Contacts of the helix formed by residues 52 - 65 (chain B) in PDB entry 1JG0
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 LEU 52 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B PHE* 3.8 30.1 - - + -
44B LEU* 3.6 37.2 - - + -
51B HIS* 1.3 79.0 - - - +
53B ARG* 1.3 65.5 + - - +
54B SER 3.3 3.1 - - - -
55B ILE* 3.1 19.3 + - + -
56B ILE* 2.8 45.1 + - + +
176B PHE* 4.5 5.8 - - + -
179B ALA* 3.7 15.3 - - + +
183B LEU* 5.8 2.9 - - + -
230B LEU* 6.4 0.2 - - + -
249B ILE* 4.5 18.6 - - + -
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Residues in contact with ARG 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B HIS* 3.5 9.4 - - + +
52B LEU* 1.3 78.3 - - - +
54B SER* 1.3 76.9 + - - +
56B ILE* 4.7 0.9 - - - +
57B HIS* 3.3 32.6 + - + +
75B ASN 2.8 24.7 + - - -
76B ASN* 2.8 33.2 + - - +
77B VAL* 4.1 5.2 - - - +
244B PHE* 3.4 32.5 - - + -
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Residues in contact with SER 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B HIS* 4.9 2.5 + - - +
52B LEU 3.3 0.2 - - - -
53B ARG* 1.3 90.6 + - - +
55B ILE* 1.3 57.9 + - - +
57B HIS* 3.4 2.4 + - - +
58B GLU* 2.8 30.7 + - - +
77B VAL* 3.9 26.5 - - - +
78B THR 5.3 0.5 + - - -
79B ILE* 3.8 25.4 - - - +
306B DDT 4.2 22.6 + - - -
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Residues in contact with ILE 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B LEU* 3.1 26.6 + - + +
54B SER* 1.3 74.1 - - - +
56B ILE* 1.3 63.1 + - - +
58B GLU* 3.5 15.2 + - - +
59B LEU* 2.9 28.1 + - + +
79B ILE* 4.6 0.9 - - + -
176B PHE* 3.6 35.9 - - + +
179B ALA* 4.5 2.0 - - + -
180B SER* 3.1 46.5 + - - +
183B LEU* 4.7 8.3 - - + -
306B DDT 3.6 30.7 - - + -
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Residues in contact with ILE 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B LEU* 2.8 39.5 + - + +
53B ARG* 3.8 4.3 - - - +
55B ILE* 1.3 73.1 - - - +
57B HIS* 1.3 66.9 - - - +
59B LEU* 3.1 4.0 + - - +
60B LEU* 2.9 24.8 + - + +
183B LEU* 3.7 25.4 - - + -
244B PHE* 3.6 32.8 - - + +
247B PHE* 3.6 48.9 - - + +
249B ILE* 6.3 2.2 - - + -
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Residues in contact with HIS 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B ARG* 3.3 28.0 + - + -
54B SER 3.8 5.8 - - - +
56B ILE* 1.3 78.4 - - - +
58B GLU* 1.3 64.4 + - - +
60B LEU* 3.2 3.8 + - - +
61B TRP* 2.9 24.5 + - - +
71B TYR* 2.8 44.7 - + + -
72B LEU* 4.3 2.9 - - + -
75B ASN* 3.6 28.7 + - + -
77B VAL* 3.8 22.5 - - + +
244B PHE* 3.3 45.4 - + + +
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Residues in contact with GLU 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B SER 2.8 18.9 + - - +
55B ILE* 3.7 20.9 - - - +
57B HIS* 1.3 76.7 - - - +
59B LEU* 1.3 57.1 + - - +
61B TRP* 3.1 15.8 + - + +
62B PHE* 2.8 59.6 + - + -
72B LEU* 4.1 8.4 - - + +
79B ILE* 3.9 19.6 - - + +
80B TRP* 2.8 29.7 + - + +
147B HIS* 5.7 3.0 + - - -
180B SER* 4.4 6.4 + - - -
306B DDT 4.4 9.9 - - - -
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Residues in contact with LEU 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ILE* 2.9 18.5 + - + +
56B ILE* 3.1 5.1 + - - +
58B GLU* 1.3 76.0 - - - +
60B LEU* 1.3 65.7 + - + +
62B PHE* 3.2 12.9 + - + +
63B LEU* 3.1 28.1 + - + +
98B TRP* 3.9 30.7 - - + -
180B SER* 3.8 27.4 - - - +
183B LEU* 4.0 13.7 - - + -
184B LEU* 3.9 22.2 - - + +
187B MET* 3.7 27.4 - - - -
247B PHE* 6.4 0.2 - - + -
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Residues in contact with LEU 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B ILE* 2.9 23.0 + - + +
57B HIS* 3.6 7.2 - - - +
59B LEU* 1.3 77.9 - - + +
61B TRP* 1.3 60.8 + - - +
63B LEU* 3.4 9.4 + - + +
64B GLN* 3.2 29.4 + - + +
71B TYR* 4.0 20.2 - - + +
187B MET* 4.3 12.1 - - + -
242B TYR* 3.8 33.2 - - + +
243B ARG* 3.7 6.7 - - - -
244B PHE* 3.3 37.7 - - + +
247B PHE* 4.2 10.1 - - + -
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Residues in contact with TRP 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B HIS 2.9 13.4 + - - +
58B GLU* 3.2 16.8 - - + +
60B LEU* 1.3 75.5 - - - +
62B PHE* 1.3 102.5 + + - +
64B GLN* 3.4 7.1 + - - +
65B GLY 3.5 1.4 + - - -
66B ASP* 2.8 66.6 + - - +
67B THR* 3.7 19.5 - - + -
68B ASN 3.0 21.8 + - - -
69B ILE* 4.4 0.4 - - + +
71B TYR* 3.8 29.3 - + + -
72B LEU* 3.9 23.8 - - + +
80B TRP* 3.5 24.9 - + - -
90B LEU* 3.4 26.0 - - + -
93B VAL* 4.8 5.6 - - + -
95B GLY 6.1 0.2 - - - -
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Residues in contact with PHE 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B GLU* 2.8 44.2 + - + -
59B LEU* 3.2 17.9 + - + +
61B TRP* 1.3 108.9 - + - +
63B LEU* 1.3 56.8 + - - +
65B GLY* 2.9 17.5 + - - -
80B TRP* 4.4 0.9 - + - -
93B VAL* 6.0 0.2 - - + -
94B TYR* 3.7 43.5 - + + -
95B GLY* 3.3 21.2 - - - +
98B TRP* 3.6 37.4 - + + -
99B ARG* 4.1 2.8 - - - +
147B HIS* 3.9 20.0 - + - -
180B SER* 5.9 4.9 - - - -
181B TYR* 6.2 1.1 - + - -
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Residues in contact with LEU 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B LEU* 3.1 22.1 + - + +
60B LEU* 3.7 13.2 - - + +
61B TRP 3.3 0.2 - - - -
62B PHE* 1.3 80.9 - - - +
64B GLN* 1.3 60.1 + - - +
98B TRP* 3.9 24.2 - - + -
99B ARG* 2.8 32.2 + - - +
112B ILE* 4.2 26.9 - - + -
184B LEU* 4.5 10.8 - - + -
187B MET* 3.5 32.3 - - + -
239B ILE* 3.9 18.6 - - + +
240B PHE* 3.4 13.4 - - + -
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Residues in contact with GLN 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B LEU 3.2 15.7 + - - +
61B TRP* 3.8 3.8 - - - +
62B PHE 3.2 1.0 - - - -
63B LEU* 1.3 78.9 - - - +
65B GLY* 1.3 61.8 + - - +
66B ASP* 3.4 21.7 + - - +
99B ARG* 4.0 11.0 + - - +
240B PHE* 2.9 38.4 + - - +
242B TYR 5.9 0.2 + - - -
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Residues in contact with GLY 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B TRP 3.5 0.6 + - - -
62B PHE 2.9 11.2 + - - -
63B LEU 3.1 0.6 - - - -
64B GLN* 1.3 79.0 - - - +
66B ASP* 1.3 60.4 + - - +
67B THR 4.1 0.9 + - - -
95B GLY 3.3 26.0 - - - +
96B LYS* 3.9 20.8 + - - +
99B ARG* 3.6 12.1 - - - +
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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