Contacts of the helix formed by residues 105 - 119 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77B ALA* 5.2 1.7 - - + +
103B ASN 5.2 2.5 - - - +
104B SER* 1.3 73.5 - - - +
106B TYR* 1.3 68.4 + - + +
107B ARG* 4.5 14.7 + - + +
108B ASP* 2.9 38.2 + - - +
109B THR* 3.1 9.9 + - - -
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Residues in contact with TYR 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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104B SER 3.4 3.0 + - - -
105B GLU* 1.3 74.1 - - + +
107B ARG* 1.3 102.9 + - + +
109B THR* 3.2 8.3 + - - -
110B THR* 2.9 34.3 + - - -
177B GLU 4.5 0.5 - - - +
178B GLY 3.8 9.0 - - - +
181B HIS* 4.1 6.0 - - + +
182B PHE* 3.6 58.2 - + + +
185B MET* 4.4 10.3 - - + -
270B SER* 4.1 12.0 + - - -
274B TYR* 3.0 32.6 + - - -
349B PHE* 4.0 12.1 - + - -
351B TRP* 4.4 12.8 - + - -
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Residues in contact with ARG 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B GLU* 3.2 13.9 + - + +
106B TYR* 1.3 118.2 + - + +
108B ASP* 1.3 65.4 + - - +
110B THR* 3.6 6.0 + - - -
111B ARG* 3.2 21.8 + - - +
270B SER* 5.1 1.2 + - - -
273B GLU* 2.6 36.4 + - - -
274B TYR* 4.6 6.1 + - - -
349B PHE* 5.5 5.3 - - + -
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Residues in contact with ASP 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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78B GLY* 5.4 5.5 - - - -
105B GLU* 2.9 33.1 + - + +
107B ARG* 1.3 78.5 - - - +
109B THR* 1.3 59.0 + - - +
111B ARG* 3.1 26.6 + - - +
112B ARG* 2.8 61.4 + - - +
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Residues in contact with THR 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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104B SER* 3.9 6.2 - - - -
105B GLU 3.1 11.2 + - - -
106B TYR* 3.2 8.0 + - - -
108B ASP* 1.3 76.0 - - - +
110B THR* 1.3 57.3 + - - +
112B ARG* 3.5 7.4 + - - +
113B CYS* 2.9 28.3 + - + +
123B PHE* 3.5 24.0 - - + -
125B GLY* 3.6 10.5 - - - +
177B GLU 4.6 0.2 - - - -
178B GLY* 3.5 23.6 - - - +
181B HIS* 2.6 37.0 + - + +
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Residues in contact with THR 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 TYR* 2.9 17.3 + - - -
107B ARG* 3.8 7.7 - - - -
109B THR* 1.3 77.3 - - - +
111B ARG* 1.3 61.8 + - - +
113B CYS* 3.2 2.3 + - - +
114B ARG* 3.1 60.1 + - - +
177B GLU* 2.6 40.9 + - + +
349B PHE* 5.5 5.4 - - + -
351B TRP* 3.6 13.3 - - + -
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Residues in contact with ARG 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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82B ASP* 3.2 36.8 + - - -
107B ARG 3.2 10.3 + - - +
108B ASP* 3.1 30.3 + - - +
110B THR* 1.3 81.1 - - - +
112B ARG* 1.3 77.2 + - - +
114B ARG* 3.5 7.6 + - - +
115B ASP* 3.0 51.3 + - - +
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Residues in contact with ARG 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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78B GLY 3.5 27.3 + - - +
81B VAL* 3.7 13.9 - - - +
82B ASP* 2.8 32.4 + - - +
85B ILE* 3.6 25.6 - - + -
100B ASP* 3.7 19.2 + - - -
104B SER* 3.9 10.9 + - - -
108B ASP* 2.8 53.9 + - - +
109B THR* 3.9 9.7 + - - +
111B ARG* 1.3 81.1 - - - +
113B CYS* 1.3 61.9 + - - +
115B ASP* 4.1 5.6 - - - +
116B LEU* 3.0 32.1 + - + +
123B PHE* 3.9 21.5 - - + -
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Residues in contact with CYS 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 THR 2.9 19.2 + - - +
110B THR 3.2 5.6 + - - +
112B ARG* 1.3 77.4 - - - +
114B ARG* 1.3 58.0 + - - +
116B LEU* 4.0 0.7 - - - +
117B LYS* 3.0 33.8 + - - +
121B ILE 5.2 0.2 - - - +
123B PHE* 3.8 22.5 + - + +
145B GLY* 3.7 33.2 - - - -
146B ASN* 4.2 10.5 + - - -
177B GLU* 3.9 24.0 - - + -
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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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110B THR* 3.1 36.5 + - - +
111B ARG* 4.1 7.1 - - - +
113B CYS* 1.3 74.0 - - - +
115B ASP* 1.3 70.9 + - - +
117B LYS* 3.3 19.1 + - - +
118B ALA* 3.2 22.9 + - - +
177B GLU* 2.7 40.7 + - + +
349B PHE* 4.9 14.3 + - - -
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Residues in contact with ASP 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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111B ARG* 3.0 42.9 + - - +
112B ARG* 4.1 4.7 - - - +
114B ARG* 1.3 83.2 - - - +
116B LEU* 1.3 63.8 + - + +
118B ALA* 3.7 5.9 + - - +
119B LYS* 3.5 30.3 + - - +
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Residues in contact with LEU 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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85B ILE* 3.8 26.2 - - + -
86B GLU* 6.0 0.4 - - - +
89B VAL* 3.6 30.1 - - + -
98B ILE* 4.3 11.7 - - + -
112B ARG* 3.0 19.0 + - - +
115B ASP* 1.3 79.1 - - + +
117B LYS* 1.3 64.0 + - - +
118B ALA 3.2 0.7 - - - -
119B LYS* 3.2 15.6 + - + +
121B ILE* 2.8 48.5 + - + +
123B PHE* 3.5 39.0 - - + -
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Residues in contact with LYS 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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113B CYS* 3.0 21.2 + - - +
114B ARG* 3.3 18.5 + - - +
116B LEU* 1.3 77.9 - - - +
118B ALA* 1.3 59.8 + - - +
120B GLY* 3.3 12.2 + - - -
121B ILE 3.6 8.6 + - - -
146B ASN* 3.9 24.5 - - - +
177B GLU* 5.0 10.7 + - - +
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Residues in contact with ALA 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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114B ARG 3.2 15.2 + - - +
115B ASP* 3.9 7.2 - - - +
116B LEU 3.2 0.6 - - - -
117B LYS* 1.3 77.1 - - - +
119B LYS* 1.3 60.8 + - + +
120B GLY 3.3 1.6 + - - -
462D GLY* 3.8 11.8 - - - +
464D PHE* 5.4 3.8 - - - -
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Residues in contact with LYS 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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86B GLU* 4.4 16.8 + - - -
89B VAL* 4.1 27.3 - - + +
94B THR* 4.5 1.9 + - - -
115B ASP* 3.5 19.5 + - - +
116B LEU* 3.2 17.2 + - + +
118B ALA* 1.3 78.7 - - + +
120B GLY* 1.3 60.3 + - - +
121B ILE* 3.3 14.3 + - + +
461D PRO 3.6 7.6 - - - +
462D GLY* 3.4 28.0 - - - +
463D GLN* 4.3 9.9 + - - +
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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