Contacts of the helix formed by residues 101 - 113 (chain A) in PDB entry 2AJQ
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 ASN 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A HIS* 3.0 2.3 - - - +
100A SER* 1.3 84.6 - - - +
102A LEU* 1.3 63.2 + - - +
103A LYS* 3.0 9.0 + - - +
104A ASP* 3.1 42.0 + - - +
105A THR* 3.4 15.3 + - - +
426A VAL* 4.3 6.8 - - - +
591A ARG* 5.7 0.2 - - - +
602A HIS* 3.3 46.9 + - + +
604A ARG* 5.5 1.6 + - - -
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Residues in contact with LEU 102 (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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99A HIS* 3.6 26.9 + - + +
100A SER 3.7 0.8 - - - -
101A ASN* 1.3 76.5 - - - +
103A LYS* 1.3 63.3 + - + +
105A THR* 4.0 11.0 - - + -
106A ASP* 2.8 49.7 + - - +
109A LEU* 5.8 0.2 - - + -
121A GLY* 4.2 10.8 - - - +
122A SER 3.9 4.5 - - - +
123A HIS* 3.3 43.7 - - + +
128A TRP* 4.2 13.5 - - + -
131A ARG* 3.7 32.3 - - - +
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Residues in contact with LYS 103 (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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101A ASN* 3.0 5.8 + - - +
102A LEU* 1.3 78.8 - - + +
104A ASP* 1.3 66.7 + - - +
106A ASP* 4.7 0.2 - - - -
107A MET* 3.7 5.5 + - - +
120A PHE* 3.1 63.3 + - + -
121A GLY* 4.5 16.3 + - - -
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Residues in contact with ASP 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ASN* 3.1 34.8 + - - +
103A LYS* 1.3 79.4 - - - +
105A THR* 1.3 59.8 + - - +
106A ASP 2.8 10.9 + - - -
107A MET* 2.9 29.1 + - - +
108A GLY 4.2 1.2 + - - -
591A ARG* 5.2 7.9 + - - +
602A HIS* 4.5 5.4 + - - -
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Residues in contact with THR 105 (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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99A HIS* 5.9 4.7 + - - +
101A ASN* 3.4 17.0 + - - +
102A LEU* 4.1 14.3 - - + -
104A ASP* 1.3 76.6 - - - +
106A ASP* 1.3 63.3 + - - +
108A GLY* 4.1 5.3 + - - -
109A LEU* 3.6 17.4 + - + +
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Residues in contact with ASP 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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102A LEU* 2.8 32.6 + - - +
103A LYS 3.8 0.2 - - - +
104A ASP 2.8 1.8 + - - -
105A THR* 1.3 79.0 - - - +
107A MET* 1.3 56.2 + - - +
108A GLY 3.0 3.4 - - - -
109A LEU* 2.6 35.2 + - + +
110A LEU* 2.7 12.8 + - - +
115A LEU* 5.4 3.2 - - + +
119A ARG 4.3 1.7 - - - +
120A PHE* 3.6 22.4 - - + -
121A GLY 3.0 22.1 + - - +
131A ARG* 2.5 37.4 + - - -
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Residues in contact with MET 107 (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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103A LYS 3.7 7.3 + - - +
104A ASP* 2.9 24.3 + - - +
106A ASP* 1.3 75.6 - - - +
108A GLY* 1.3 63.5 + - - +
110A LEU* 3.2 10.8 + - + +
111A ARG* 3.1 38.6 + - + +
120A PHE* 3.6 26.7 - - - -
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Residues in contact with GLY 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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104A ASP 4.2 1.4 + - - -
105A THR 4.1 6.5 + - - -
106A ASP 3.0 1.0 - - - -
107A MET* 1.3 78.8 - - - +
109A LEU* 1.3 58.4 + - - +
111A ARG* 4.0 4.8 - - - +
112A SER* 2.9 34.3 + - - -
240F GLU* 4.8 12.0 - - - +
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Residues in contact with LEU 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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102A LEU* 5.8 0.2 - - + -
105A THR* 3.6 16.6 - - + +
106A ASP* 2.6 43.0 + - + +
108A GLY* 1.3 71.4 - - - +
110A LEU* 1.3 60.8 + - - -
112A SER* 4.1 0.7 - - - -
113A GLY* 3.2 16.5 + - - -
114A LYS* 3.3 43.7 + - + +
115A LEU* 3.4 24.0 + - + -
131A ARG* 3.3 29.4 - - + +
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Residues in contact with LEU 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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106A ASP 2.7 9.5 + - - +
107A MET* 3.5 16.8 - - + +
109A LEU* 1.3 76.2 - - - +
111A ARG* 1.3 83.7 + - + +
113A GLY* 3.5 11.3 + - - -
115A LEU* 4.0 12.6 - - + +
116A PRO 4.5 1.1 - - - +
117A GLY* 3.8 29.4 - - - +
120A PHE* 4.2 24.5 - - + -
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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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107A MET* 3.1 28.6 + - + +
108A GLY* 4.0 6.1 - - - +
110A LEU* 1.3 99.4 - - - +
112A SER* 1.3 62.0 + - - +
113A GLY 3.5 0.3 + - - -
244F VAL* 3.8 40.8 - - + +
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Residues in contact with SER 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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108A GLY 2.9 19.0 + - - -
109A LEU* 4.3 4.0 - - - -
111A ARG* 1.3 78.0 - - - +
113A GLY* 1.3 60.9 + - - +
114A LYS* 3.5 12.6 - - - -
240F GLU* 4.4 17.3 + - - +
243F TYR* 4.9 26.5 + - - -
244F VAL* 4.6 8.5 - - - +
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Residues in contact with GLY 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 LEU 3.2 7.0 + - - -
110A LEU 3.5 7.4 + - - -
111A ARG 3.3 3.0 - - - -
112A SER* 1.3 80.9 - - - +
114A LYS* 1.3 63.7 + - - +
115A LEU 3.2 6.9 + - - -
116A PRO* 5.6 0.7 - - - +
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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