Contacts of the helix formed by residues 110 - 124 (chain X) 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 110 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109X LEU* 1.3 79.8 - - - +
111X ASP* 1.3 64.7 + - - +
112X GLU* 3.8 6.2 + - - +
113X ASP* 3.1 32.3 + - - +
114X ALA* 3.2 16.8 + - - +
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Residues in contact with ASP 111 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109X LEU 4.5 0.8 - - - +
110X SER* 1.3 74.7 - - - +
112X GLU* 1.3 63.1 + - - +
114X ALA* 3.4 5.3 + - - +
115X ARG* 3.1 23.4 + - - +
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Residues in contact with GLU 112 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12670 C 4.0 9.9 + - - -
110X SER* 3.2 6.8 + - - +
111X ASP* 1.3 80.0 - - - +
113X ASP* 1.3 60.9 + - - +
115X ARG* 2.5 49.5 + - - +
116X LEU* 3.0 46.3 + - + +
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Residues in contact with ASP 113 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109X LEU* 4.0 18.6 - - + +
110X SER* 3.1 27.7 + - - +
112X GLU* 1.3 81.6 - - - +
114X ALA* 1.3 57.0 + - - +
116X LEU* 3.2 5.0 + - - -
117X LEU* 2.8 30.1 + - - +
173X ALA* 3.6 24.8 - - - +
174X VAL* 3.6 5.9 - - - +
177X LYS* 3.5 25.0 + - - +
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Residues in contact with ALA 114 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109X LEU* 4.2 17.6 - - + +
110X SER 3.2 12.8 + - - +
111X ASP* 3.9 5.8 - - - +
113X ASP* 1.3 78.9 - - - +
115X ARG* 1.3 58.3 + - - +
117X LEU* 3.8 9.5 - - + +
118X THR* 3.0 33.3 + - - -
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Residues in contact with ARG 115 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5950 U 5.2 14.3 - - - +
12660 U 2.7 52.8 + - - -
12670 C 4.0 0.8 + - - -
85170 CL 3.8 26.7 - - + +
111X ASP 3.1 17.4 + - - +
112X GLU* 2.5 55.1 + - - +
113X ASP 3.1 0.2 - - - -
114X ALA* 1.3 79.3 - - - +
116X LEU* 1.3 77.5 + - + +
118X THR* 3.3 7.3 + - - +
119X GLN* 2.9 26.8 + - - +
122X ARG* 5.0 1.4 + - - -
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Residues in contact with LEU 116 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12660 U 4.4 2.7 - - - +
12670 C 3.7 33.4 - - - +
12680 C 6.0 0.2 - - - +
112X GLU* 3.0 35.6 + - + +
113X ASP 3.7 3.8 - - - +
115X ARG* 1.3 95.0 - - - +
117X LEU* 1.3 65.8 + - - +
119X GLN* 3.2 10.7 + - - +
120X ARG* 3.0 24.1 + - - +
171X PRO* 4.2 18.8 - - + +
173X ALA* 3.7 26.5 - - + -
174X VAL* 3.8 13.5 - - + +
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Residues in contact with LEU 117 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109X LEU* 4.4 10.8 - - + -
113X ASP 2.8 16.7 + - - +
114X ALA* 3.8 7.6 - - - +
116X LEU* 1.3 77.4 - - - +
118X THR* 1.3 64.4 + - - +
120X ARG* 3.5 21.7 + - - +
121X HIS* 3.2 23.0 + - + +
174X VAL* 3.2 30.7 - - + +
177X LYS* 4.4 5.6 - - + -
178X HIS 4.4 2.2 - - - +
179X PRO 3.8 15.0 - - - +
180X SER 4.3 3.4 - - - +
181X GLY* 3.8 31.2 - - - +
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Residues in contact with THR 118 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5950 U 3.7 41.7 - - - +
5960 C 4.0 14.9 + - - +
114X ALA* 3.0 23.5 + - - +
115X ARG* 3.6 6.5 - - - +
117X LEU* 1.3 81.3 - - - +
119X GLN* 1.3 60.5 + - - +
121X HIS* 3.5 8.8 + - - +
122X ARG* 3.0 22.6 + - + +
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Residues in contact with GLN 119 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12650 G 5.7 1.0 - - - +
12660 U 2.5 39.9 + - - +
12670 C 3.2 27.4 + - - +
115X ARG* 2.9 18.2 + - + +
116X LEU* 3.5 17.7 - - - +
117X LEU 3.2 0.4 - - - -
118X THR* 1.3 73.4 - - - +
120X ARG* 1.3 58.8 + - - +
122X ARG* 2.9 26.9 + - - +
123X VAL* 2.7 53.3 + - + +
171X PRO* 3.8 11.2 - - + +
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Residues in contact with ARG 120 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13260 U 3.5 14.8 + - - -
13270 G 2.8 40.6 + - - +
116X LEU 3.0 13.1 + - - +
117X LEU* 3.7 19.1 + - - +
119X GLN* 1.3 78.7 - - - +
121X HIS* 1.3 60.0 + - - +
123X VAL* 5.0 2.5 - - - -
124X GLY* 3.0 31.0 + - - +
170X SER* 4.2 19.5 - - - -
171X PRO* 4.3 11.8 - - + +
174X VAL* 3.3 31.7 + - + +
177X LYS 3.0 29.3 + - - +
179X PRO* 4.0 14.1 - - - +
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Residues in contact with HIS 121 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5550 U 3.6 22.8 + - - -
5560 C 3.2 29.2 + - - -
6070 G 5.2 14.7 + - - -
117X LEU* 3.2 14.8 + - + +
118X THR* 3.8 9.3 + - - +
119X GLN 3.2 0.6 - - - -
120X ARG* 1.3 84.1 - - - +
122X ARG* 1.3 66.0 + - - +
124X GLY* 4.4 3.3 + - - -
179X PRO* 6.2 4.0 - - + -
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Residues in contact with ARG 122 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5940 C 3.0 55.6 + - - -
5950 U 3.1 20.6 + - - +
10910 U 5.4 2.6 + - - -
12650 G 5.4 7.7 - - - +
85170 CL 3.9 7.5 - - - +
115X ARG 5.0 0.6 + - - -
118X THR* 3.0 15.1 + - + +
119X GLN* 2.9 40.3 + - - +
121X HIS* 1.3 83.0 + - - +
123X VAL* 1.3 74.0 + - - +
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Residues in contact with VAL 123 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5420 A 5.3 4.5 + - - -
10900 A 4.6 7.0 - - - +
10910 U 3.9 47.1 - - - +
119X GLN* 2.7 39.4 + - + +
120X ARG* 4.4 2.5 - - - +
122X ARG* 1.3 88.0 - - - +
124X GLY* 1.3 72.0 + - - +
125X LYS* 3.8 0.7 + - - -
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Residues in contact with GLY 124 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10900 A 5.5 0.9 + - - -
120X ARG* 3.0 19.2 + - - -
121X HIS 4.9 3.1 - - - -
122X ARG 3.6 1.0 - - - -
123X VAL* 1.3 90.9 - - - +
125X LYS* 1.3 66.2 + - - +
168X PHE* 5.6 1.9 - - - +
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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