Contacts of the helix formed by residues 97 - 109 (chain A) in PDB entry 2AA0
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 ASP 97 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A GLY 3.2 4.3 - - - +
96A ASP* 1.3 76.3 - - - +
98A PRO* 1.3 78.9 - - + +
99A ARG* 3.9 12.6 + - - +
100A GLY* 3.0 12.2 + - - -
101A GLN* 3.4 9.0 + - - +
122A GLN 4.8 2.7 - - - +
123A SER* 3.4 13.2 - - - -
124A THR* 2.7 47.3 + - - -
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Residues in contact with PRO 98 (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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97A ASP* 1.3 89.6 - - + +
99A ARG* 1.3 62.8 + - - +
101A GLN* 3.0 11.2 + - + +
102A VAL* 3.0 28.9 + - + +
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Residues in contact with ARG 99 (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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23A LEU* 3.3 35.7 - - + +
25A LEU* 5.1 5.9 - - - +
55A TYR* 4.6 13.1 - - - +
97A ASP* 3.2 13.2 + - - +
98A PRO* 1.3 79.8 - - - +
100A GLY* 1.3 62.7 + - - +
102A VAL* 3.3 9.5 + - - +
103A LEU* 3.1 22.7 + - - +
123A SER* 3.8 21.2 + - - -
124A THR* 3.1 33.1 + - + +
126A VAL* 3.6 38.7 - - - +
141A HIS* 5.5 1.8 - - - -
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Residues in contact with GLY 100 (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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94A ILE* 4.0 20.5 - - - +
95A GLY 4.3 1.8 - - - -
97A ASP* 3.0 15.2 + - - -
99A ARG* 1.3 76.1 - - - +
101A GLN* 1.3 57.8 + - - +
103A LEU* 3.3 3.6 + - - +
104A LYS* 3.0 28.9 + - - +
124A THR* 3.1 24.4 + - - -
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Residues in contact with GLN 101 (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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97A ASP 3.4 7.2 + - - +
98A PRO* 3.0 13.8 + - + +
100A GLY* 1.3 74.8 - - - +
102A VAL* 1.3 66.1 + - + +
104A LYS* 3.5 21.2 + - - +
105A GLU* 3.0 25.8 + - + +
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Residues in contact with VAL 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 4.2 22.4 - - + -
65A SER* 4.5 10.8 - - - +
98A PRO* 3.0 22.6 + - + +
99A ARG* 3.6 10.8 - - - +
100A GLY 3.2 0.2 - - - -
101A GLN* 1.3 78.2 - - + +
103A LEU* 1.3 57.3 + - - +
105A GLU* 3.5 3.3 + - - +
106A LEU* 2.7 47.8 + - + +
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Residues in contact with LEU 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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21A PRO* 3.8 41.7 - - + +
22A ILE 3.8 13.7 - - - +
23A LEU* 4.2 14.6 - - + -
67A PRO* 3.8 32.8 - - + -
72A LEU* 4.3 8.3 - - + -
94A ILE* 4.4 7.0 - - + -
99A ARG 3.1 16.8 + - - +
100A GLY 3.7 4.3 - - - +
101A GLN 3.3 0.2 - - - -
102A VAL* 1.3 73.9 - - - +
104A LYS* 1.3 67.5 + - - +
106A LEU* 3.2 4.8 + - - +
107A CYS* 3.1 27.5 + - - -
116A PHE* 4.9 3.6 - - + -
124A THR* 4.0 15.5 - - + -
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Residues in contact with LYS 104 (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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94A ILE* 4.1 11.4 - - - +
100A GLY 3.0 15.5 + - - +
101A GLN* 3.8 20.2 - - - +
103A LEU* 1.3 76.3 - - - +
105A GLU* 1.3 58.3 + - - +
107A CYS* 3.3 3.1 + - - +
108A ASP* 2.8 46.8 + - - +
114A THR* 5.3 0.7 - - - +
116A PHE* 3.5 58.9 + - + +
118A VAL* 5.0 5.9 - - - +
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Residues in contact with GLU 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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101A GLN* 3.0 20.1 + - + +
102A VAL* 3.8 5.8 - - - +
104A LYS* 1.3 75.6 - - - +
106A LEU* 1.3 69.9 + - + +
108A ASP* 3.3 8.0 + - - +
109A LYS* 3.1 27.2 + - - +
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Residues in contact with LEU 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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23A LEU* 5.3 1.6 - - + -
65A SER 4.7 12.1 - - - +
66A LEU* 5.2 3.8 - - + -
67A PRO* 4.1 36.6 - - + -
102A VAL* 2.7 39.6 + - + +
103A LEU* 3.2 9.8 + - - +
105A GLU* 1.3 82.2 - - + +
107A CYS* 1.3 60.6 + - - +
109A LYS* 3.4 42.7 - - + +
110A GLU* 3.6 16.4 - - - +
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Residues in contact with CYS 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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67A PRO* 4.6 6.7 - - - -
72A LEU* 3.9 30.7 - - - -
76A ARG* 5.0 4.0 - - - +
103A LEU* 3.1 21.1 + - - +
104A LYS 3.6 7.6 - - - +
106A LEU* 1.3 75.7 - - - +
108A ASP* 1.3 64.1 + - - +
110A GLU* 3.1 18.1 + - - +
112A LEU* 3.5 25.3 + - + +
114A THR* 4.5 11.4 - - + +
116A PHE* 3.9 27.1 - - + -
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Residues in contact with ASP 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 LYS* 2.8 41.3 + - - +
105A GLU* 3.3 7.7 + - - +
107A CYS* 1.3 75.2 - - - +
109A LYS* 1.3 62.4 + - - +
111A GLY* 3.1 14.3 + - - +
112A LEU 4.4 9.9 - - - +
114A THR* 4.2 13.3 + - - -
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Residues in contact with LYS 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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105A GLU 3.1 14.5 + - - +
106A LEU* 3.4 40.0 - - + +
107A CYS 3.2 0.4 - - - -
108A ASP* 1.3 76.0 - - - +
110A GLU* 1.3 67.5 + - + +
111A GLY 3.2 0.8 + - - -
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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