Contacts of the helix formed by residues 75 - 85 (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 75 (chain s).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73s ALA* 3.4 0.6 - - - +
74s GLU* 1.3 78.9 - - - +
76s VAL* 1.3 65.9 + - - +
77s ASP* 4.3 8.5 - - - -
78s GLU* 2.9 42.4 + - - +
79s LYS* 3.4 23.8 + - - +
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Residues in contact with VAL 76 (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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75s SER* 1.3 74.4 - - - +
77s ASP* 1.3 64.2 + - - +
79s LYS* 3.2 12.3 + - + +
80s LEU* 2.9 38.9 + - + +
288s THR* 5.0 3.1 - - + -
341s MET 3.2 25.6 - - - +
342s TYR* 3.6 23.3 - - - +
343s GLN* 4.9 1.1 - - - -
344s GLY* 4.1 15.5 - - - +
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Residues in contact with ASP 77 (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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75s SER* 3.2 7.2 - - - -
76s VAL* 1.3 80.2 + - - +
78s GLU* 1.3 58.2 + - + +
80s LEU* 3.2 13.1 + - - +
81s ARG* 2.9 28.8 + - - +
288s THR* 2.5 42.2 + - - +
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Residues in contact with GLU 78 (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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73s ALA* 4.1 17.4 - - + +
74s GLU* 4.4 4.5 + - - +
75s SER* 2.9 29.6 + - - +
76s VAL 3.2 0.6 - - - -
77s ASP* 1.3 81.4 - - + +
79s LYS* 1.3 58.1 + - - +
81s ARG* 3.2 9.5 + - - +
82s ILE* 2.9 39.0 + - + +
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Residues in contact with LYS 79 (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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70s VAL* 3.3 32.8 - - + +
71s HIS* 3.5 17.0 + - - +
73s ALA* 3.0 27.5 + - + -
74s GLU 5.6 0.4 - - - -
75s SER 3.4 14.5 + - - +
76s VAL* 3.2 13.8 + - + +
78s GLU* 1.3 79.5 - - - +
80s LEU* 1.3 58.6 + - + +
82s ILE* 3.2 6.7 + - - +
83s LEU* 2.9 35.8 + - + +
344s GLY* 5.3 14.5 - - - -
345s PHE 5.7 0.8 - - - +
346s TRP* 4.0 20.6 - - - +
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Residues in contact with LEU 80 (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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76s VAL* 2.9 23.9 + - + +
77s ASP* 3.3 8.3 - - - +
79s LYS* 1.3 77.3 - - + +
81s ARG* 1.3 57.9 + - - +
83s LEU* 3.2 9.7 + - + +
84s THR* 2.9 36.4 + - + +
282s ILE* 4.5 22.5 - - + +
288s THR* 4.0 26.7 - - + -
341s MET* 3.5 49.1 - - + +
342s TYR* 4.8 11.7 - - + -
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Residues in contact with ARG 81 (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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2442A U 2.7 23.5 + - - -
2443A C 3.1 25.7 + - - -
77s ASP 2.9 13.0 + - - +
78s GLU* 3.2 13.2 + - - +
80s LEU* 1.3 75.7 - - - +
82s ILE* 1.3 56.6 + - + +
84s THR* 2.6 24.1 + - - +
85s LYS* 2.6 41.1 + - - +
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Residues in contact with ILE 82 (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 2.8 32.6 + - - +
66s TRP* 3.6 14.3 + - + +
69s THR* 4.5 8.5 - - - +
70s VAL* 3.3 44.6 - - + +
73s ALA* 4.3 11.0 - - + -
78s GLU* 2.9 30.3 + - + +
79s LYS* 3.2 6.9 + - - +
81s ARG* 1.3 78.3 - - + +
83s LEU* 1.3 61.6 + - - +
85s LYS* 3.7 16.7 + - + +
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Residues in contact with LEU 83 (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 4.0 10.7 - - - +
66s TRP* 4.8 18.9 - - + -
70s VAL* 4.1 13.9 - - + -
79s LYS* 2.9 22.8 + - + +
80s LEU* 3.2 12.1 + - + +
82s ILE* 1.3 78.6 - - - +
84s THR* 1.3 61.7 + - - +
209s TYR* 4.3 14.9 + - + -
282s ILE* 4.8 3.1 - - + -
341s MET* 3.6 33.2 - - + -
346s TRP* 3.9 42.0 - - + +
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Residues in contact with THR 84 (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 5.0 0.2 - - - +
80s LEU* 2.9 18.1 + - + +
81s ARG* 2.6 29.5 + - - +
82s ILE 4.0 0.4 - - - -
83s LEU* 1.3 79.4 - - - +
85s LYS* 1.3 54.2 + - - -
86s MET* 2.6 20.9 + - - +
209s TYR* 5.0 2.2 + - + -
280s ASN* 3.1 55.4 + - + +
281s HIS* 4.4 0.9 - - - +
282s ILE* 3.8 27.6 - - + +
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Residues in contact with LYS 85 (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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2441A C 3.8 7.3 + - - +
2442A U 3.6 23.6 + - - +
2443A C 2.8 38.8 + - - +
2446A A 3.5 28.0 + - - +
81s ARG* 2.6 44.2 + - - +
82s ILE* 3.7 15.2 + - + +
84s THR* 1.3 70.6 + - - +
86s MET* 1.3 70.6 - - + +
87s GLN* 3.0 14.3 + - - +
280s ASN* 5.1 0.4 - - - -
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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