7.6 - + - -
221B PHE* 3.6 44.6 - + + -
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Residues in contact with LYS 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B GLU* 3.1 35.8 + - - +
112B GLU* 3.1 20.3 + - - +
114B TYR* 1.3 84.9 - - + +
116B ARG* 1.3 62.5 + - + +
117B GLY* 3.2 1.7 + - - -
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Residues in contact with ARG 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B GLU* 2.7 40.3 + - - +
113B CYS* 3.1 11.6 + - - +
114B TYR 3.1 1.4 - - - -
115B LYS* 1.3 76.5 - - + +
117B GLY* 1.3 58.4 + - - +
118B ASP* 3.5 13.7 + - - +
274B SER 2.9 29.9 + - - -
275B LEU* 3.4 26.7 + - - +
276B GLY* 3.9 4.2 - - - +
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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