Contacts of the helix formed by residues 112 - 124 (chain A) in PDB entry 2AYO
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 112 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107A THR 4.8 0.3 + - - -
108A ASN* 4.1 1.2 + - - -
109A LEU* 3.0 34.5 + - - +
110A GLY 3.4 11.7 - - - +
111A ASN* 1.3 83.8 - - - +
113A CYS* 1.3 62.5 + - - +
114A TYR* 2.9 15.3 - - + +
115A MET* 3.0 13.9 + - + +
116A ASN* 2.5 40.3 + - - -
175A LEU* 3.7 29.1 - - + +
179A HIS* 5.7 2.2 - - + -
194A TYR* 5.9 2.2 - - + -
195A LEU 5.7 0.2 - - - +
76B GLZ 2.9 1.6 + - - -
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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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112A THR* 1.3 69.6 - - - +
114A TYR* 1.3 53.2 + - - +
116A ASN* 3.2 11.7 - - - +
117A ALA* 2.3 40.4 + - - +
434A HIS* 3.8 5.8 - - - +
435A TYR* 3.0 44.8 - - - +
451A ASP* 2.9 21.1 - - - +
76B GLZ 2.3 64.7 + - - +
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Residues in contact with TYR 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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111A ASN 3.7 16.6 + - - -
112A THR* 2.9 6.2 - - + +
113A CYS* 1.3 82.3 - - - +
115A MET* 1.3 111.8 + - + +
117A ALA* 3.5 0.5 - - - +
118A THR* 2.8 30.5 + - - -
178A LEU* 5.7 0.2 - - - +
179A HIS* 4.5 8.0 - - - -
185A PHE* 3.7 31.1 - + - +
195A LEU 5.1 2.3 + - - -
196A GLN* 4.2 0.9 - - - -
197A GLN* 2.8 50.1 - - + +
198A ASP 4.8 0.7 - - - -
199A ALA* 3.9 3.5 - - - +
202A CYS* 4.5 17.5 - - + -
435A TYR* 3.1 38.8 - - + -
75B GLY 3.3 13.2 - - - +
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Residues in contact with MET 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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112A THR* 3.0 14.3 + - + +
114A TYR* 1.3 110.7 - - + +
116A ASN* 1.3 58.2 + - - +
118A THR* 3.7 0.5 - - - -
119A VAL* 2.7 51.3 + - + +
171A PRO* 5.2 2.9 - - - -
174A LEU* 2.9 43.5 - - + -
175A LEU* 4.1 26.7 - - + -
178A LEU* 3.2 34.3 - - + -
179A HIS* 6.5 0.2 - - + -
202A CYS* 4.3 7.2 - - - -
206A MET* 4.6 5.4 - - + -
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Residues in contact with ASN 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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106A LEU* 3.3 42.3 + - + +
107A THR 4.3 1.2 - - - +
108A ASN* 4.3 11.1 - - - +
112A THR* 2.5 43.5 + - - -
113A CYS* 3.2 11.0 - - - +
115A MET* 1.3 79.5 - - - +
117A ALA* 1.3 67.3 + - - +
119A VAL* 3.3 0.7 + - - +
120A GLN* 3.0 32.4 + - - +
171A PRO* 3.7 15.2 - - - +
451A ASP* 3.6 15.4 + - - +
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Residues in contact with ALA 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 2.3 30.7 + - - +
114A TYR* 3.5 3.8 - - - +
116A ASN* 1.3 65.5 - - - +
118A THR* 1.3 56.4 + - - +
120A GLN* 2.5 30.3 + - - +
121A CYS* 3.2 8.0 + - - -
423A LEU* 3.9 19.3 - - + -
435A TYR* 3.8 23.6 - - + +
436A VAL 4.4 0.4 - - - -
437A SER* 3.6 27.4 + - - +
449A PHE 5.8 0.4 - - - -
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Residues in contact with THR 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 TYR 2.8 16.2 + - - -
115A MET 3.8 0.2 - - - -
117A ALA* 1.3 73.2 - - - +
119A VAL* 1.3 61.9 + - - +
120A GLN 3.1 0.7 + - - -
121A CYS* 3.3 1.9 + - - +
122A ILE* 3.2 29.7 + - + +
199A ALA* 3.0 35.3 + - - +
202A CYS* 3.2 26.5 - - - -
203A TRP* 3.5 32.7 - - + +
206A MET* 3.3 12.8 - - + -
423A LEU* 4.0 8.4 - - - +
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Residues in contact with VAL 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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106A LEU* 4.3 15.5 - - + -
115A MET* 2.7 46.9 + - + +
116A ASN* 3.7 5.8 - - - +
117A ALA 2.8 2.2 + - - -
118A THR* 1.3 71.8 - - - +
120A GLN* 1.3 57.4 + - + +
122A ILE* 4.2 4.9 - - - +
123A ARG* 3.4 20.1 + - + +
155A LEU* 4.7 9.2 - - + -
158A LEU* 4.8 11.4 - - + -
159A PHE* 4.0 22.7 - - + -
162A MET* 5.4 2.2 - - - -
171A PRO* 6.1 0.7 - - + -
174A LEU* 4.6 10.3 - - + -
206A MET* 3.6 23.1 - - + -
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Residues in contact with GLN 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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104A CYS 3.7 5.7 + - - -
105A GLY* 3.9 5.9 - - - -
106A LEU* 3.7 19.9 + - + +
116A ASN* 3.0 25.5 - - - +
117A ALA 2.5 12.8 + - - +
119A VAL* 1.3 75.7 - - + +
121A CYS* 1.3 60.8 + - - +
123A ARG* 2.9 23.0 - - - +
124A SER 3.3 3.6 + - - -
162A MET* 3.6 25.0 - - + +
437A SER* 3.8 11.4 - - - +
439A VAL* 3.5 11.8 - - - +
449A PHE* 2.8 63.6 - - + +
451A ASP 5.1 3.5 + - - +
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Residues in contact with CYS 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 ALA 3.2 5.6 + - - -
118A THR 3.3 3.8 + - - +
120A GLN* 1.3 71.4 - - - +
122A ILE* 1.3 67.4 + - - +
123A ARG 2.9 1.4 + - - -
124A SER* 2.2 33.2 + - - -
125A VAL* 4.1 1.9 + - - +
203A TRP* 3.2 29.4 - - + -
421A ALA* 4.1 15.0 - - + -
422A VAL 3.1 30.1 - - - -
423A LEU* 3.2 25.6 - - - -
437A SER* 3.5 8.1 - - - -
439A VAL* 4.6 0.7 - - - -
478A LEU* 4.5 1.3 - - - +
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Residues in contact with ILE 122 (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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118A THR* 3.2 19.1 - - + +
119A VAL* 4.2 5.8 - - - +
121A CYS* 1.3 80.0 - - - +
123A ARG* 1.3 63.5 + - - +
125A VAL* 3.2 22.8 + - - +
128A LEU* 3.1 34.0 - - + +
129A LYS* 5.6 0.2 - - - +
132A LEU* 5.9 0.9 - - + -
155A LEU* 5.0 8.1 - - + -
159A PHE* 4.6 11.4 - - + -
203A TRP* 4.3 24.4 - - + +
206A MET* 3.8 41.7 - - + -
207A MET* 4.7 6.3 - - + -
210A LEU* 4.3 15.3 - - + -
246A PHE* 6.2 0.7 - - - -
478A LEU* 6.3 0.2 - - - -
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Residues in contact with ARG 123 (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 CYS* 4.9 4.2 + - - +
119A VAL 3.4 12.1 + - - +
120A GLN* 2.9 19.0 + - - +
122A ILE* 1.3 79.9 - - - +
124A SER* 1.3 54.1 + - - +
125A VAL 2.9 7.4 + - - -
129A LYS* 3.0 56.2 - - - +
159A PHE* 3.5 27.9 + - + -
162A MET* 2.9 60.6 + - - +
163A ASP* 3.3 23.0 + - - +
441A ARG* 3.8 23.9 - - - +
449A PHE* 4.1 18.2 - - - -
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Residues in contact with SER 124 (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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120A GLN 3.3 0.4 + - - -
121A CYS 2.2 27.4 + - - -
123A ARG* 1.3 75.5 - - - +
125A VAL* 1.3 49.2 + - - +
126A PRO* 2.7 24.5 - - - +
129A LYS* 5.2 1.1 - - - +
420A GLN* 4.2 17.2 + - - +
421A ALA* 3.8 4.0 - - - +
439A VAL* 3.6 37.2 - - - -
441A ARG* 5.0 6.5 - - - +
478A LEU* 3.7 16.3 - - - +
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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