Contacts of the helix formed by residues 104 - 122 (chain B) in PDB entry 4Q9U
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 ASN 104 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28B GLU* 5.6 3.4 + - - +
31B VAL* 5.6 4.2 - - - +
101B ASP* 3.1 24.8 + - + +
102B ILE 3.2 0.4 - - - -
103B THR* 1.3 96.3 + - - +
105B GLU* 1.3 58.4 + - - +
106B GLU* 2.9 10.3 - - + +
107B SER* 2.5 47.2 + - - +
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Residues in contact with GLU 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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104B ASN* 1.3 71.1 - - - +
106B GLU* 1.3 56.5 + - - +
108B PHE* 2.9 22.7 + - + +
109B ALA* 2.9 15.0 + - - +
142B ALA* 2.9 42.7 - - + +
143B VAL* 3.7 19.7 - - + +
144B ASP* 5.2 1.7 - - - +
147B GLU* 5.1 7.4 - - - +
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Residues in contact with GLU 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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28B GLU* 4.6 10.8 - - - +
104B ASN* 2.9 6.9 + - + +
105B GLU* 1.3 78.1 - - - +
107B SER* 1.3 57.1 + - - +
109B ALA* 3.2 9.8 + - - +
110B ARG* 2.5 71.7 + - + +
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Residues in contact with SER 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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28B GLU* 4.1 18.1 + - - -
31B VAL* 4.1 9.4 - - - -
99B VAL 3.9 2.6 - - - +
100B TYR* 3.2 14.0 - - - +
101B ASP* 2.5 43.2 + - - +
104B ASN* 2.5 29.8 + - - +
106B GLU* 1.3 76.8 - - - +
108B PHE* 1.3 56.3 + - - +
110B ARG* 3.5 11.1 - - - +
111B ALA* 2.9 20.4 + - - +
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Residues in contact with PHE 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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100B TYR* 3.3 48.0 - + + -
105B GLU* 2.9 17.3 + - + +
107B SER* 1.3 80.8 + - - +
109B ALA* 1.3 59.2 + - + +
111B ALA* 3.0 6.0 - - + +
112B LYS* 2.9 59.3 + - + +
130B LEU* 4.4 9.2 - - + -
143B VAL* 4.2 15.3 - - + -
147B GLU* 4.4 16.8 - - + -
148B ALA* 3.7 35.2 - - + -
151B TYR* 4.5 14.6 - + + -
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Residues in contact with ALA 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 GLU 2.9 11.3 + - - +
106B GLU* 3.2 15.7 + - - +
108B PHE* 1.3 72.3 - - + +
110B ARG* 1.3 71.2 + - - +
111B ALA 3.0 1.3 - - - -
112B LYS* 3.0 27.5 + - - +
113B ASN* 3.0 16.7 + - - +
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Residues in contact with ARG 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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28B GLU* 3.5 28.9 - - + -
80B GLU* 5.7 3.6 - - - -
83B HIS* 4.5 6.9 + - - -
106B GLU* 2.5 58.3 + - - +
107B SER* 3.5 8.3 - - - +
109B ALA* 1.3 78.5 + - - +
111B ALA* 1.3 64.0 + - - +
113B ASN* 3.4 29.0 + - - +
114B TRP* 2.8 58.0 + - + +
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Residues in contact with ALA 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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98B VAL* 3.6 24.8 - - + +
99B VAL 4.6 0.2 - - - +
100B TYR* 3.5 19.1 - - + -
107B SER 2.9 15.8 + - - +
108B PHE* 3.0 15.3 - - + +
109B ALA 3.0 0.2 - - - -
110B ARG* 1.3 75.6 - - - +
112B LYS* 1.3 54.0 + - - +
114B TRP* 3.1 7.4 + - - +
115B VAL* 2.9 32.4 + - - +
130B LEU* 3.7 12.1 - - + -
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Residues in contact with LYS 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 PHE* 2.9 43.6 + - + +
109B ALA* 3.0 17.6 + - - +
111B ALA* 1.3 70.0 - - - +
113B ASN* 1.3 64.2 + - - +
115B VAL* 3.0 14.3 + - - +
116B LYS* 3.0 28.0 + - - +
147B GLU* 5.1 5.3 + - - -
151B TYR* 3.5 51.3 - - + +
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Residues in contact with ASN 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 ALA 3.0 12.0 + - - +
110B ARG* 3.7 29.8 - - - +
112B LYS* 1.3 75.5 - - - +
114B TRP* 1.3 67.1 + - + +
116B LYS* 3.2 20.4 + - - +
117B GLU* 3.0 27.2 + - - +
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Residues in contact with TRP 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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26B LEU* 3.5 42.9 - - + +
27B GLY* 4.2 12.9 - - - -
28B GLU 4.3 0.4 - - - +
83B HIS* 3.1 67.1 - + + -
86B ALA* 6.3 2.2 - - + -
98B VAL* 3.8 17.0 - - + -
99B VAL 5.0 1.6 - - - -
110B ARG* 2.8 55.3 + - + +
111B ALA* 3.2 14.4 - - - +
113B ASN* 1.3 78.0 - - + +
115B VAL* 1.3 56.7 + - - +
117B GLU* 3.8 26.0 - - + +
118B LEU* 2.9 30.9 + - - +
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Residues in contact with VAL 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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98B VAL* 5.0 10.5 - - + -
111B ALA 2.9 24.0 + - - +
112B LYS* 3.0 8.9 + - - +
114B TRP* 1.3 77.9 - - - +
116B LYS* 1.3 58.3 + - - +
118B LEU* 2.9 23.7 + - + +
119B GLN* 2.9 45.4 + - + +
128B ILE* 5.1 12.6 - - + -
130B LEU* 5.2 7.6 - - + -
151B TYR* 3.6 27.1 - - + +
155B ASN* 5.7 1.1 - - + -
157B LEU* 4.9 15.3 - - + -
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Residues in contact with LYS 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 LYS* 3.0 35.9 + - - +
113B ASN* 3.2 26.0 + - - +
115B VAL* 1.3 76.0 - - - +
117B GLU* 1.3 63.5 - - - +
119B GLN* 3.5 12.1 + - - +
120B ARG* 3.1 27.2 + - - +
151B TYR* 3.6 17.4 + - - +
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Residues in contact with GLU 117 (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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83B HIS 5.3 3.1 - - - +
86B ALA* 4.9 13.2 - - - +
87B PRO* 4.9 7.4 - - - +
90B TYR* 5.0 10.6 + - + +
113B ASN 3.0 16.1 + - - +
114B TRP* 3.8 28.3 - - - +
116B LYS* 1.3 75.9 - - - +
118B LEU* 1.3 58.5 + - - +
121B GLN* 2.8 47.1 + - + +
122B ALA 3.7 2.8 + - - -
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Residues in contact with LEU 118 (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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24B VAL* 6.1 1.8 - - + -
26B LEU* 5.6 4.7 - - + -
90B TYR* 6.1 2.9 - - + -
96B ALA* 4.5 19.7 - - + -
97B ILE 5.8 0.4 - - - +
98B VAL* 4.0 26.5 - - + -
114B TRP 2.9 13.8 + - - +
115B VAL* 2.9 16.1 + - + +
117B GLU* 1.3 74.8 - - - +
119B GLN* 1.3 66.1 + - + +
122B ALA* 3.1 52.3 + - + +
126B ILE* 4.1 21.1 - - + +
128B ILE* 4.3 27.6 - - + -
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Residues in contact with GLN 119 (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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115B VAL* 2.9 47.1 + - - +
116B LYS* 3.5 12.0 - - - +
118B LEU* 1.3 78.2 - - - +
120B ARG* 1.3 65.3 + - - +
122B ALA 4.1 4.5 - - - +
124B PRO* 4.5 14.8 - - - +
126B ILE* 5.9 2.2 - - - -
128B ILE* 4.1 23.0 - - + +
155B ASN* 4.1 29.4 + - - +
157B LEU* 4.8 2.4 - - - +
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Residues in contact with ARG 120 (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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116B LYS 3.1 15.2 + - - +
118B LEU 3.1 1.2 - - - -
119B GLN* 1.3 84.2 + - - +
121B GLN* 1.3 91.7 + - + +
122B ALA 3.8 3.8 - - - +
124B PRO* 4.7 6.1 - - - +
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Residues in contact with GLN 121 (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 TYR* 3.3 15.6 + - - +
91B ARG* 3.3 18.2 + - - -
117B GLU* 2.8 30.5 + - + +
120B ARG* 1.3 99.1 - - + +
122B ALA* 1.3 63.2 + - - +
124B PRO* 5.7 0.2 - - - -
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Residues in contact with ALA 122 (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 TYR* 3.5 31.7 + - + -
117B GLU 3.7 2.8 + - - -
118B LEU* 3.1 47.7 + - + +
119B GLN 4.1 0.5 - - - +
120B ARG 3.8 3.3 - - - +
121B GLN* 1.3 78.9 - - - +
123B SER* 1.3 70.2 + - - +
124B PRO* 2.8 11.1 - - - +
126B ILE* 5.0 4.9 - - + -
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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