Contacts of the helix formed by residues 101 - 113 (chain A) in PDB entry 1UZL
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 THR 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A MET* 1.3 85.8 - - - +
102A GLU* 1.3 59.4 + - - +
103A GLU* 3.5 10.4 + - - +
104A LYS* 3.0 43.1 + - - +
105A PHE* 2.9 30.2 + - - +
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Residues in contact with GLU 102 (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 MET 4.2 0.2 + - - -
101A THR* 1.3 72.3 - - - +
103A GLU* 1.3 57.1 + - - +
105A PHE* 3.3 5.7 + - - +
106A GLU* 2.9 61.1 + - + +
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Residues in contact with GLU 103 (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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101A THR* 3.1 9.9 + - - +
102A GLU* 1.3 80.2 + - - +
104A LYS* 1.3 63.1 + - + +
106A GLU* 4.1 5.0 - - - +
107A LYS* 3.1 33.2 + - + +
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Residues in contact with LYS 104 (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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94A ASP 5.7 3.7 + - - +
100A MET* 3.3 26.0 - - + +
101A THR* 3.0 36.3 + - - +
103A GLU* 1.3 74.9 - - + +
105A PHE* 1.3 66.5 + - - +
107A LYS* 3.6 11.4 - - + +
108A VAL* 3.4 17.5 + - + +
152A ASN* 3.3 13.5 - - - +
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Residues in contact with PHE 105 (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 MET* 3.6 10.9 - - + +
101A THR 2.9 18.1 + - - +
102A GLU* 3.7 7.6 - - - +
104A LYS* 1.3 78.2 - - - +
106A GLU* 1.3 65.5 - - + +
108A VAL* 3.9 2.1 - - - +
109A ILE* 3.0 50.8 + - + +
151A ALA* 3.9 13.5 - - + -
152A ASN* 3.6 35.7 - - + +
155A ALA* 4.0 18.2 - - + -
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Residues in contact with GLU 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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102A GLU* 2.9 45.5 + - + +
103A GLU* 4.1 4.8 - - - +
105A PHE* 1.3 85.1 - - + +
107A LYS* 1.3 57.3 + - - +
109A ILE* 3.7 6.7 - - - +
110A ASN* 2.8 31.4 + - - +
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Residues in contact with LYS 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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91A LEU* 3.3 28.8 - - + +
103A GLU* 3.1 26.7 + - + +
104A LYS* 3.6 15.9 - - + +
106A GLU* 1.3 72.7 - - - +
108A VAL* 1.3 72.6 + - + +
110A ASN* 3.8 5.5 - - - +
111A ALA* 3.1 19.1 + - - +
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Residues in contact with VAL 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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91A LEU* 3.8 14.6 - - + -
104A LYS* 3.4 10.3 + - - +
105A PHE 3.4 3.4 + - - +
106A GLU 3.3 0.2 - - - -
107A LYS* 1.3 78.6 - - + +
109A ILE* 1.3 61.3 + - - +
112A ASN* 2.8 56.6 + - - +
152A ASN* 3.4 38.4 - - + +
153A TYR* 3.7 36.1 - - + +
156A SER* 4.1 2.0 - - - +
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Residues in contact with ILE 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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105A PHE* 3.0 54.6 + - + +
106A GLU* 3.7 7.0 - - - +
108A VAL* 1.3 78.3 - - - +
110A ASN* 1.3 58.8 + - - +
113A LEU* 2.9 41.2 + - + -
114A THR* 3.0 18.8 + - - +
152A ASN 4.2 5.2 - - - +
155A ALA* 4.2 3.8 - - + -
156A SER* 3.8 32.8 - - - +
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Residues in contact with ASN 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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63A THR* 3.6 28.5 + - + +
106A GLU 2.8 19.4 + - - +
107A LYS* 3.8 6.7 - - - +
108A VAL 3.2 0.2 - - - -
109A ILE* 1.3 79.0 - - - +
111A ALA* 1.3 56.6 + - - +
114A THR* 3.5 9.6 - - - +
115A GLY 2.8 24.4 + - - -
118A ARG* 3.1 32.1 + - - +
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Residues in contact with ALA 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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62A VAL* 3.5 26.6 - - + +
63A THR* 4.1 16.4 - - + +
89A ALA 3.9 6.8 - - - +
90A GLY* 4.9 5.2 - - - -
91A LEU* 3.6 25.6 - - + -
107A LYS 3.1 16.7 + - - +
110A ASN* 1.3 78.7 - - - +
112A ASN* 1.3 66.0 + - - +
115A GLY* 3.6 6.6 - - - -
116A ALA 4.2 1.2 + - - -
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Residues in contact with ASN 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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89A ALA* 4.3 12.9 - - - +
90A GLY* 2.9 31.1 + - - +
91A LEU* 3.8 1.4 - - - +
108A VAL* 2.8 26.2 + - - +
111A ALA* 1.3 79.5 - - - +
113A LEU* 1.3 58.3 + - - +
116A ALA* 3.5 10.8 - - - +
140A SER* 4.3 1.6 + - - -
153A TYR* 3.6 29.3 - - - -
156A SER* 3.2 24.6 + - - +
157A LYS* 3.9 18.2 + - + +
160A VAL* 3.4 17.7 - - - +
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Residues in contact with LEU 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 ILE* 2.9 29.6 + - + +
112A ASN* 1.3 77.7 - - - +
114A THR* 1.3 61.5 + - - +
115A GLY 3.3 0.7 - - - -
116A ALA* 3.0 6.2 + - - +
117A PHE* 2.9 25.3 + - - +
155A ALA 4.7 1.6 - - - +
156A SER* 4.2 19.3 - - - +
159A GLY* 3.4 21.1 - - - +
160A VAL* 3.4 34.3 - - + +
163A MET* 4.4 11.8 - - + +
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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