Contacts of the helix formed by residues 101 - 115 (chain B) in PDB entry 2CLS
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 101 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97B PRO 4.7 2.4 + - - -
98B GLU 4.1 5.5 + - - +
100B VAL* 1.3 95.7 - - - +
102B SER* 1.3 66.7 + - - +
103B ALA 3.3 0.7 + - - -
105B LYS* 3.3 19.6 + - - +
158B GLN* 4.6 13.9 + - - +
159B LEU* 5.4 1.4 - - - +
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Residues in contact with SER 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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98B GLU 4.7 6.3 + - - -
101B ASP* 1.3 79.7 - - - +
103B ALA* 1.3 60.7 + - - +
105B LYS* 3.5 7.2 - - - +
106B LYS* 3.2 31.4 + - - +
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Residues in contact with ALA 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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21B ASP* 3.8 24.0 - - - +
98B GLU 5.3 0.4 + - - -
99B THR* 2.9 28.5 + - - +
101B ASP 3.3 0.8 + - - -
102B SER* 1.3 75.4 - - - +
104B LEU* 1.3 60.0 + - + +
106B LYS* 3.2 25.8 - - - +
107B TRP* 3.0 33.8 + - + -
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Residues in contact with LEU 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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90B LEU* 3.3 36.6 - - + +
91B CYS 4.1 2.2 - - - +
92B PHE* 4.0 29.4 - - + -
99B THR 3.5 9.2 + - - +
100B VAL* 3.4 44.0 - - + +
101B ASP 3.6 0.6 + - - -
103B ALA* 1.3 79.7 - - + +
105B LYS* 1.3 53.4 + - - +
107B TRP* 3.4 8.5 + - + +
108B ARG* 2.8 34.7 + - - +
122B LEU* 4.3 4.3 - - + -
155B ILE* 3.9 7.9 - - + -
159B LEU* 3.6 24.6 - - + +
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Residues in contact with LYS 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 ASP 3.3 13.3 + - - +
102B SER* 3.5 13.0 - - - +
103B ALA 3.2 0.2 - - - -
104B LEU* 1.3 75.6 - - - +
106B LYS* 1.3 58.2 + - - +
108B ARG* 3.3 2.7 + - - +
109B THR* 2.7 44.2 + - - +
159B LEU* 4.1 13.3 - - + +
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Residues in contact with LYS 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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21B ASP* 5.2 3.2 + - - -
102B SER* 3.2 23.5 + - - +
103B ALA* 3.2 27.2 + - - +
105B LYS* 1.3 78.2 - - - +
107B TRP* 1.3 65.5 + - + +
109B THR* 3.8 5.1 - - - -
110B GLU* 3.0 24.3 + - - +
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Residues in contact with TRP 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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19B VAL* 4.0 19.1 - - + -
20B GLY* 3.5 26.2 - - - -
21B ASP* 2.8 30.1 + - - +
70B GLY* 3.5 29.2 - - - -
75B ASP* 5.3 0.2 - - - -
78B ARG* 3.4 48.5 - - - -
82B TYR* 4.8 0.4 - - - -
90B LEU* 3.6 24.7 - - + -
103B ALA* 3.0 30.4 + - + +
104B LEU* 3.7 9.0 - - + +
105B LYS 3.3 0.2 - - - -
106B LYS* 1.3 78.2 - - + +
108B ARG* 1.3 63.7 + - - +
110B GLU* 3.4 18.6 + - - +
111B ILE* 3.2 29.6 + - - +
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Residues in contact with ARG 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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90B LEU* 4.2 5.1 - - + +
104B LEU 2.8 21.1 + - - +
105B LYS* 3.3 4.9 + - - +
107B TRP* 1.3 73.4 - - - +
109B THR* 1.3 56.7 + - - +
111B ILE* 3.5 16.8 + - - +
112B LEU* 3.0 59.1 + - + +
115B CYS 5.6 0.6 + - - -
116B PRO* 5.0 7.1 + - - +
118B THR 4.5 7.3 + - - -
120B VAL* 3.8 34.3 - - - +
159B LEU* 2.9 44.8 + - + +
160B GLY* 4.2 10.9 + - - -
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Residues in contact with THR 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 LYS* 2.7 29.3 + - - +
106B LYS* 3.8 6.1 - - - -
108B ARG* 1.3 73.8 - - - +
110B GLU* 1.3 56.4 + - - +
112B LEU* 3.2 12.2 + - + +
113B ASP* 2.7 60.3 + - - +
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Residues in contact with GLU 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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75B ASP* 4.0 8.3 - - - +
78B ARG* 3.0 40.2 + - - +
79B PRO* 4.3 17.6 - - + +
82B TYR* 2.5 34.2 + - + +
106B LYS 3.0 13.7 + - - +
107B TRP* 3.6 18.8 - - - +
109B THR* 1.3 75.2 - - - +
111B ILE* 1.3 57.3 + - - +
113B ASP* 3.4 8.5 + - - +
114B TYR* 3.0 26.7 + - - +
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Residues in contact with ILE 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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19B VAL* 4.1 10.3 - - + -
82B TYR* 4.0 24.2 - - + +
88B VAL* 3.6 42.4 - - + -
90B LEU* 4.2 12.3 - - + -
107B TRP 3.2 22.7 + - - +
108B ARG* 3.8 11.7 - - - +
110B GLU* 1.3 75.1 - - - +
112B LEU* 1.3 57.8 + - - +
114B TYR* 3.2 4.9 + - + +
115B CYS 3.0 30.4 + - - +
118B THR* 4.3 14.1 - - - +
120B VAL* 3.8 28.7 - - + -
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Residues in contact with LEU 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 ARG* 3.0 39.1 + - + +
109B THR* 3.5 13.0 - - + +
111B ILE* 1.3 77.4 - - - +
113B ASP* 1.3 66.1 + - - +
115B CYS 3.4 12.2 + - - -
116B PRO* 3.4 47.6 - - + +
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Residues in contact with ASP 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 THR* 2.7 43.5 + - - +
110B GLU* 3.7 7.3 + - - +
112B LEU* 1.3 73.7 - - - +
114B TYR* 1.3 64.6 + - - +
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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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79B PRO* 3.7 31.4 - - + -
80B LEU* 5.7 0.4 - - + -
82B TYR* 3.5 39.9 - + + -
83B SER* 3.1 33.6 - - - -
84B ASP 4.6 1.2 + - - -
110B GLU 3.0 9.1 + - - +
111B ILE* 3.2 8.0 + - + +
112B LEU 4.0 0.2 - - - -
113B ASP* 1.3 79.9 - - - +
115B CYS* 1.3 79.2 + - + +
116B PRO* 4.8 0.2 - - - -
118B THR* 4.3 8.7 - - - -
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Residues in contact with CYS 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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108B ARG* 5.6 0.3 + - - -
111B ILE* 3.0 11.2 + - - +
112B LEU* 3.4 4.4 + - - -
114B TYR* 1.3 103.1 - - + +
116B PRO* 1.4 72.6 - - - +
117B SER* 3.1 27.4 - - - -
118B THR* 3.1 25.2 + - - +
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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