Contacts of the helix formed by residues 105 - 116 (chain B) in PDB entry 4AUP
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 ALA 105 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111A THR* 3.9 7.0 - - + -
115A ASN* 3.6 21.3 - - - +
1212A ACT 3.0 28.8 + - + +
104B THR* 1.3 74.3 - - - +
106B MET* 1.3 67.8 + - - +
107B PRO* 3.4 5.2 - - + -
108B ALA 2.9 13.9 + - - -
109B PHE 3.1 8.8 + - - -
146B ARG* 4.5 0.9 - - - +
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Residues in contact with MET 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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105B ALA* 1.3 70.9 - - - +
107B PRO* 1.4 72.4 - - + +
109B PHE* 2.9 17.5 + - - +
110B LEU* 2.9 46.3 + - + +
142B ASP* 3.5 40.2 - - + +
143B SER* 3.7 5.4 - - - +
146B ARG* 3.6 16.9 - - + +
175B ASP* 3.6 37.2 - - + +
178B ASN* 6.6 0.4 - - + -
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Residues in contact with PRO 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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111A THR* 3.8 20.0 - - + +
114A ARG* 5.2 6.3 - - - +
105B ALA* 3.5 11.4 - - + -
106B MET* 1.4 93.6 - - + +
108B ALA* 1.3 58.9 + - - +
110B LEU* 3.4 10.8 + - + +
111B THR* 2.9 28.6 + - - -
114B ARG* 4.7 1.5 + - - +
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Residues in contact with ALA 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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108A ALA* 4.1 26.3 - - + +
111A THR* 3.8 17.6 - - + +
1212A ACT 3.8 15.7 - - - +
100B LEU* 5.1 0.3 - - - +
104B THR* 3.5 20.9 - - + -
105B ALA 2.9 4.9 + - - +
107B PRO* 1.3 80.6 - - - +
109B PHE* 1.3 57.6 + - - +
111B THR* 3.3 1.6 + - - -
112B ALA* 2.9 29.3 + - - +
1212B SCN 4.5 1.1 + - - +
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Residues in contact with PHE 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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100B LEU* 3.6 25.1 - - + -
104B THR* 3.5 7.6 - - + +
105B ALA 3.1 5.3 + - - +
106B MET* 2.9 24.9 + - - +
108B ALA* 1.3 76.7 - - - +
110B LEU* 1.3 66.4 + - + +
112B ALA* 3.4 5.6 + - - +
113B LYS* 2.9 39.4 + - + +
123B TRP* 3.7 25.6 - + - -
145B LYS 4.1 3.6 - - - -
146B ARG* 3.4 62.4 - - + +
149B PHE* 3.8 32.5 - + + -
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Residues in contact with LEU 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 MET* 2.9 35.8 + - + +
107B PRO* 4.0 7.2 - - + +
108B ALA 3.3 0.2 - - - -
109B PHE* 1.3 91.8 - - + +
111B THR* 1.3 58.2 + - - +
113B LYS* 3.7 7.4 - - + +
114B ARG* 2.9 57.9 + - - +
142B ASP* 3.5 45.1 - - + +
145B LYS* 4.1 20.9 - - + +
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Residues in contact with THR 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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105A ALA* 3.9 13.2 - - + -
107A PRO* 3.6 22.0 - - + +
108A ALA* 3.7 32.7 + - + +
107B PRO* 2.9 21.0 + - - +
108B ALA 3.6 4.5 - - - -
109B PHE 3.2 0.2 - - - -
110B LEU* 1.3 75.2 - - - +
112B ALA* 1.3 64.5 + - - +
114B ARG* 3.5 18.2 + - - +
115B ASN* 2.8 44.1 + - - +
1212B SCN 4.0 0.9 - - - -
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Residues in contact with ALA 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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100B LEU* 3.7 19.7 - - + -
108B ALA 2.9 14.7 + - - +
109B PHE 3.6 4.5 - - - +
111B THR* 1.3 78.4 - - - +
113B LYS* 1.3 50.4 + - - +
115B ASN 3.3 1.2 + - - -
116B LYS 2.7 30.3 + - - -
117B ASN 3.0 28.2 + - - +
123B TRP* 3.9 6.1 - - + -
1212B SCN 3.6 26.6 - - - +
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Residues in contact with LYS 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 PHE* 2.9 27.6 + - + +
110B LEU* 3.7 10.5 - - + +
111B THR 3.3 0.2 - - - -
112B ALA* 1.3 75.5 - - - +
114B ARG* 1.3 56.4 + - + +
116B LYS* 2.7 42.6 + - - +
123B TRP* 2.7 57.2 + - + +
125B ASP* 2.7 33.4 + - - +
145B LYS* 3.7 41.8 + - + +
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Residues in contact with ARG 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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107A PRO* 5.6 2.4 - - - +
107B PRO* 4.7 1.0 + - - +
110B LEU* 2.9 43.3 + - + +
111B THR* 3.5 35.9 + - - +
112B ALA 3.4 0.2 - - - -
113B LYS* 1.3 76.4 - - + +
115B ASN* 1.3 63.8 + - - +
116B LYS* 3.7 14.8 + - - +
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Residues in contact with ASN 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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105A ALA* 3.9 17.4 - - - +
111B THR* 2.8 42.5 + - - +
112B ALA 3.8 2.9 - - - +
114B ARG* 1.3 83.4 - - - +
116B LYS* 1.4 70.2 + - - +
117B ASN* 4.1 6.0 - - + +
1212B SCN 4.1 10.5 - - - -
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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 ALA 2.7 11.3 + - - -
113B LYS* 2.7 31.4 + - - +
114B ARG* 3.7 14.3 + - - +
115B ASN* 1.4 76.8 - - - +
117B ASN* 1.3 55.8 + - - +
119B GLY* 3.0 24.6 + - - -
123B TRP* 3.5 44.6 + - + +
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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