Contacts of the helix formed by residues 110 - 120 (chain R) in PDB entry 3J0S
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 PRO 110 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78R LYS* 2.7 33.4 - - - +
79R ASP* 4.6 6.3 - - - +
80R CYS 5.7 0.2 - - - +
108R SER 3.9 1.3 - - - +
109R ALA* 1.4 79.0 - - + +
111R LEU* 1.3 66.4 + - - +
112R LYS* 3.3 5.3 + - + +
113R SER* 3.5 13.7 + - - +
114R LYS* 3.1 22.5 + - - +
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Residues in contact with LEU 111 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25G ASP* 4.2 25.6 - - + +
144G ALA 6.1 0.4 - - - +
334G GLU* 4.1 34.5 - - + +
341G ILE* 5.5 4.3 - - + -
345G ILE* 6.5 0.4 - - + -
107R GLU* 5.9 4.5 - - - +
109R ALA 3.1 6.4 + - - +
110R PRO* 1.3 72.2 - - - +
112R LYS* 1.3 68.2 + - + +
114R LYS* 4.4 10.8 - - + -
115R MET* 2.9 69.7 + - + +
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Residues in contact with LYS 112 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23G GLY 5.3 7.0 - - - +
25G ASP* 3.7 27.7 + - - +
345G ILE* 5.8 1.6 - - + +
44R LYS* 4.4 2.1 - - - -
110R PRO* 3.3 4.0 - - + -
111R LEU* 1.3 88.2 - - + +
113R SER* 1.3 62.5 + - - +
115R MET* 4.0 4.4 + - - +
116R ILE* 3.9 18.4 + - - +
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Residues in contact with SER 113 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40R LEU* 5.7 2.1 - - - +
44R LYS* 3.8 29.8 + - - +
80R CYS* 4.5 17.0 + - - +
110R PRO* 3.5 16.2 + - - +
112R LYS* 1.3 77.1 - - - +
114R LYS* 1.3 66.1 + - - +
115R MET 3.5 0.3 + - - -
116R ILE 3.5 2.4 + - - -
117R TYR* 3.3 18.8 + - - +
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Residues in contact with LYS 114 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144G ALA 3.1 25.6 - - - -
145G SER* 3.2 22.9 + - - +
146G GLY* 3.4 13.1 - - - -
80R CYS* 4.0 21.1 - - + +
105R ALA* 3.6 17.2 + - - +
106R PRO 3.2 22.6 + - - +
107R GLU* 4.2 15.3 - - - +
109R ALA* 4.0 11.0 - - + +
110R PRO 3.1 22.0 + - - +
111R LEU* 4.0 11.2 - - + +
113R SER* 1.3 78.1 - - - +
115R MET* 1.3 59.5 + - - +
117R TYR* 3.1 4.0 + - - +
118R ALA* 2.9 30.0 + - - +
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Residues in contact with MET 115 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144G ALA* 4.5 26.0 - - + +
341G ILE* 3.1 32.8 - - + +
342G GLY* 4.7 3.8 - - - +
345G ILE* 3.4 50.2 - - + +
111R LEU* 2.9 41.0 + - + +
112R LYS* 4.4 3.4 - - - +
114R LYS* 1.3 83.3 - - - +
116R ILE* 1.3 61.3 + - - +
118R ALA* 3.5 5.3 + - + +
119R SER* 3.1 32.0 + - - +
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Residues in contact with ILE 116 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345G ILE* 3.3 31.4 - - + +
346G LEU* 4.9 6.7 - - + +
349G LEU* 3.9 37.2 - - + -
4R GLY* 5.8 1.3 - - - +
5R VAL* 4.8 3.8 - - + -
40R LEU* 3.6 14.6 - - + -
44R LYS* 3.3 42.2 - - + -
112R LYS 3.9 11.8 + - - +
113R SER 3.5 1.4 + - - -
114R LYS 3.3 0.4 - - - -
115R MET* 1.3 75.7 - - - +
117R TYR* 1.3 56.1 + - - +
119R SER* 3.4 4.6 + - - -
120R SER* 2.9 35.5 + - - -
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Residues in contact with TYR 117 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146G GLY 4.9 2.0 - - - -
40R LEU* 4.6 7.1 - - + +
80R CYS* 3.1 30.3 - - + +
81R ARG 2.9 19.0 + - - -
82R TYR* 3.0 70.1 + + - -
103R PHE* 3.2 24.6 - + + -
104R TRP 2.9 39.1 + - - -
105R ALA* 3.4 19.7 - - + -
113R SER 3.3 10.2 + - - +
114R LYS 3.1 8.9 + - - +
116R ILE* 1.3 79.3 - - - +
118R ALA* 1.3 67.0 + - - +
120R SER* 3.2 5.4 + - - -
121R LYS* 3.5 6.1 + - + +
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Residues in contact with ALA 118 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143G TYR* 2.8 50.5 - - - +
144G ALA* 3.8 3.8 - - - +
146G GLY* 3.3 27.7 - - - +
148G THR* 5.1 0.5 + - - -
114R LYS* 2.9 24.2 + - - +
115R MET* 3.8 6.3 - - - +
117R TYR* 1.3 81.2 - - - +
119R SER* 1.3 54.6 + - - +
120R SER 3.3 0.2 + - - -
121R LYS* 3.5 10.3 + - - +
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Residues in contact with SER 119 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143G TYR* 3.1 32.5 + - - -
144G ALA* 5.8 1.0 - - - -
342G GLY* 4.9 1.2 + - - -
345G ILE* 5.5 1.1 - - - +
346G LEU* 3.4 31.1 - - - +
1R MET* 3.4 25.5 - - - +
2R ALA 4.7 1.2 - - - +
3R SER* 4.8 0.3 - - - -
4R GLY 3.8 11.8 + - - -
115R MET* 3.1 21.6 + - - +
116R ILE* 3.8 3.8 - - - -
117R TYR 3.3 0.2 - - - -
118R ALA* 1.3 78.1 - - - +
120R SER* 1.3 56.8 + - - +
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Residues in contact with SER 120 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4R GLY* 4.3 10.3 - - - +
5R VAL* 3.2 35.7 - - - +
40R LEU* 5.0 1.5 - - - +
47R ILE* 4.3 3.8 - - - +
82R TYR* 3.0 23.2 + - - -
116R ILE* 2.9 17.1 + - - -
117R TYR* 3.2 1.0 + - - -
119R SER* 1.3 75.3 - - - +
121R LYS* 1.3 57.8 + - - +
122R ASP 3.3 2.9 - - - -
123R ALA* 3.1 4.3 + - - +
124R ILE* 2.7 26.3 + - - +
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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