Contacts of the helix formed by residues 119 - 134 (chain P) in PDB entry 2JA7
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 ARG 119 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118P THR* 1.3 73.2 - - + +
120P GLU* 1.3 72.8 + - + +
121P LYS 3.0 0.2 - - - -
122P GLU* 2.9 26.2 + - - +
123P LEU* 3.6 14.2 + - + +
149P THR* 5.8 1.0 - - - +
150P ASN* 5.2 10.1 - - - +
221P TYR* 3.6 52.5 - - + +
142S ARG* 6.1 2.9 - - - +
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Residues in contact with GLU 120 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118P THR 2.8 2.7 + - - +
119P ARG* 1.3 87.2 - - + +
121P LYS* 1.3 59.2 - - + +
122P GLU 3.3 0.4 + - - -
123P LEU* 3.7 32.4 + - + +
124P GLU* 4.1 6.6 + - - +
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Residues in contact with LYS 121 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118P THR* 2.8 41.8 + - + +
120P GLU* 1.3 79.9 - - + +
122P GLU* 1.3 60.1 + - - +
124P GLU* 3.9 6.0 + - - +
125P SER* 3.5 19.6 + - - -
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Residues in contact with GLU 122 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56P ARG* 3.2 21.3 + - - -
60P LYS* 3.0 26.5 + - - +
118P THR 4.3 9.4 + - - +
119P ARG* 2.9 13.1 + - - +
121P LYS* 1.3 75.7 - - - +
123P LEU* 1.3 62.0 + - - +
124P GLU 3.3 0.7 - - - -
125P SER* 2.9 28.8 + - - +
126P ILE* 2.9 31.1 + - + +
149P THR* 2.8 29.7 + - + +
155P ARG* 4.8 16.7 + - - +
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Residues in contact with LEU 123 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119P ARG* 3.9 13.7 - - + +
120P GLU* 3.8 26.7 - - + +
121P LYS 3.4 0.6 - - - -
122P GLU* 1.3 78.7 - - - +
124P GLU* 1.3 56.4 + - - +
126P ILE* 4.0 3.0 - - - +
127P ASP* 3.1 38.7 + - - +
146P GLN* 5.0 11.7 - - + +
149P THR* 3.6 30.7 - - + -
150P ASN* 4.4 17.5 - - - +
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Residues in contact with GLU 124 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120P GLU 4.1 5.9 + - - +
121P LYS* 3.9 8.8 + - - +
123P LEU* 1.3 80.6 - - - +
125P SER* 1.3 60.4 + - - +
126P ILE 3.3 0.9 + - - -
127P ASP* 3.9 8.2 - - + +
128P VAL* 3.5 30.0 + - + +
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Residues in contact with SER 125 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67P ARG* 5.3 2.1 + - - -
121P LYS 3.5 12.7 + - - -
122P GLU* 2.9 34.7 + - - +
124P GLU* 1.3 80.0 - - - +
126P ILE* 1.3 59.1 + - - +
128P VAL* 4.2 7.0 - - - +
129P LEU* 3.8 15.2 + - - +
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Residues in contact with ILE 126 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56P ARG* 5.2 1.6 - - + -
60P LYS* 5.0 13.9 - - + -
122P GLU* 2.9 38.3 + - + +
123P LEU* 4.1 2.9 - - - +
125P SER* 1.3 78.5 - - - +
127P ASP* 1.3 75.6 + - - +
128P VAL 2.9 2.0 - - - -
129P LEU* 2.7 27.0 + - + +
130P LEU* 3.0 18.7 + - + +
145P MET* 3.6 51.8 - - + -
149P THR* 4.3 12.1 - - + +
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Residues in contact with ASP 127 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123P LEU* 3.1 24.7 + - - +
124P GLU* 3.9 8.8 - - + +
126P ILE* 1.3 81.9 - - - +
128P VAL* 1.3 58.9 + - + +
130P LEU* 3.2 13.9 + - - +
131P GLU* 3.0 41.0 + - - +
142P LYS* 5.7 2.9 - - - +
146P GLN* 5.7 6.1 + - - +
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Residues in contact with VAL 128 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67P ARG* 4.0 17.5 - - - +
124P GLU* 3.5 19.2 + - + +
125P SER* 4.2 6.7 - - - +
126P ILE 2.9 0.4 - - - -
127P ASP* 1.3 75.3 - - + +
129P LEU* 1.3 63.9 + - - +
130P LEU 2.8 6.3 + - - -
131P GLU* 3.1 17.1 + - - +
132P GLN* 2.9 38.6 - - + +
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Residues in contact with LEU 129 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60P LYS* 4.1 10.8 - - + +
63P LEU* 3.1 50.1 - - + +
64P VAL* 3.6 28.7 - - + -
67P ARG* 4.1 32.1 - - + +
125P SER 3.8 10.6 + - - +
126P ILE* 2.7 23.2 + - + +
128P VAL* 1.3 75.6 - - - +
130P LEU* 1.3 57.5 + - + +
132P GLN* 4.0 1.7 - - - +
133P THR* 2.6 34.6 + - + +
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Residues in contact with LEU 130 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63P LEU* 3.7 15.9 - - + -
126P ILE* 3.0 24.2 + - + +
127P ASP* 3.4 14.6 - - - +
128P VAL 2.8 1.2 + - - -
129P LEU* 1.3 76.2 - - + +
131P GLU* 1.3 53.8 - - + +
132P GLN 2.2 21.3 + - - -
133P THR 2.8 10.9 + - - -
134P THR* 2.8 46.4 + - + +
136P GLY* 5.5 1.5 + - - -
141P LEU* 4.4 16.4 - - + +
142P LYS* 3.5 47.1 - - + +
145P MET* 4.6 10.1 - - + -
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Residues in contact with GLU 131 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127P ASP* 3.0 26.4 + - - +
128P VAL* 3.1 11.2 + - - +
130P LEU* 1.3 71.5 - - + +
132P GLN* 1.3 65.3 + - + +
134P THR 5.8 0.7 - - - -
136P GLY* 6.0 5.8 - - - -
142P LYS* 5.7 10.5 + - - -
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Residues in contact with GLN 132 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67P ARG* 3.2 33.3 + - + +
70P PHE* 4.2 14.9 - - - -
71P LYS* 5.1 9.4 + - - +
128P VAL* 2.9 36.2 - - + +
129P LEU* 4.0 5.2 - - - +
130P LEU 2.2 20.4 + - - -
131P GLU* 1.3 72.6 + - - +
133P THR* 1.3 66.4 + - + +
134P THR 3.7 2.8 + - - +
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Residues in contact with THR 133 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63P LEU* 2.9 23.7 + - - +
66P ARG* 2.9 45.0 + - + +
67P ARG* 3.3 48.9 - - + +
70P PHE* 4.6 14.4 - - + -
129P LEU 2.6 22.4 + - - +
130P LEU 2.8 1.0 + - - -
132P GLN* 1.3 80.7 - - + +
134P THR* 1.3 61.9 + - - +
31S LEU* 5.4 1.2 - - - +
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Residues in contact with THR 134 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63P LEU* 3.4 8.7 - - - +
66P ARG* 4.7 3.4 - - - +
130P LEU* 2.8 54.9 + - + +
131P GLU* 5.8 0.5 - - - -
132P GLN 5.0 1.6 - - - +
133P THR* 1.3 81.6 + - - +
135P GLY* 1.3 74.2 + - - +
136P GLY* 3.2 16.2 + - - +
138P ASN* 3.7 24.9 - - + +
141P LEU* 4.2 10.0 - - + +
142P LYS* 6.1 1.3 - - + -
35S GLU* 5.1 2.7 - - - +
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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