Contacts of the helix formed by residues 105 - 115 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A THR* 1.3 75.9 - - - +
106A MET* 1.3 66.6 - - - +
107A PRO* 3.5 5.8 - - + -
108A ALA 3.0 13.5 + - - -
109A PHE 3.1 9.0 + - - -
146A ARG* 4.5 0.9 - - - +
111B THR* 3.9 13.9 - - + -
115B ASN* 3.9 15.7 - - - +
117B ASN* 4.7 0.4 - - - +
1212B SCN 3.4 23.1 - - - -
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Residues in contact with MET 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A THR 3.5 2.0 + - - -
105A ALA* 1.3 69.4 - - - +
107A PRO* 1.4 70.6 - - + +
109A PHE* 3.0 17.3 + - - +
110A LEU* 2.9 35.9 + - + +
142A ASP* 3.6 51.1 - - + +
143A SER* 3.8 5.4 - - - +
146A ARG* 3.7 14.7 - - + +
175A ASP* 3.5 37.5 - - + +
178A ASN* 6.6 0.2 - - + -
182A LYS* 6.4 0.4 - - - +
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Residues in contact with PRO 107 (chain A).
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* 3.6 11.2 - - + -
106A MET* 1.4 93.0 - - + +
108A ALA* 1.3 57.3 + - - +
110A LEU* 3.4 9.8 + - + +
111A THR* 2.9 31.6 + - - -
114A ARG* 5.0 0.9 + - - -
111B THR* 3.6 20.9 - - + +
114B ARG* 5.6 2.2 - - - +
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Residues in contact with ALA 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A LEU* 5.0 0.3 - - - +
104A THR* 3.5 21.5 - - + +
105A ALA 3.0 5.2 + - - +
107A PRO* 1.3 78.3 - - - +
109A PHE* 1.4 58.3 + - - +
111A THR* 3.3 2.6 + - - -
112A ALA* 3.0 27.9 + - - +
1212A ACT 4.7 0.2 - - - +
108B ALA* 4.1 24.6 - - + +
111B THR* 3.7 23.1 - - + +
1212B SCN 3.7 14.1 - - - +
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Residues in contact with PHE 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A LEU* 3.6 25.1 - - + +
104A THR* 3.7 6.6 - - + +
105A ALA 3.1 6.1 + - - +
106A MET* 3.0 23.8 + - - +
108A ALA* 1.4 76.6 - - - +
110A LEU* 1.3 65.1 + - + +
112A ALA* 3.3 6.8 + - - +
113A LYS* 2.9 40.0 + - + +
123A TRP* 3.7 19.7 - + - -
145A LYS 4.1 4.0 - - - -
146A ARG* 3.6 52.0 - - + +
149A PHE* 3.6 47.1 - + + -
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Residues in contact with LEU 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A MET* 2.9 33.0 + - + +
107A PRO* 3.9 7.2 - - + +
109A PHE* 1.3 94.1 - - + +
111A THR* 1.3 55.8 + - - +
113A LYS* 3.5 9.1 - - + +
114A ARG* 2.9 48.2 + - - +
142A ASP* 3.5 41.5 - - + +
145A LYS* 4.2 23.3 - - + +
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Residues in contact with THR 111 (chain A).
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 2.9 18.2 + - - -
108A ALA 3.7 5.2 - - - -
109A PHE 3.2 0.2 - - - -
110A LEU* 1.3 76.1 - - - +
112A ALA* 1.4 57.1 + - - +
114A ARG* 3.3 22.6 + - - +
115A ASN* 2.9 45.0 + - - +
1212A ACT 3.3 17.9 - - - +
105B ALA* 3.9 7.2 - - + -
107B PRO* 3.8 20.7 - - + +
108B ALA* 3.8 24.3 + - + +
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Residues in contact with ALA 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A LEU* 3.7 22.7 - - + -
108A ALA 3.0 14.2 + - - +
109A PHE 3.3 8.0 + - - +
111A THR* 1.4 73.5 - - - +
113A LYS* 1.3 51.7 - - - +
115A ASN 3.4 0.7 + - - -
116A LYS* 2.9 13.9 + - - -
117A ASN 2.8 43.7 + - - +
123A TRP* 3.9 6.8 - - + -
1212A ACT 3.6 20.7 + - - +
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Residues in contact with LYS 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A PHE* 2.9 27.7 + - + +
110A LEU* 3.5 10.8 - - + +
112A ALA* 1.3 73.2 - - - +
114A ARG* 1.3 61.5 + - - +
116A LYS* 2.9 27.4 + - - +
123A TRP* 2.9 52.8 + - + +
124A SER 4.4 0.4 + - - -
125A ASP* 2.7 36.1 + - - +
145A LYS* 3.7 42.6 + - + +
149A PHE* 6.3 0.6 - - - +
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Residues in contact with ARG 114 (chain A).
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 5.0 0.8 + - - -
110A LEU* 2.9 43.8 + - - +
111A THR* 3.5 34.9 + - - +
113A LYS* 1.3 75.4 - - - +
115A ASN* 1.3 62.9 + - - +
116A LYS* 3.6 5.4 + - - +
107B PRO* 5.2 6.9 - - - +
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Residues in contact with ASN 115 (chain A).
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* 2.9 38.4 + - - +
112A ALA 4.0 0.2 - - - +
114A ARG* 1.3 82.4 - - - +
116A LYS* 1.3 70.3 + - - +
117A ASN* 4.1 3.0 - - + +
1212A ACT 3.3 33.7 + - + -
105B ALA* 3.6 12.5 - - - +
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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