Contacts of the helix formed by residues 63 - 80 (chain o) in PDB entry 3J7Y
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 ALA 63 (chain o).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2081A U 2.6 41.3 + - - +
2082A G 3.2 25.6 - - - +
101Z LYS* 5.0 1.3 - - - +
83j GLU* 4.5 5.4 - - - -
62o HIS* 1.3 79.8 - - + +
64o ALA* 1.3 61.2 + - - +
65o VAL 3.5 0.9 - - - -
66o ARG* 3.1 14.3 + - - +
67o ARG* 3.0 26.4 + - + +
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Residues in contact with ALA 64 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2080A U 6.1 0.9 - - - -
2081A U 3.2 17.4 + - - +
61o GLY* 3.2 19.0 + - - +
63o ALA* 1.3 74.4 - - - +
65o VAL* 1.3 66.6 + - + +
67o ARG* 3.5 6.7 + - - +
68o ARG* 3.0 33.4 + - - +
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Residues in contact with VAL 65 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61o GLY 4.9 0.8 + - - -
62o HIS 5.0 1.2 + - - +
63o ALA 3.3 0.6 + - - -
64o ALA* 1.3 76.3 - - + +
66o ARG* 1.3 60.5 + - - +
68o ARG* 3.2 22.8 + - - +
69o GLU* 2.9 46.4 + - - +
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Residues in contact with ARG 66 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2082A G 3.0 35.5 + - - -
2083A U 3.0 30.5 + - - -
101Z LYS* 3.4 8.3 - - - +
79j LEU* 6.0 7.4 - - + +
80j LEU* 4.8 7.2 - - - +
83j GLU* 2.8 41.0 + - - +
62o HIS 5.5 0.2 + - - -
63o ALA* 3.1 10.8 + - - +
65o VAL* 1.3 80.2 - - - +
67o ARG* 1.3 63.9 + - - +
69o GLU* 3.2 9.5 + - + +
70o ALA* 2.9 32.1 + - - +
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Residues in contact with ARG 67 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2055A U 5.1 5.5 + - - -
2056A G 4.0 1.8 + - - -
2057A C 4.9 0.4 - - - +
2080A U 5.9 1.0 + - - -
2081A U 3.2 41.7 + - - -
2082A G 2.6 47.1 + - - +
2083A U 2.6 41.0 + - + +
2084A A 4.5 3.8 + - - +
63o ALA* 3.0 32.7 + - + +
64o ALA* 3.7 7.0 - - - +
65o VAL 3.2 0.2 - - - -
66o ARG* 1.3 81.1 - - - +
68o ARG* 1.3 59.2 + - - +
70o ALA* 3.2 8.8 + - - +
71o PHE* 2.9 28.8 + - - +
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Residues in contact with ARG 68 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64o ALA* 3.0 29.3 + - - +
65o VAL* 3.3 31.0 - - - +
67o ARG* 1.3 77.7 - - - +
69o GLU* 1.3 57.7 + - - +
71o PHE* 3.2 10.1 + - + +
72o GLU* 2.9 50.0 + - + +
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Residues in contact with GLU 69 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65o VAL* 2.9 29.3 + - - +
66o ARG* 3.2 13.6 + - + +
68o ARG* 1.3 78.4 - - - +
70o ALA* 1.3 57.3 + - - +
72o GLU* 3.0 29.4 + - + +
73o ALA* 2.9 30.3 + - - +
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Residues in contact with ALA 70 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2083A U 5.8 4.0 - - + +
2084A A 5.3 6.7 - - - +
66o ARG* 2.9 17.4 + - - +
67o ARG* 3.3 12.8 - - - +
69o GLU* 1.3 77.3 - - - +
71o PHE* 1.3 61.1 + - - +
73o ALA* 3.4 7.1 + - - +
74o ILE* 3.3 32.2 + - + +
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Residues in contact with PHE 71 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2054A U 3.2 49.4 - + - -
2055A U 3.3 37.2 - + - +
2084A A 3.0 39.4 - + - +
2085A A 5.1 1.1 - + - -
67o ARG 2.9 10.9 + - - +
68o ARG* 3.5 13.2 - - + +
70o ALA* 1.3 75.5 - - - +
72o GLU* 1.3 60.8 + - + +
74o ILE* 3.2 12.1 + - + +
75o LYS* 2.9 54.6 + - + +
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Residues in contact with GLU 72 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68o ARG* 2.9 30.1 + - + +
69o GLU* 3.0 30.8 - - + +
71o PHE* 1.3 80.0 - - + +
73o ALA* 1.3 56.2 + - - +
75o LYS* 3.2 22.2 + - - +
76o ALA* 2.9 29.3 + - - +
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Residues in contact with ALA 73 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69o GLU 2.9 11.2 + - - +
70o ALA* 3.7 11.0 - - - +
72o GLU* 1.3 76.9 - - - +
74o ILE* 1.3 57.1 - - + +
76o ALA* 3.2 8.9 + - - +
77o ALA* 2.9 29.3 + - - +
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Residues in contact with ILE 74 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2054A U 5.2 0.4 - - - +
2084A A 3.7 57.9 - - + +
2085A A 4.2 32.5 - - + +
70o ALA* 3.4 18.4 - - + +
71o PHE* 3.2 12.0 + - + +
73o ALA* 1.3 79.3 - - + +
75o LYS* 1.3 58.8 + - - +
77o ALA* 3.2 9.0 + - - +
78o ALA* 2.9 27.0 + - - +
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Residues in contact with LYS 75 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2054A U 3.4 59.5 - - + +
134g LYS* 6.1 2.2 - - - +
71o PHE* 2.9 43.9 + - + +
72o GLU* 3.3 22.4 - - - +
74o ILE* 1.3 77.7 - - - +
76o ALA* 1.3 56.4 + - - +
78o ALA* 3.2 3.8 + - - +
79o THR* 2.9 40.6 + - + +
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Residues in contact with ALA 76 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134g LYS* 5.9 1.8 - - - +
72o GLU 2.9 12.9 + - - +
73o ALA* 3.3 12.8 - - - +
75o LYS* 1.3 75.3 - - - +
77o ALA* 1.3 54.3 + - - +
79o THR* 2.6 23.9 + - - -
80o SER* 2.7 29.2 + - - +
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Residues in contact with ALA 77 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73o ALA 2.9 12.7 + - - +
74o ILE* 3.2 12.5 + - - +
76o ALA* 1.3 78.2 - - - +
78o ALA* 1.3 63.4 + - - +
80o SER* 3.5 19.8 - - - +
81o LYS* 3.9 5.9 - - - +
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Residues in contact with ALA 78 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2052A A 4.4 5.5 + - - -
2053A U 3.6 19.3 - - + +
2054A U 3.5 9.0 - - - +
2085A A 3.3 30.1 - - - +
74o ILE 2.9 9.6 + - - +
75o LYS 3.3 8.5 - - - +
77o ALA* 1.3 76.8 - - - +
79o THR* 1.3 64.6 + - + +
81o LYS* 3.4 22.3 + - - +
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Residues in contact with THR 79 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2053A U 4.2 29.2 - - + +
2054A U 5.6 2.0 - - + -
134g LYS* 3.9 26.7 + - - +
137g VAL* 5.4 0.4 - - - -
150g LYS* 2.8 32.7 + - - +
75o LYS* 2.9 26.5 + - + +
76o ALA* 2.6 27.5 + - - -
78o ALA* 1.3 76.4 - - + +
80o SER* 1.3 56.9 + - - -
81o LYS* 2.5 20.4 + - - +
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Residues in contact with SER 80 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137g VAL* 3.9 29.6 - - - +
76o ALA* 2.7 24.8 + - - +
77o ALA* 3.5 8.8 + - - +
79o THR* 1.3 71.2 + - - +
81o LYS* 1.3 59.9 + - - +
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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