Contacts of the helix formed by residues 108 - 125 (chain O) in PDB entry 6AH0
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 108 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106O MET 4.9 2.6 - - - +
107O GLU* 1.3 78.2 + - - +
109O LYS* 1.3 67.0 + - - +
110O GLN 3.2 2.9 - - - +
111O GLU* 3.9 5.6 + - - +
112O MET* 3.5 14.6 + - - -
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Residues in contact with LYS 109 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44O VAL* 5.7 5.4 - - - +
107O GLU 4.3 0.2 + - - -
108O ASP* 1.3 72.5 - - - +
110O GLN* 1.3 62.7 + - - +
112O MET* 3.2 3.9 + - - +
113O VAL* 3.1 17.5 + - - -
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Residues in contact with GLN 110 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108O ASP* 3.2 1.2 - - - +
109O LYS* 1.3 77.4 - - - +
111O GLU* 1.3 58.1 + - - +
113O VAL* 2.9 18.5 + - - +
114O ASP* 3.0 11.3 + - - -
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Residues in contact with GLU 111 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108O ASP* 3.9 8.7 + - - +
109O LYS 3.4 0.4 - - - -
110O GLN* 1.3 73.7 - - - +
112O MET* 1.3 57.7 + - - +
114O ASP* 4.0 3.4 - - - +
115O ILE* 3.7 12.8 + - - -
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Residues in contact with MET 112 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108O ASP 3.5 10.0 + - - -
109O LYS 3.2 7.0 + - - -
110O GLN 3.1 1.0 - - - -
111O GLU* 1.3 75.3 - - - +
113O VAL* 1.3 63.0 + - - +
114O ASP 3.2 0.2 - - - -
115O ILE* 3.3 3.0 + - - +
116O ILE* 3.2 17.7 + - - -
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Residues in contact with VAL 113 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109O LYS 3.1 9.6 + - - -
110O GLN* 2.9 7.7 + - - +
112O MET* 1.3 75.3 - - - +
114O ASP* 1.3 57.5 + - - +
116O ILE* 3.4 1.5 + - - +
117O GLU* 2.9 26.2 + - - -
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Residues in contact with ASP 114 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110O GLN 3.0 13.0 + - - -
111O GLU* 4.0 3.3 - - - +
112O MET 3.2 0.4 - - - -
113O VAL* 1.3 76.2 - - - +
115O ILE* 1.3 51.4 + - - +
117O GLU* 3.2 1.4 + - - +
118O THR* 2.7 33.4 + - - -
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Residues in contact with ILE 115 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111O GLU 3.7 10.1 + - - -
112O MET* 3.3 6.1 + - - +
113O VAL 3.2 0.8 - - - -
114O ASP* 1.3 75.1 - - - +
116O ILE* 1.3 57.5 + - - +
118O THR* 3.2 1.3 + - - +
119O VAL* 2.9 26.9 + - - -
132O SER* 5.9 6.7 - - - +
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Residues in contact with ILE 116 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112O MET 3.2 11.9 + - - -
113O VAL* 3.9 2.7 - - - +
115O ILE* 1.3 75.4 - - - +
117O GLU* 1.3 57.8 + - - +
119O VAL* 3.3 2.0 + - - +
120O TYR* 3.0 26.7 + - - -
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Residues in contact with GLU 117 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113O VAL 2.9 14.8 + - - -
114O ASP* 3.6 3.4 - - - +
116O ILE* 1.3 78.9 - - - +
118O THR* 1.3 61.7 + - - +
120O TYR* 4.0 0.8 - - - +
121O ARG* 3.0 20.1 + - - -
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Residues in contact with THR 118 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114O ASP 2.7 20.5 + - - -
115O ILE* 3.7 1.6 - - - +
117O GLU* 1.3 73.0 - - - +
119O VAL* 1.3 63.5 + - - +
121O ARG* 3.3 0.6 + - - +
122O GLY* 3.0 22.9 + - - -
131O VAL 6.1 1.1 - - - -
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Residues in contact with VAL 119 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115O ILE 2.9 14.7 + - - -
116O ILE* 3.8 2.9 - - - +
118O THR* 1.3 77.0 - - - +
120O TYR* 1.3 55.6 + - - +
122O GLY* 5.3 0.2 - - - -
123O ALA* 2.8 26.9 + - - -
130O VAL* 6.3 2.9 - - - +
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Residues in contact with TYR 120 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116O ILE 3.0 15.4 + - - -
117O GLU* 4.0 1.6 - - - +
119O VAL* 1.3 77.7 - - - +
121O ARG* 1.3 52.2 + - - +
123O ALA* 3.2 1.5 + - - +
124O ARG* 2.8 32.7 + - - -
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Residues in contact with ARG 121 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117O GLU 3.0 16.1 + - - -
118O THR 3.9 0.4 - - - -
120O TYR* 1.3 77.4 - - - +
122O GLY* 1.3 62.1 + - - +
124O ARG* 3.3 9.6 + - - +
125O LYS* 3.8 5.4 + - - -
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Residues in contact with GLY 122 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118O THR 3.0 14.7 + - - -
119O VAL 4.2 0.2 - - - -
121O ARG* 1.3 74.6 - - - +
123O ALA* 1.3 63.9 + - - +
125O LYS* 3.2 12.3 + - - -
127O ARG* 3.6 18.9 + - - -
129O LEU 5.9 2.9 - - - -
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Residues in contact with ALA 123 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119O VAL 2.8 20.6 + - - -
120O TYR* 3.6 1.6 - - - +
122O GLY* 1.3 74.9 - - - +
124O ARG* 1.3 66.3 + - - +
126O GLY* 2.8 17.2 + - - -
127O ARG 4.0 12.6 - - - -
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Residues in contact with ARG 124 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120O TYR 2.8 19.4 + - - -
121O ARG* 3.3 4.2 + - - +
122O GLY 3.2 0.8 - - - -
123O ALA* 1.3 73.4 - - - +
125O LYS* 1.3 56.8 + - - +
126O GLY 3.3 3.6 + - - -
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Residues in contact with LYS 125 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121O ARG 3.8 5.0 + - - -
122O GLY 3.2 8.0 + - - -
123O ALA 3.0 1.2 - - - -
124O ARG* 1.3 76.0 - - - +
126O GLY* 1.3 53.9 + - - +
127O ARG 3.1 9.5 + - - -
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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