Contacts of the helix formed by residues 58 - 70 (chain V) 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 58 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57V PRO* 1.3 75.6 - - - +
59V GLN* 1.3 66.2 + - - +
60V GLU* 3.8 10.1 + - - +
61V THR* 3.0 15.9 + - - -
62V LEU* 3.1 22.0 + - - +
101V LEU* 4.2 0.7 - - - -
143V THR* 3.7 12.2 - - - +
147V ASP* 2.5 31.1 + - - -
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Residues in contact with GLN 59 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58V SER* 1.3 72.3 - - - +
60V GLU* 1.3 67.5 + - + +
62V LEU* 3.5 3.1 + - - +
63V GLU* 3.0 47.3 + - - +
94V SER* 3.1 22.2 + - - -
97V ALA* 3.2 16.1 - - - +
98V PHE* 3.2 31.4 - - - +
101V LEU* 3.7 19.4 - - + +
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Residues in contact with GLU 60 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58V SER* 3.2 8.7 - - - +
59V GLN* 1.3 83.1 - - + +
61V THR* 1.3 65.7 + - - +
63V GLU* 2.8 22.4 + - - +
64V THR* 2.9 17.2 + - - +
151V GLU* 5.7 1.1 - - - +
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Residues in contact with THR 61 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58V SER* 3.0 11.8 + - - -
60V GLU* 1.3 78.1 - - - +
62V LEU* 1.3 64.9 + - - +
64V THR* 3.0 9.5 + - - -
65V VAL* 3.0 23.1 + - + +
147V ASP* 2.8 32.9 + - - +
150V LEU* 3.6 41.3 - - + -
151V GLU* 2.6 33.4 + - + +
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Residues in contact with LEU 62 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1V MET* 3.7 26.7 - - + -
3V ALA* 6.3 0.2 - - + -
34V LEU* 4.1 26.2 - - + -
57V PRO* 4.6 11.8 - - + +
58V SER 3.1 16.7 + - - +
59V GLN 3.7 4.7 - - - +
61V THR* 1.3 78.1 - - - +
63V GLU* 1.3 53.0 + - - +
65V VAL* 3.7 4.7 - - + +
66V LEU* 2.7 58.1 + - + +
97V ALA* 3.8 19.7 - - + +
100V LEU* 4.2 6.3 - - + -
101V LEU* 3.7 17.9 - - + -
116V LEU* 4.9 6.3 - - + -
150V LEU* 6.0 2.9 - - + -
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Residues in contact with GLU 63 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59V GLN* 3.0 41.9 + - - +
60V GLU* 2.8 13.6 + - - +
62V LEU* 1.3 75.7 - - - +
64V THR* 1.3 63.6 + - - +
66V LEU* 3.8 0.7 - - - +
67V ALA* 3.0 26.9 + - - +
93V ILE* 3.8 17.1 - - + +
94V SER* 2.7 36.2 + - - -
97V ALA* 3.7 15.5 - - + -
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Residues in contact with THR 64 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60V GLU* 2.9 13.7 + - - +
61V THR* 3.0 10.1 + - - -
63V GLU* 1.3 76.1 - - - +
65V VAL* 1.3 60.1 + - + +
67V ALA* 3.8 3.9 - - - +
68V THR* 2.9 31.2 + - - +
151V GLU* 5.1 12.1 + - + +
154V ARG* 4.2 27.6 - - + +
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Residues in contact with VAL 65 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32V CYS* 5.8 0.2 - - - -
61V THR* 3.0 19.3 + - + +
62V LEU* 4.0 6.5 - - + +
64V THR* 1.3 76.6 - - + +
66V LEU* 1.3 58.1 + - - +
68V THR* 3.3 9.6 - - + -
69V ARG* 2.6 33.5 + - + +
70V ALA 3.8 0.5 + - - -
116V LEU* 3.6 29.1 - - + +
118V LEU* 4.0 20.9 - - + -
150V LEU* 3.8 45.3 - - + +
151V GLU* 5.3 0.7 - - + -
154V ARG* 4.8 5.2 - - + -
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Residues in contact with LEU 66 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34V LEU* 4.8 0.4 - - + -
62V LEU* 2.7 39.8 + - + +
63V GLU 3.8 3.1 - - - +
65V VAL* 1.3 73.6 - - - +
67V ALA* 1.3 63.7 + - - +
70V ALA* 2.8 41.3 + - + +
79V VAL* 4.1 5.0 - - + +
93V ILE* 4.0 14.1 - - + -
96V LEU* 4.5 11.2 - - + -
97V ALA* 3.9 26.2 - - + +
100V LEU* 3.8 24.0 - - + -
107V LEU* 4.1 25.1 - - + -
116V LEU* 4.3 12.8 - - + -
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Residues in contact with ALA 67 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63V GLU 3.0 18.2 + - - +
64V THR* 3.8 4.5 - - - +
66V LEU* 1.3 80.0 - - - +
68V THR* 1.3 62.3 + - - +
70V ALA 4.4 2.1 + - - +
78V ASP* 5.9 1.0 - - - +
79V VAL 3.7 16.4 + - - +
80V ASP* 5.7 0.4 - - - -
93V ILE* 3.4 28.0 - - + +
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Residues in contact with THR 68 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5670 U 5.1 1.6 + - - -
64V THR* 2.9 27.5 + - - +
65V VAL* 3.2 15.0 - - - +
67V ALA* 1.3 79.7 - - - +
69V ARG* 1.3 76.4 + - + +
70V ALA 5.3 0.7 - - - +
154V ARG* 3.1 45.2 + - + +
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Residues in contact with ARG 69 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5660 A 3.4 11.6 + - - -
5670 U 2.7 29.3 + - - -
12630 C 3.1 40.2 + - - -
12640 U 4.4 6.3 + - - -
65V VAL 2.6 17.8 + - - +
68V THR* 1.3 86.2 + - + +
70V ALA* 1.3 62.1 + - - +
71V GLU* 3.9 8.4 + - - +
115V THR 4.4 1.0 - - - +
116V LEU* 3.8 19.2 - - + -
117V ARG* 3.3 27.6 + - - +
118V LEU* 4.0 23.3 - - + -
119V HIS* 3.6 20.7 + - - +
154V ARG 2.7 25.5 + - - +
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Residues in contact with ALA 70 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65V VAL 3.8 0.2 + - - -
66V LEU* 2.8 41.8 + - + +
67V ALA 4.4 1.2 + - - +
68V THR 3.8 0.9 - - - +
69V ARG* 1.3 79.6 - - - +
71V GLU* 1.3 65.9 + - - +
77V ALA 4.6 1.6 - - - +
78V ASP* 5.2 0.9 - - - -
79V VAL* 3.2 36.2 + - + +
107V LEU* 5.5 0.9 - - + -
112V LEU* 4.5 8.3 - - + -
116V LEU* 4.0 9.9 - - + -
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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