Contacts of the helix formed by residues 99 - 113 (chain B) in PDB entry 5WC9
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 SER 99 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97B THR* 3.9 3.0 + - - -
98B ILE* 1.3 79.2 - - - +
100B ILE* 1.3 64.5 + - - +
101B ALA* 3.9 5.0 + - - +
102B ALA* 3.1 33.6 + - - +
103B LYS* 3.1 12.1 + - - +
130B LEU* 6.0 0.8 - - - +
126E GLU 5.6 0.9 - - - -
127E GLU 4.1 0.2 - - - -
128E LEU* 3.9 15.1 + - - -
129E ASN* 3.5 33.0 - - - +
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Residues in contact with ILE 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 ILE 3.7 0.9 + - - +
99B SER* 1.3 73.1 - - - +
101B ALA* 1.3 61.9 + - - +
103B LYS* 3.4 35.7 + - + +
104B ASP* 3.4 15.2 + - + +
126E GLU* 4.6 11.8 + - + +
127E GLU* 3.6 21.5 + - + +
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Residues in contact with ALA 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 SER* 3.2 4.2 - - - +
100B ILE* 1.3 79.4 - - - +
102B ALA* 1.3 59.4 + - - +
104B ASP* 2.6 21.9 - - - +
105B ALA* 3.4 10.9 + - - +
101E ALA* 6.1 4.6 - - + +
105E ALA* 5.7 2.7 - - + -
127E GLU* 3.0 27.6 + - + +
128E LEU* 3.7 23.6 - - + -
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Residues in contact with ALA 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 ILE* 3.5 19.7 - - + -
99B SER* 3.1 21.5 + - - +
101B ALA* 1.3 76.1 - - - +
103B LYS* 1.3 54.1 + - - +
105B ALA* 3.1 6.7 + - - +
106B LEU* 2.7 41.2 + - + +
128B LEU* 4.4 26.0 - - + +
130B LEU* 4.5 6.7 - - + -
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Residues in contact with LYS 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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97B THR* 4.8 5.7 - - - +
98B ILE* 3.4 23.9 + - + -
99B SER 3.1 11.8 + - - +
100B ILE* 3.4 27.9 + - + +
101B ALA 3.4 0.4 - - - -
102B ALA* 1.3 76.6 - - - +
104B ASP* 1.3 58.3 + - - +
106B LEU* 3.8 7.2 - - - +
107B GLU* 2.8 33.0 + - - +
138B TRP* 4.4 12.9 - - + +
182C T 3.8 18.5 + - - +
183C C 3.2 37.7 + - - +
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Residues in contact with ASP 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 ILE* 3.4 6.8 + - + +
101B ALA* 2.6 37.2 - - - +
103B LYS* 1.3 78.5 - - - +
105B ALA* 1.3 56.5 + - - +
107B GLU* 3.8 5.8 - - - +
108B ARG* 2.9 63.6 + - - +
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Residues in contact with ALA 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 ALA 3.6 10.8 - - - +
102B ALA* 3.1 10.9 + - - +
104B ASP* 1.3 79.3 + - - +
106B LEU* 1.3 55.1 + - - +
108B ARG* 3.0 19.3 + - - +
109B HIS* 2.7 45.1 + - + +
128B LEU* 4.4 17.5 - - + -
101E ALA* 5.8 3.6 - - + -
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Residues in contact with LEU 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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98B ILE* 4.5 16.2 - - + -
102B ALA* 2.7 28.0 + - + +
103B LYS* 3.8 2.5 - - - +
105B ALA* 1.3 71.8 - - - +
107B GLU* 1.3 52.1 + - - +
109B HIS* 3.1 9.1 + - - +
110B PHE* 2.7 34.5 + - - +
124B MET* 4.3 6.5 - - - -
128B LEU* 3.5 28.7 - - + -
130B LEU* 4.9 3.4 - - + -
135B VAL* 3.9 23.3 - - + -
138B TRP* 3.8 45.2 - - + +
139B PHE* 4.0 14.8 - - + -
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Residues in contact with GLU 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 LYS 2.8 21.3 + - - +
104B ASP* 4.0 5.2 - - - +
106B LEU* 1.3 72.8 - - - +
108B ARG* 1.3 62.1 + - - +
110B PHE* 3.3 5.8 + - - +
111B GLY* 3.2 18.7 + - - -
138B TRP* 3.6 9.9 - - + -
142B ARG* 2.5 53.0 + - - -
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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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104B ASP* 2.9 49.2 + - - +
105B ALA* 3.0 16.8 + - - +
107B GLU* 1.3 74.7 - - - +
109B HIS* 1.3 67.3 + - + +
111B GLY* 3.3 10.4 + - - -
112B GLU* 3.8 13.0 + - - +
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Residues in contact with HIS 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 ALA* 2.7 26.2 + - + +
106B LEU* 3.5 12.6 - - - +
108B ARG* 1.3 75.9 - - + +
110B PHE* 1.3 62.2 + - - +
112B GLU* 3.2 29.3 + - - +
113B GLN* 3.1 23.4 + - - +
124B MET* 3.7 36.4 - - + +
127B GLU* 4.1 21.2 + - - -
128B LEU* 5.8 5.3 - - + +
139B PHE* 4.4 11.8 - - + -
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Residues in contact with PHE 110 (chain B).
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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106B LEU 2.7 19.9 + - - +
107B GLU* 3.5 12.6 - - - +
108B ARG 3.2 0.4 - - - -
109B HIS* 1.3 75.4 - - - +
111B GLY* 1.3 60.1 + - - +
112B GLU 3.3 0.7 + - - -
113B GLN 3.5 7.3 + - - -
114B ASN* 2.9 66.3 + - + +
138B TRP* 4.3 2.2 - - + -
139B PHE* 3.5 23.3 - + + -
142B ARG* 3.5 66.0 - - + -
143B ARG* 4.0 17.9 - - + -
146B GLU* 4.2 8.5 - - + -
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Residues in contact with GLY 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 GLU* 3.2 13.8 + - - -
108B ARG 3.3 5.5 + - - -
109B HIS 3.3 0.6 - - - -
110B PHE* 1.3 80.1 - - - +
112B GLU* 1.3 56.6 + - - +
114B ASN* 4.6 3.8 - - - +
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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 ARG* 3.8 7.2 + - - +
109B HIS* 3.2 45.0 + - - +
111B GLY* 1.3 76.8 - - - +
113B GLN* 1.3 67.9 + - + +
114B ASN* 4.3 0.9 - - - -
120B GLU* 5.7 0.5 - - - +
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Residues in contact with GLN 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 HIS 3.1 15.7 + - - +
110B PHE* 3.5 8.2 + - - +
111B GLY 3.6 0.2 - - - -
112B GLU* 1.3 87.3 + - + +
114B ASN* 1.3 70.3 + - - +
115B LYS* 3.5 28.5 + - - +
116B PRO* 3.7 17.1 - - + +
117B SER 5.8 0.6 - - - +
120B GLU* 4.6 20.4 + - - +
139B PHE* 4.0 8.0 - - - -
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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