Contacts of the helix formed by residues 55 - 73 (chain s) 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 SER 55 (chain s).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2325A U 3.4 34.3 + - - -
2326A C 2.6 27.5 + - - -
53s ALA* 3.2 4.0 + - - +
54s ASP* 1.3 78.2 + - - +
56s LYS* 1.3 61.4 + - - +
58s ALA* 3.1 15.8 + - - +
59s ARG* 3.0 26.7 + - - +
62s ARG* 4.8 2.5 + - - +
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Residues in contact with LYS 56 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2324A U 3.2 53.4 + - - +
2325A U 3.2 12.6 + - - +
55s SER* 1.3 72.6 - - - +
57s ALA* 1.3 60.9 + - - +
59s ARG* 3.2 11.7 + - - +
60s LEU* 2.9 35.9 + - + +
226s ILE* 4.4 24.2 - - + -
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Residues in contact with ALA 57 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1480 PRO* 5.7 1.1 - - + -
1490 PHE* 4.2 9.0 - - + -
2325A U 2.8 36.6 + - - +
2326A C 4.7 0.4 - - - +
49s ALA* 3.7 21.5 - - + +
55s SER* 4.5 0.4 - - - +
56s LYS* 1.3 75.4 - - - +
58s ALA* 1.3 58.5 + - - +
60s LEU* 3.2 11.6 + - - +
61s ARG* 2.9 28.8 + - - +
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Residues in contact with ALA 58 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2326A C 4.3 0.4 - - - +
49s ALA* 4.1 1.9 - - - +
50s SER 3.2 26.3 - - - +
53s ALA* 3.0 32.3 - - + +
55s SER* 3.1 18.7 + - - +
56s LYS 3.2 0.4 - - - -
57s ALA* 1.3 78.7 - - - +
59s ARG* 1.3 56.3 + - - +
61s ARG* 3.2 4.9 + - - +
62s ARG* 2.9 38.9 + - - +
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Residues in contact with ARG 59 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2446A A 4.5 1.7 - - - +
2447A A 2.8 42.6 + - - +
55s SER 3.0 15.2 + - - +
56s LYS* 3.2 13.4 + - - +
58s ALA* 1.3 75.7 - - - +
60s LEU* 1.3 68.5 + - - +
62s ARG* 3.2 19.7 + - - +
63s ILE* 2.9 56.0 + - + +
226s ILE* 3.5 52.4 + - - +
227s ASP* 5.2 0.2 - - - +
228s ASP* 4.3 19.0 + - - +
382s GLN* 6.1 0.2 - - - +
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Residues in contact with LEU 60 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56s LYS* 2.9 19.6 + - + +
57s ALA* 3.2 13.9 + - - +
59s ARG* 1.3 93.0 - - - +
61s ARG* 1.3 57.9 + - - +
63s ILE* 3.2 10.4 + - + +
64s GLU* 2.9 45.1 + - - +
226s ILE* 6.4 0.9 - - + -
382s GLN* 4.3 21.7 + - + +
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Residues in contact with ARG 61 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46s PRO* 5.7 1.6 - - - +
48s VAL* 3.1 41.9 - - - +
49s ALA* 2.8 36.9 + - + +
50s SER* 3.7 3.1 - - - +
51s MET* 3.6 33.1 - - + +
57s ALA 2.9 13.3 + - - +
58s ALA* 3.4 11.0 - - - +
60s LEU* 1.3 75.9 - - - +
62s ARG* 1.3 57.6 + - - +
64s GLU* 3.2 21.8 + - - +
65s ARG* 2.9 27.6 + - + +
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Residues in contact with ARG 62 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2328A C 4.9 1.2 - - - +
2329A C 5.6 1.8 - - - +
2446A A 3.4 44.0 + - - +
2447A A 5.3 6.2 + - - -
2448A G 5.6 3.8 + - - -
2449A G 5.8 0.4 + - - -
3338A MG 3.7 20.6 - - - -
51s MET* 2.8 25.4 + - + +
52s THR* 3.4 15.2 + - - +
53s ALA 2.3 35.9 + - - -
54s ASP* 4.4 3.4 + - - +
55s SER 4.8 3.0 + - - +
58s ALA* 2.9 20.9 + - - +
59s ARG* 3.2 23.1 + - - +
61s ARG* 1.3 76.1 - - - +
63s ILE* 1.3 56.8 - - - +
65s ARG* 3.2 21.4 + - - +
66s TRP* 2.9 29.5 + - - +
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Residues in contact with ILE 63 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2446A A 3.8 22.2 - - - +
2447A A 4.9 0.2 - - - +
59s ARG* 2.9 58.0 + - - +
60s LEU* 3.4 12.1 - - + +
62s ARG* 1.3 76.3 - - - +
64s GLU* 1.3 57.0 + - + +
66s TRP* 3.2 27.5 + - + -
67s GLN* 2.9 42.7 + - - +
382s GLN* 4.0 24.9 - - - +
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Residues in contact with GLU 64 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60s LEU* 2.9 36.7 + - - +
61s ARG* 3.3 26.2 + - - +
63s ILE* 1.3 77.2 - - + +
65s ARG* 1.3 59.0 + - - +
67s GLN* 3.2 16.5 + - - +
68s ALA* 2.9 28.6 + - - +
348s GLU* 6.2 0.2 - - - +
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Residues in contact with ARG 65 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2444A A 5.1 0.2 + - - -
2445A U 2.4 42.9 + - - -
2446A A 4.4 10.8 + - - -
51s MET* 3.3 47.0 - - + +
61s ARG 2.9 12.6 + - - +
62s ARG* 3.3 20.1 - - - +
64s GLU* 1.3 76.7 - - - +
66s TRP* 1.3 62.9 + - - +
68s ALA* 3.2 22.6 + - - +
69s THR* 3.2 15.4 + - + +
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Residues in contact with TRP 66 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2446A A 3.2 82.8 - + + +
62s ARG 2.9 13.0 + - - +
63s ILE* 3.3 42.0 - - + +
65s ARG* 1.3 80.8 - - - +
67s GLN* 1.3 79.8 - - + +
69s THR* 2.5 31.1 + - - -
70s VAL* 3.2 24.6 - - + +
82s ILE* 3.6 11.0 - - + +
83s LEU* 4.8 17.3 - - + -
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Residues in contact with GLN 67 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63s ILE* 2.9 34.8 + - - +
64s GLU* 3.4 17.5 - - - +
66s TRP* 1.3 99.2 - - + +
68s ALA* 1.3 58.0 + - - +
70s VAL* 3.2 7.1 + - - -
71s HIS* 2.9 28.0 + - + +
346s TRP* 3.0 23.9 - - + -
347s SER* 4.8 4.4 + - - -
348s GLU* 3.2 47.9 + - - +
382s GLN* 4.0 11.0 + - - +
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Residues in contact with ALA 68 (chain s).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64s GLU 2.9 13.3 + - - +
65s ARG* 3.2 14.6 - - - +
67s GLN* 1.3 75.8 - - - +
69s THR* 1.3 57.0 + - + +
71s HIS* 3.2 12.6 + - - +
72s ALA* 2.9 29.4 + - - +
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Residues in contact with THR 69 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65s ARG* 3.2 17.2 + - + +
66s TRP* 2.5 25.9 + - - -
68s ALA* 1.3 75.3 - - + +
70s VAL* 1.3 69.6 + - - +
72s ALA* 3.1 10.1 + - - +
73s ALA* 3.1 20.6 + - - +
82s ILE* 4.5 9.7 - - - +
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Residues in contact with VAL 70 (chain s).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66s TRP* 3.2 31.0 - - + +
67s GLN* 3.2 6.2 + - + +
69s THR* 1.3 81.7 + - - +
71s HIS* 1.3 60.8 + - - +
73s ALA* 3.2 9.5 + - - +
79s LYS* 3.3 53.0 - - + +
82s ILE* 3.3 32.8 - - + -
83s LEU* 4.1 10.1 - - + -
346s TRP* 3.2 30.1 - - + -
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Residues in contact with HIS 71 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67s GLN* 2.9 12.8 + - + -
68s ALA* 3.2 13.6 + - - +
70s VAL* 1.3 77.9 - - - +
72s ALA* 1.3 61.8 + - - +
73s ALA 3.3 1.6 + - - +
79s LYS* 3.5 20.4 + - - +
346s TRP* 3.0 48.3 - + - -
348s GLU* 4.3 17.0 - - + -
349s ALA* 3.8 21.7 + - + +
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Residues in contact with ALA 72 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68s ALA 2.9 12.9 + - - +
69s THR* 3.1 14.3 + - - +
71s HIS* 1.3 76.4 - - - +
73s ALA* 1.3 65.9 + - - +
74s GLU* 3.3 17.8 + - - +
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Residues in contact with ALA 73 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69s THR 3.1 10.7 + - - +
70s VAL 3.2 13.8 + - - +
71s HIS 3.6 0.7 - - - +
72s ALA* 1.3 77.6 - - - +
74s GLU* 1.3 61.5 + - - +
75s SER 3.4 0.9 - - - +
78s GLU* 4.1 19.3 - - + +
79s LYS* 3.0 37.6 - - + -
82s ILE* 4.3 16.2 - - + -
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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