Contacts of the helix formed by residues 109 - 121 (chain A) in PDB entry 2R5Y
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 109 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107A SER 4.9 4.0 - - - +
108A TYR* 1.3 74.3 - - - +
110A ARG* 1.3 66.2 + - - +
111A TYR* 3.1 9.1 + - - +
112A GLN* 2.9 41.1 + - - +
113A THR* 2.9 24.7 + - - -
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Residues in contact with ARG 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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108A TYR 4.1 0.2 + - - -
109A THR* 1.3 71.8 - - - +
111A TYR* 1.3 53.6 + - - +
113A THR* 3.9 4.6 - - - -
114A LEU* 2.7 40.0 + - + +
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Residues in contact with TYR 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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109A THR* 3.1 7.7 + - - +
110A ARG* 1.3 77.8 - - - +
112A GLN* 1.3 70.9 + - + +
114A LEU* 3.7 6.5 - - + +
115A GLU* 2.8 61.1 + - + +
137A ALA* 4.4 9.8 + - - +
138A LEU* 3.4 26.7 - - + +
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Residues in contact with GLN 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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107A SER 4.4 1.2 - - - +
108A TYR* 3.3 18.1 - - + +
109A THR* 2.9 45.4 + - - +
111A TYR* 1.3 79.3 - - + +
113A THR* 1.3 65.0 + - - +
115A GLU* 3.3 1.4 + - - +
116A LEU* 2.9 29.2 + - - +
138A LEU* 2.8 45.5 + - + +
139A SER* 4.6 4.9 + - - -
140A LEU* 3.3 33.5 - - + +
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Residues in contact with THR 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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108A TYR* 3.6 20.5 + - - +
109A THR 2.9 21.1 + - - -
110A ARG* 3.9 4.3 - - - -
112A GLN* 1.3 73.9 - - - +
114A LEU* 1.3 63.7 + - - +
116A LEU* 3.2 9.5 + - - +
117A GLU* 2.8 40.6 + - + +
148A TRP* 4.7 7.7 + - + +
12C T 4.5 6.1 + - - +
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Residues in contact with LEU 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 ARG* 2.7 24.4 + - + +
111A TYR* 3.7 7.0 - - + +
113A THR* 1.3 74.2 - - - +
115A GLU* 1.3 69.4 + - - +
117A GLU* 3.3 8.1 + - + +
118A LYS* 2.8 34.7 + - + +
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Residues in contact with GLU 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 TYR* 2.8 69.0 + - + +
112A GLN 3.7 2.7 - - - +
114A LEU* 1.3 81.5 - - - +
116A LEU* 1.3 52.7 + - - +
118A LYS* 2.8 32.7 + - - +
119A GLU* 2.7 36.2 + - - +
134A ILE* 5.5 1.6 - - + -
138A LEU* 3.9 15.5 - - + -
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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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108A TYR* 4.2 15.5 - - + -
112A GLN 2.9 26.8 + - - +
113A THR* 3.6 4.7 - - - +
115A GLU* 1.3 71.5 - - - +
117A GLU* 1.3 64.3 + - - +
119A GLU* 3.1 6.7 + - - +
120A PHE* 2.9 25.1 + - - +
134A ILE* 3.8 17.5 - - + -
138A LEU* 4.0 4.9 - - + -
140A LEU* 4.6 9.0 - - + -
145A ILE* 3.7 24.9 - - + -
148A TRP* 3.5 51.8 - - + +
149A PHE* 3.9 16.9 - - + -
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Residues in contact with GLU 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 THR* 2.8 29.5 + - + +
114A LEU* 3.4 9.2 - - + +
116A LEU* 1.3 73.9 - - - +
118A LYS* 1.3 63.7 + - - +
120A PHE* 3.5 5.9 + - - +
121A HIS* 3.4 20.4 + - - +
148A TRP* 3.7 18.6 - - - -
152A ARG* 2.8 40.5 + - - -
155A LYS* 5.1 6.7 + - - -
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Residues in contact with LYS 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 LEU* 2.8 19.7 + - + +
115A GLU* 3.0 40.2 + - - +
117A GLU* 1.3 74.6 - - - +
119A GLU* 1.3 63.2 + - - +
121A HIS* 3.5 13.6 + - - +
122A PHE* 3.7 8.5 + - - +
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Residues in contact with GLU 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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115A GLU 2.7 13.9 + - - +
116A LEU 3.1 7.4 + - - +
118A LYS* 1.3 70.2 - - - +
120A PHE* 1.3 58.0 + - - +
122A PHE* 2.7 50.1 + - - +
123A ASN* 3.2 17.7 + - - -
126A LEU* 3.3 26.5 - - - +
130A ARG* 2.5 49.6 + - - +
134A ILE* 3.7 23.6 - - + -
149A PHE* 4.0 9.0 - - + -
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Residues in contact with PHE 120 (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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116A LEU 2.9 16.6 + - - +
117A GLU* 3.7 7.4 - - - +
119A GLU* 1.3 76.7 - - - +
121A HIS* 1.3 61.5 + - - +
122A PHE 3.1 1.1 + - - -
123A ASN 3.8 0.9 - - - -
124A ARG* 3.3 72.4 + - + +
148A TRP* 4.1 7.4 - - + -
149A PHE* 3.7 23.5 - + + -
152A ARG* 3.4 58.3 - - + -
153A ARG* 4.1 11.2 - - + -
156A TRP* 3.8 25.4 - + + -
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Residues in contact with HIS 121 (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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117A GLU 3.4 10.0 + - - +
118A LYS* 3.8 10.8 - - - +
119A GLU 3.1 0.8 + - - -
120A PHE* 1.3 79.8 - - + +
122A PHE* 1.3 60.8 + - - +
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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