Contacts of the helix formed by residues 45 - 53 (chain L) 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 ARG 45 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3800 A 4.0 14.3 + - - +
3810 G 2.6 35.5 + - - -
8L ILE* 4.3 4.3 - - - -
9L ARG* 5.7 2.2 + - - +
12L TRP* 3.5 64.8 + - + +
43L PRO* 3.2 3.3 - - - -
44L THR* 1.3 77.3 - - - +
46L LEU* 1.3 66.3 + - - +
47L ASP* 3.2 15.0 + - - +
48L ARG* 2.9 44.2 + - + +
49L ALA* 3.0 11.8 + - - +
118L TYR* 3.8 19.7 + - + +
119L SER 2.9 32.1 + - - +
120L VAL* 4.2 3.1 - - + -
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Residues in contact with LEU 46 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2630 U 3.4 26.7 - - - +
2640 G 3.2 30.5 - - - +
59F ILE* 4.1 18.4 - - + -
5L TYR* 3.5 15.5 - - + -
8L ILE* 3.9 15.3 - - + +
42L ARG* 6.2 0.9 - - - -
43L PRO* 3.8 19.3 + - + +
44L THR 3.7 3.6 + - - -
45L ARG* 1.3 73.3 - - - +
47L ASP* 1.3 62.2 + - - +
49L ALA* 3.4 0.3 + - - +
50L ARG* 3.0 44.6 + - + +
54L TYR* 4.0 15.9 - - + -
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Residues in contact with ASP 47 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2410 A 4.6 1.7 + - - -
3800 A 5.0 2.1 + - - -
5L TYR* 3.7 37.0 - - + +
8L ILE* 3.4 21.6 - - + +
9L ARG* 3.1 44.6 + - + +
12L TRP* 5.5 0.2 - - - -
45L ARG* 3.6 11.6 + - - +
46L LEU* 1.3 75.6 - - - +
48L ARG* 1.3 85.2 + - - +
50L ARG* 4.0 3.4 - - - +
51L SER* 2.9 26.1 + - - -
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Residues in contact with ARG 48 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3790 G 4.1 0.9 + - - -
3800 A 3.1 32.7 + - - +
3810 G 3.1 31.8 + - - -
4300 A 4.0 4.4 + - - -
4310 G 2.5 47.3 + - - -
45L ARG* 3.1 48.9 - - + +
47L ASP* 1.3 84.9 + - - +
49L ALA* 1.3 61.7 + - - +
51L SER* 3.2 11.1 + - - -
52L LEU* 3.0 41.4 + - - +
117L SER 5.5 0.6 + - - -
118L TYR* 3.8 23.9 - - + +
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Residues in contact with ALA 49 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43L PRO* 3.8 25.1 - - + -
45L ARG 3.0 6.7 + - - +
46L LEU 3.7 6.3 - - - +
48L ARG* 1.3 73.8 - - - +
50L ARG* 1.3 64.4 + - - +
52L LEU* 3.0 11.4 + - - +
53L GLY 3.0 0.5 + - - -
54L TYR* 2.8 45.8 + - + +
118L TYR* 4.1 11.4 - - + -
132L ILE* 3.9 13.0 - - + +
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Residues in contact with ARG 50 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2400 C 5.3 0.2 + - - -
2410 A 3.4 37.0 + - - +
2420 A 3.0 33.5 + - - -
2640 G 3.0 32.3 + - - -
2650 U 2.7 38.8 + - - -
5L TYR* 3.7 25.5 + - + -
46L LEU* 3.0 39.8 + - + +
47L ASP* 4.0 4.0 - - - +
49L ALA* 1.3 74.9 - - - +
51L SER* 1.3 62.7 + - - +
53L GLY* 3.1 13.2 + - - -
54L TYR* 3.6 24.7 + - + +
55L LYS* 4.7 2.6 - - - +
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Residues in contact with SER 51 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2400 C 4.6 0.2 - - - +
2410 A 3.5 17.9 + - - +
3790 G 2.8 66.1 + - - +
4310 G 3.4 9.9 + - - +
47L ASP 2.9 20.3 + - - -
48L ARG* 3.3 11.0 - - - -
50L ARG* 1.3 78.4 - - - +
52L LEU* 1.3 62.0 + - - +
53L GLY 3.7 0.2 + - - -
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Residues in contact with LEU 52 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4310 G 3.0 52.2 + - - +
4320 G 4.9 1.9 - - - +
48L ARG* 3.0 26.5 + - - +
49L ALA 3.0 8.1 + - - +
51L SER* 1.3 77.6 - - - +
53L GLY* 1.3 57.1 + - - +
54L TYR 3.8 0.2 - - - -
115L LEU* 3.0 18.4 - - - +
116L ASN* 3.4 34.6 + - + +
117L SER* 3.4 33.0 - - - +
118L TYR* 3.9 16.4 - - + -
132L ILE* 4.0 6.1 - - + -
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Residues in contact with GLY 53 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2400 C 5.3 8.1 - - - -
2410 A 6.1 0.2 - - - -
49L ALA 3.0 0.4 + - - -
50L ARG 3.1 9.4 + - - -
51L SER 3.4 0.8 + - - -
52L LEU* 1.3 80.5 - - - +
54L TYR* 1.3 66.6 + - - +
55L LYS* 3.5 8.3 + - - +
60L ILE* 4.9 0.5 - - - +
115L LEU* 4.1 11.4 - - - +
132L ILE* 5.4 0.4 - - - -
147L LEU* 4.1 22.2 - - - +
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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