Contacts of the helix formed by residues 115 - 128 (chain O) in PDB entry 1JJ2
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 SER 115 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114O LEU* 1.3 73.5 - - - +
116O SER* 1.3 56.9 + - - +
117O SER* 2.7 27.2 + - - -
118O GLN* 2.6 49.9 + - - +
119O TYR* 2.9 10.5 + - - +
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Residues in contact with SER 116 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15930 C 3.4 18.6 + - - +
15940 C 3.5 20.8 + - - -
109O ARG* 4.5 9.9 - - - +
114O LEU 3.8 1.4 + - - -
115O SER* 1.3 70.3 - - - +
117O SER* 1.3 57.1 + - - +
119O TYR* 4.2 7.9 - - - -
120O ARG* 3.2 25.1 + - - +
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Residues in contact with SER 117 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15930 C 2.7 37.7 + - - -
115O SER* 2.7 24.6 + - - -
116O SER* 1.3 78.4 + - - +
118O GLN* 1.3 64.4 + - - +
120O ARG* 3.6 2.5 - - - +
121O ASP* 3.1 22.9 + - - +
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Residues in contact with GLN 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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113O THR 4.1 5.1 + - - +
114O LEU* 3.5 24.9 - - + +
115O SER* 2.6 49.8 + - - +
117O SER* 1.3 76.3 - - - +
119O TYR* 1.3 67.4 + - - +
121O ASP* 3.0 8.1 + - - +
122O LEU* 2.8 30.6 + - + +
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Residues in contact with TYR 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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15940 C 3.1 30.5 - - - -
15950 G 2.6 28.2 + - - -
15960 U 5.4 0.3 + - - -
102O ARG 5.0 1.1 + - - -
105O LEU* 3.5 46.7 - - + -
106O ARG* 4.0 12.5 + - - +
109O ARG* 3.0 36.9 + - + -
114O LEU* 4.3 17.8 - - + +
115O SER 2.9 14.4 + - - +
116O SER* 4.1 5.4 - - - +
118O GLN* 1.3 76.0 - - - +
120O ARG* 1.3 63.0 + - - +
122O LEU* 3.0 4.9 + - - +
123O TYR* 2.6 62.2 + + + +
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Residues in contact with ARG 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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15930 C 3.7 44.1 - - + +
15940 C 2.8 53.5 + - - +
15950 G 2.9 35.6 + - - -
116O SER 3.2 16.6 + - - +
117O SER 3.6 6.3 - - - +
119O TYR* 1.3 83.6 - - - +
121O ASP* 1.3 58.2 + - - +
123O TYR* 2.8 37.7 - - - +
124O ASP* 2.9 62.4 + - - +
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Residues in contact with ASP 121 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8020 G 5.0 3.2 + - - -
117O SER 3.1 11.5 + - - +
118O GLN* 3.0 13.3 + - - +
120O ARG* 1.3 80.4 - - - +
122O LEU* 1.3 66.9 + - + +
124O ASP* 4.0 4.8 - - - +
125O LYS* 3.3 50.3 + - - +
140O TYR* 5.6 0.2 - - - -
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Residues in contact with LEU 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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105O LEU* 3.7 16.4 - - + -
114O LEU* 3.8 37.5 - - + -
118O GLN* 2.8 19.9 + - + +
119O TYR 3.6 4.7 - - - +
121O ASP* 1.3 79.3 - - - +
123O TYR* 1.3 61.0 + - - +
125O LYS* 3.2 5.5 + - + +
126O ALA* 2.8 30.1 + - - +
131O PHE* 3.6 10.7 - - + -
137O LEU* 4.4 6.3 - - + -
140O TYR* 3.5 38.1 - - + -
141O ILE* 4.1 16.8 - - + -
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Residues in contact with TYR 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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15950 G 3.4 27.0 - + - -
15960 U 2.5 53.2 + + - -
102O ARG* 3.6 37.0 + - + -
105O LEU* 3.4 16.3 - - + +
106O ARG* 5.7 0.7 - - - -
119O TYR* 2.6 51.3 + + + +
120O ARG* 2.8 38.6 - - - +
122O LEU* 1.3 71.9 - - - +
124O ASP* 1.3 65.3 + - - +
126O ALA* 3.0 5.0 + - - +
127O GLY* 3.0 20.9 + - - -
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Residues in contact with ASP 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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8000 G 4.0 2.1 + - - +
8010 U 3.4 34.6 + - - +
15930 C 5.6 3.5 + - - -
15940 C 5.1 1.5 + - - -
15950 G 4.0 6.0 - - - +
120O ARG* 2.9 59.4 + - - +
121O ASP* 4.0 6.1 - - - +
123O TYR* 1.3 77.4 - - - +
125O LYS* 1.3 62.8 + - + +
127O GLY* 3.4 2.8 + - - -
128O GLY 3.1 16.1 + - - -
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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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8010 U 3.8 18.6 - - - +
8020 G 3.4 26.4 - - - +
121O ASP* 3.3 34.8 + - - +
122O LEU* 3.2 9.0 + - - +
124O ASP* 1.3 75.4 - - + +
126O ALA* 1.3 67.4 + - - +
128O GLY 3.1 6.8 + - - -
129O GLY 3.1 0.3 + - - -
130O GLU* 3.0 42.7 + - + +
131O PHE* 3.9 16.2 - - + -
140O TYR* 2.7 31.5 + - + +
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Residues in contact with ALA 126 (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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94O TRP* 3.9 8.5 - - - -
98O ILE* 4.3 13.8 - - + +
101O GLN* 3.6 25.7 - - + +
102O ARG* 5.6 2.2 - - + -
105O LEU* 4.6 8.7 - - + -
122O LEU 2.8 13.4 + - - +
123O TYR* 3.4 11.7 - - - +
125O LYS* 1.3 77.9 - - - +
127O GLY* 1.3 54.7 + - - +
129O GLY* 2.7 25.6 + - - -
130O GLU 4.4 0.9 - - - +
131O PHE* 3.5 17.4 - - + -
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Residues in contact with GLY 127 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8000 G 3.7 13.5 + - - +
8140 G 5.2 4.5 + - - +
8150 U 5.5 1.9 - - - +
15960 U 5.1 5.2 - - - -
15980 A 4.8 2.4 + - - -
94O TRP* 4.0 15.5 - - - -
98O ILE* 4.4 4.8 - - - +
102O ARG* 4.2 21.5 - - - -
123O TYR* 3.0 14.0 + - - -
124O ASP* 3.4 3.6 + - - -
126O ALA* 1.3 75.6 - - - +
128O GLY* 1.3 57.7 + - - +
129O GLY 3.1 1.4 + - - -
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Residues in contact with GLY 128 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8000 G 3.0 35.5 + - - -
8010 U 3.2 31.2 - - - -
8130 C 4.6 0.7 - - - +
8140 G 4.5 4.8 + - - -
124O ASP 3.1 5.9 + - - -
125O LYS 3.1 8.2 + - - -
126O ALA 3.0 1.2 - - - -
127O GLY* 1.3 77.1 - - - +
129O GLY* 1.3 61.0 + - - +
130O GLU* 3.6 3.5 - - - +
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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