Contacts of the helix formed by residues 105 - 118 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103C ASN 5.1 3.1 - - - +
104C SER* 1.3 73.7 - - - +
106C TYR* 1.3 69.3 + - + +
107C ARG* 4.5 13.1 + - + +
108C ASP* 2.9 36.6 + - - +
109C THR* 3.2 9.2 + - - -
266C TRP* 4.8 24.3 + - + -
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Residues in contact with TYR 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C SER 3.6 2.2 + - - -
105C GLU* 1.3 73.9 - - + +
107C ARG* 1.3 109.2 + - + +
109C THR* 3.2 4.3 + - - -
110C THR* 2.8 34.1 + - - -
177C GLU 4.5 0.5 - - - +
178C GLY 4.0 6.1 - - - +
181C HIS* 4.1 10.6 + - - +
182C PHE* 3.5 57.4 - + + +
185C MET* 4.1 21.8 - - + -
270C SER* 4.0 11.2 + - - -
274C TYR* 3.5 11.3 + - - -
349C PHE* 3.7 25.8 - + - -
351C TRP* 4.3 11.7 - + + -
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Residues in contact with ARG 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C GLU* 3.1 12.4 + - + +
106C TYR* 1.3 121.4 + - + +
108C ASP* 1.3 64.3 + - - +
110C THR* 3.5 6.7 + - - -
111C ARG* 3.1 23.9 + - - +
266C TRP* 6.1 4.0 - - - -
270C SER* 5.9 0.2 - - - -
273C GLU* 2.8 37.9 + - - -
274C TYR* 5.0 1.8 + - - -
349C PHE* 5.4 6.3 - - + -
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Residues in contact with ASP 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C GLY* 5.2 6.2 - - - +
82C ASP* 4.7 1.4 - - - +
105C GLU* 2.9 35.8 + - - +
107C ARG* 1.3 79.8 - - - +
109C THR* 1.3 57.6 + - - +
111C ARG* 3.2 31.6 + - - +
112C ARG* 3.0 58.9 + - - +
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Residues in contact with THR 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C SER* 3.8 6.2 - - - -
105C GLU 3.2 10.3 + - - -
106C TYR* 3.2 8.0 + - - -
108C ASP* 1.3 75.0 - - - +
110C THR* 1.3 60.6 + - - +
112C ARG* 3.3 7.3 + - - +
113C CYS* 2.8 29.4 + - + +
123C PHE* 3.5 25.1 - - + -
125C GLY* 3.6 8.3 - - - +
145C GLY* 5.7 0.2 - - - -
177C GLU 4.5 0.4 - - - -
178C GLY* 3.5 26.0 - - - -
181C HIS* 2.7 34.1 + - + +
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Residues in contact with THR 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C TYR* 2.8 19.6 + - - -
107C ARG* 3.8 7.9 - - - -
109C THR* 1.3 75.7 - - - +
111C ARG* 1.3 62.3 + - - +
113C CYS* 3.5 1.8 + - - +
114C ARG* 3.2 45.6 + - - +
177C GLU* 2.8 49.4 + - + +
349C PHE* 5.5 7.8 - - + -
351C TRP* 3.9 12.8 - - + -
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Residues in contact with ARG 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C ASP* 3.1 38.0 + - - -
107C ARG 3.1 12.4 + - - +
108C ASP* 3.3 44.4 + - - +
109C THR 3.2 0.2 - - - -
110C THR* 1.3 74.0 - - - +
112C ARG* 1.3 78.5 + - - +
113C CYS 3.2 0.2 + - - -
114C ARG* 3.3 6.6 + - - +
115C ASP* 2.7 45.9 + - - +
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Residues in contact with ARG 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C GLY* 3.7 24.0 + - - +
81C VAL* 3.5 17.8 - - - +
82C ASP* 3.1 23.5 + - - +
85C ILE* 3.6 25.1 - - + -
100C ASP* 3.5 19.6 + - - -
104C SER* 3.7 17.4 + - - -
108C ASP* 3.0 52.8 + - - +
109C THR* 3.8 5.1 + - - +
111C ARG* 1.3 82.5 - - - +
113C CYS* 1.3 62.7 + - - +
115C ASP* 4.9 2.7 - - - -
116C LEU* 3.0 34.9 + - + +
123C PHE* 3.7 25.7 - - + -
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Residues in contact with CYS 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C THR 2.8 17.9 + - - +
110C THR 3.8 4.0 - - - +
111C ARG 3.2 0.2 - - - -
112C ARG* 1.3 77.4 - - - +
114C ARG* 1.3 57.6 + - - +
116C LEU* 4.3 0.7 - - - +
117C LYS* 3.0 36.0 + - - +
123C PHE* 3.9 21.0 + - + +
145C GLY* 3.5 38.1 - - - -
146C ASN* 4.0 10.0 + - - -
176C ASP* 4.5 0.9 - - - -
177C GLU* 3.9 22.4 - - + -
178C GLY 4.8 0.2 - - - +
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Residues in contact with ARG 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C THR* 3.2 36.1 + - - +
111C ARG* 4.0 4.6 - - - +
113C CYS* 1.3 75.4 - - - +
115C ASP* 1.3 67.9 + - - +
117C LYS* 3.3 8.6 + - - +
118C ALA* 3.2 23.2 + - - +
177C GLU* 2.6 44.8 + - + +
349C PHE* 5.3 9.7 + - - -
325E LYS* 4.4 15.3 - - - +
401E ASN* 3.4 35.4 + - - +
404E ASP* 5.6 0.7 - - - +
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Residues in contact with ASP 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C ARG* 2.7 44.8 + - + +
112C ARG* 4.5 2.9 - - - +
114C ARG* 1.3 80.1 - - - +
116C LEU* 1.3 61.1 + - + +
118C ALA* 4.0 6.3 + - - +
119C LYS* 3.2 29.6 + - + +
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Residues in contact with LEU 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C ILE* 3.8 25.6 - - + -
89C VAL* 3.6 28.0 - - + -
98C ILE* 4.6 3.1 - - + -
112C ARG* 3.0 21.2 + - + +
113C CYS 4.3 1.1 - - - +
115C ASP* 1.3 78.6 - - + +
117C LYS* 1.3 61.0 + - - +
118C ALA 3.2 1.8 - - - -
119C LYS* 3.1 25.0 + - - +
120C GLY 3.2 0.2 + - - -
121C ILE* 2.9 49.9 + - + +
123C PHE* 3.6 36.6 - - + -
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Residues in contact with LYS 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C CYS* 3.0 23.3 + - - +
114C ARG* 3.7 7.9 - - - +
116C LEU* 1.3 77.1 - - - +
118C ALA* 1.3 61.8 + - - +
120C GLY* 3.4 11.7 + - - -
121C ILE 3.5 9.3 + - - -
122C LEU* 6.1 0.4 - - + -
146C ASN* 4.1 25.7 + - - +
148C GLU* 6.0 2.0 - - - -
176C ASP* 5.9 1.2 + - - -
318E SER* 5.6 7.9 - - - -
404E ASP* 5.5 1.1 - - - +
408E ARG* 3.0 48.6 - - - +
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Residues in contact with ALA 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C ARG 3.2 14.4 + - - +
115C ASP* 4.2 7.9 - - - +
116C LEU 3.2 0.8 - - - -
117C LYS* 1.3 77.2 - - - +
119C LYS* 1.3 60.6 + - + +
120C GLY 3.3 1.3 + - - -
404E ASP* 4.5 9.3 + - + +
309F LYS* 3.3 54.7 - - + +
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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