Contacts of the helix formed by residues 108 - 122 (chain A) in PDB entry 5AIS
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 LYS 108 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A GLU* 3.1 22.1 + - - +
107A LYS* 1.3 78.8 - - + +
109A GLN* 1.3 59.5 + - - +
110A ASP* 3.4 7.2 - - - +
111A VAL* 3.2 23.5 + - + -
112A LYS* 2.9 25.1 + - - +
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Residues in contact with GLN 109 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A GLU 5.9 0.4 - - - +
107A LYS 3.2 10.2 + - - +
108A LYS* 1.3 72.5 - - - +
110A ASP* 1.3 58.5 + - - +
112A LYS* 3.4 11.6 + - + +
113A GLU* 2.9 29.6 + - - +
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Residues in contact with ASP 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 LYS* 3.9 9.7 - - - +
109A GLN* 1.3 72.2 + - - +
111A VAL* 1.3 76.4 + - - +
113A GLU* 3.4 11.6 + - - +
114A GLN* 3.0 47.7 + - - +
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Residues in contact with VAL 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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106A GLU* 4.1 15.7 - - + +
108A LYS* 3.2 28.2 + - + +
110A ASP* 1.3 86.8 + - - +
112A LYS* 1.3 60.4 + - - +
114A GLN* 3.4 9.7 + - - +
115A MET* 3.0 50.8 + - + +
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Residues in contact with LYS 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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103A PRO* 3.8 24.9 - - + +
104A TRP* 3.9 18.2 + - - +
106A GLU* 3.8 23.9 + - + +
108A LYS 2.9 16.8 + - - +
109A GLN* 3.6 11.2 - - + +
110A ASP 3.3 0.2 - - - -
111A VAL* 1.3 76.2 - - - +
113A GLU* 1.3 62.7 + - - +
115A MET* 3.9 0.3 - - - -
116A PHE* 3.0 58.7 + - + -
163A PHE* 5.9 5.6 - - - -
199A LEU* 5.6 7.5 - - - +
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Residues in contact with GLU 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 GLN 2.9 17.5 + - - +
110A ASP* 3.6 11.4 - - - +
112A LYS* 1.3 75.7 - - - +
114A GLN* 1.3 59.7 + - - +
116A PHE* 3.7 5.0 - - - +
117A ASN* 3.0 32.6 + - + +
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Residues in contact with GLN 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 ASP* 3.0 36.7 + - - +
111A VAL* 3.8 9.1 - - - +
113A GLU* 1.3 80.9 - - + +
115A MET* 1.3 59.5 + - + +
117A ASN* 3.5 9.0 + - - +
118A GLU* 3.0 29.9 + - - +
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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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101A CYS 4.8 7.0 - - - +
103A PRO* 3.8 41.1 - - + -
106A GLU* 5.1 2.9 - - - +
111A VAL* 3.0 39.2 + - + +
114A GLN* 1.3 74.6 - - + +
116A PHE* 1.3 66.1 + - - +
118A GLU* 3.4 15.4 + - - +
119A LEU* 3.0 33.4 + - + +
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Residues in contact with PHE 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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102A PHE* 3.7 28.9 - + + -
103A PRO* 3.6 31.6 - - + -
104A TRP* 3.7 27.8 - + - -
112A LYS* 3.0 51.3 + - + +
113A GLU* 3.7 5.4 - - - +
115A MET* 1.3 76.5 - - - +
117A ASN* 1.3 55.5 + - - +
119A LEU* 3.3 2.1 + - - +
120A LEU* 2.9 41.3 + - + +
163A PHE* 3.7 52.5 - + + -
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Residues in contact with ASN 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 GLU* 3.0 20.6 + - + +
114A GLN* 3.7 8.0 + - - +
116A PHE* 1.3 75.3 - - - +
118A GLU* 1.3 58.8 + - - +
120A LEU* 3.8 6.3 - - - +
121A THR* 2.7 49.5 + - - -
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Residues in contact with GLU 118 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114A GLN 3.0 16.9 + - - +
115A MET* 3.6 18.7 - - - +
116A PHE 3.3 0.2 - - - -
117A ASN* 1.3 79.8 - - - +
119A LEU* 1.3 64.3 + - + +
121A THR* 4.7 0.4 - - - -
122A TYR* 3.2 48.1 + - + +
123A ASN* 3.7 4.6 - - - +
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Residues in contact with LEU 119 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A PHE* 4.0 5.9 - - + -
101A CYS* 3.6 42.6 - - + +
102A PHE* 3.6 42.2 - - + -
103A PRO* 4.3 4.9 - - + -
115A MET* 3.0 24.4 + - + +
118A GLU* 1.3 79.7 - - + +
120A LEU* 1.3 57.8 + - - +
123A ASN* 3.2 34.2 + - + +
124A ALA* 2.8 28.5 + - - +
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Residues in contact with LEU 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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102A PHE* 4.0 23.6 - - + -
116A PHE* 2.9 31.6 + - + +
117A ASN* 4.1 6.1 - - - +
119A LEU* 1.3 75.8 - - - +
121A THR* 1.3 55.2 + - - +
124A ALA* 3.8 11.6 - - + +
125A PRO* 3.2 11.6 - - - +
160A LEU* 4.1 22.0 - - + +
163A PHE* 3.6 37.5 - - + +
164A LYS* 2.8 52.9 + - + +
167A LEU* 5.0 2.0 - - + -
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Residues in contact with THR 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 ASN* 2.7 39.1 + - - -
118A GLU* 4.7 0.2 - - - -
120A LEU* 1.3 79.7 - - - +
122A TYR* 1.3 91.7 + - + +
125A PRO* 3.3 16.8 - - - +
164A LYS* 4.3 6.0 + - - +
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Residues in contact with TYR 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 GLU* 3.2 36.5 + - + +
121A THR* 1.3 101.6 - - + +
123A ASN* 1.3 72.3 + - - +
124A ALA 3.5 0.4 - - - -
125A PRO* 3.6 3.9 - - - +
126A HIS* 3.2 40.1 + + + +
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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