Contacts of the helix formed by residues 105 - 119 (chain A) in PDB entry 5UQ9
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 GLU 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 SER* 1.3 74.3 - - - +
106A TYR* 1.3 68.9 + - + +
107A ARG* 3.2 12.8 + - + +
108A ASP* 3.1 33.8 + - - +
109A THR* 3.1 11.1 + - - -
266A TRP* 3.4 52.8 + - + -
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Residues in contact with TYR 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 SER 3.6 2.2 + - - -
105A GLU* 1.3 74.9 - - + +
107A ARG* 1.3 105.5 + - + +
109A THR* 3.3 3.2 + - - -
110A THR* 2.8 35.2 + - - -
177A GLU 4.4 0.7 - - - +
178A GLY 3.7 19.1 - - - +
181A HIS* 4.2 10.0 - - - +
182A PHE* 3.5 44.9 - + + +
185A MET* 4.3 20.9 - - + -
270A SER* 4.1 9.0 + - - -
273A GLU* 4.4 0.3 + - - -
274A TYR* 3.5 16.5 + - - -
349A PHE* 3.3 28.3 - + - -
351A TRP* 4.3 9.2 - + + -
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Residues in contact with ARG 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A GLU* 3.2 11.7 + - + +
106A TYR* 1.3 116.5 + - + +
108A ASP* 1.3 65.5 + - - +
110A THR* 3.5 7.7 + - - +
111A ARG* 3.1 20.8 + - - +
269A ILE* 6.2 0.6 - - - +
273A GLU* 2.4 40.3 + - - -
274A TYR* 4.0 9.9 + - - -
349A PHE* 5.6 3.9 - - + -
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Residues in contact with ASP 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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78A GLY* 5.4 6.9 - - - -
82A ASP* 5.4 0.5 - - - +
104A SER* 5.2 1.7 - - - -
105A GLU* 3.1 29.5 + - + +
107A ARG* 1.3 77.5 - - - +
109A THR* 1.3 58.1 + - - +
111A ARG* 2.7 43.0 + - - +
112A ARG* 2.8 38.7 + - - +
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Residues in contact with THR 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 ASP* 4.5 1.6 + - - -
104A SER* 3.8 6.6 - - - -
105A GLU 3.1 9.5 + - - -
106A TYR* 3.7 7.6 - - - -
108A ASP* 1.3 77.4 - - - +
110A THR* 1.3 57.6 + - - +
112A ARG* 3.4 10.2 + - - +
113A CYS* 2.9 28.1 + - - +
123A PHE* 3.4 23.3 - - + -
125A GLY* 3.7 10.1 - - - +
145A GLY* 5.9 0.2 - - - -
178A GLY* 3.5 22.4 - - - +
181A HIS* 2.5 38.1 + - + +
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Residues in contact with THR 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A TYR* 2.8 20.6 + - - -
107A ARG* 3.5 9.9 - - - +
109A THR* 1.3 76.8 - - - +
111A ARG* 1.3 62.1 + - - +
113A CYS* 3.3 1.7 + - - +
114A ARG* 3.1 60.1 + - - +
177A GLU* 2.7 39.3 + - - +
349A PHE* 6.0 3.0 - - + -
351A TRP* 4.5 6.2 - - - -
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Residues in contact with ARG 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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82A ASP* 2.9 43.0 + - - -
107A ARG 3.1 12.4 + - - +
108A ASP* 2.7 30.2 + - - +
110A THR* 1.3 73.5 - - - +
112A ARG* 1.3 83.0 + - - +
114A ARG* 4.0 4.4 - - - +
115A ASP* 3.0 51.9 + - - +
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Residues in contact with ARG 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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78A GLY 3.2 27.9 + - - +
81A VAL* 3.4 25.0 - - - +
82A ASP* 3.0 31.1 + - - +
85A ILE* 3.7 15.7 - - + +
100A ASP* 3.1 27.3 + - - -
104A SER* 4.0 8.4 + - - -
108A ASP* 2.8 44.4 + - - +
109A THR* 3.8 5.1 + - - +
111A ARG* 1.3 90.1 - - - +
113A CYS* 1.3 63.0 + - - +
115A ASP* 4.7 3.4 - - - -
116A LEU* 3.0 31.9 + - + +
123A PHE* 3.5 27.9 - - + -
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Residues in contact with CYS 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 THR 2.9 18.9 + - - +
110A THR 3.7 4.9 - - - +
111A ARG 3.3 0.2 - - - -
112A ARG* 1.3 77.6 - - - +
114A ARG* 1.3 57.3 + - - +
116A LEU* 3.8 0.9 - - - +
117A LYS* 2.9 31.1 + - - +
121A ILE 5.0 0.5 - - - +
123A PHE* 3.7 21.6 + - + +
145A GLY* 3.7 35.0 - - - -
146A ASN* 4.0 12.0 + - - -
176A ASP* 4.3 0.7 - - - -
177A GLU* 4.2 22.2 - - + -
178A GLY 5.0 0.2 - - - +
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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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110A THR* 3.1 32.2 + - - +
111A ARG* 4.1 4.3 - - - +
113A CYS* 1.3 75.1 - - - +
115A ASP* 1.3 70.6 + - - +
117A LYS* 3.2 16.2 + - - +
118A ALA* 3.3 12.8 + - - +
177A GLU* 2.6 44.6 + - + +
349A PHE* 5.9 4.9 - - - -
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Residues in contact with ASP 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 ARG* 3.0 43.5 + - - +
112A ARG* 4.2 3.8 - - - +
114A ARG* 1.3 79.5 - - - +
116A LEU* 1.3 63.6 + - + +
118A ALA* 3.5 11.9 + - - +
119A LYS* 3.5 28.8 + - - +
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Residues in contact with LEU 116 (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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85A ILE* 4.0 33.2 - - + -
89A VAL* 4.6 8.5 - - + -
98A ILE* 4.4 6.7 - - + -
112A ARG* 3.0 19.7 + - - +
113A CYS 4.3 0.9 - - - +
115A ASP* 1.3 75.1 - - + +
117A LYS* 1.3 63.9 + - - +
118A ALA 3.2 0.7 - - - -
119A LYS* 3.2 23.4 + - + +
121A ILE* 2.8 68.9 + - + +
123A PHE* 3.8 34.3 - - + -
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Residues in contact with LYS 117 (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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113A CYS* 2.9 22.2 + - - +
114A ARG* 3.4 11.0 - - - +
116A LEU* 1.3 78.4 - - - +
118A ALA* 1.3 60.6 + - - +
120A GLY* 3.4 10.0 + - - -
121A ILE 3.7 6.0 + - - +
122A LEU* 5.6 1.1 - - + -
146A ASN* 3.3 28.5 - - - +
148A GLU* 6.1 1.3 - - - -
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Residues in contact with ALA 118 (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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114A ARG 3.3 7.8 + - - +
115A ASP* 3.8 10.3 - - - +
116A LEU 3.2 0.6 - - - -
117A LYS* 1.3 80.0 - - - +
119A LYS* 1.3 60.8 + - + +
120A GLY 3.3 2.8 + - - -
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Residues in contact with LYS 119 (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 VAL* 3.9 32.8 - - + +
94A THR* 4.3 7.8 - - - +
115A ASP* 3.5 23.5 + - - +
116A LEU* 3.2 16.8 + - + +
118A ALA* 1.3 78.7 - - + +
120A GLY* 1.3 61.5 + - - +
121A ILE* 3.2 12.4 + - + +
36C VAL* 5.7 6.7 - - - +
56C GLN 5.9 0.6 + - - -
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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