Contacts of the helix formed by residues 68 - 90 (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 ASP 68 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67S PRO* 1.3 75.7 - - - +
69S PRO* 1.3 69.2 - - + +
70S VAL* 3.3 4.4 + - + +
71S GLU* 3.4 30.5 + - + +
72S GLU* 2.9 29.3 + - - +
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Residues in contact with PRO 69 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138R PRO* 5.1 19.5 - - + -
141R ILE* 5.7 9.0 - - + +
67S PRO 3.6 4.4 - - - +
68S ASP* 1.3 88.3 - - + +
70S VAL* 1.3 65.6 + - + +
72S GLU* 3.7 8.5 - - + +
73S THR* 2.9 37.6 + - + +
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Residues in contact with VAL 70 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68S ASP* 3.3 3.1 - - + -
69S PRO* 1.3 83.6 - - + +
71S GLU* 1.3 64.2 + - + +
73S THR* 2.4 24.7 + - - +
74S ARG* 2.9 31.1 + - + +
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Residues in contact with GLU 71 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67S PRO* 5.6 3.4 - - + +
68S ASP* 3.4 32.3 + - + +
70S VAL* 1.3 82.6 - - + +
72S GLU* 1.3 58.1 + - - +
74S ARG* 3.2 22.7 + - - +
75S HIS* 2.9 28.6 + - - +
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Residues in contact with GLU 72 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122R ARG* 3.1 38.0 + - - -
141R ILE* 3.8 10.9 - - + +
66S LEU* 5.5 0.5 - - - +
67S PRO* 3.2 40.8 - - + +
68S ASP 2.9 17.9 + - - +
69S PRO* 3.7 9.1 - - + +
71S GLU* 1.3 77.1 - - - +
73S THR* 1.3 57.1 + - + +
75S HIS* 3.2 11.5 + - + +
76S HIS* 2.9 55.6 + - + +
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Residues in contact with THR 73 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141R ILE* 3.4 30.5 - - + -
69S PRO* 2.9 23.4 + - + +
70S VAL* 2.4 31.9 + - - +
72S GLU* 1.3 77.3 - - - +
74S ARG* 1.3 54.2 + - - +
76S HIS* 3.2 10.5 + - + +
77S ALA* 2.9 29.3 + - - +
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Residues in contact with ARG 74 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70S VAL* 2.9 27.9 + - + +
71S GLU* 3.3 22.3 - - - +
73S THR* 1.3 77.5 + - - +
75S HIS* 1.3 57.6 + - - +
77S ALA* 3.2 9.5 + - + +
78S GLU* 2.9 51.1 + - + +
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Residues in contact with HIS 75 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71S GLU 2.9 12.2 + - - +
72S GLU* 3.4 14.1 - - + +
74S ARG* 1.3 76.1 - - - +
76S HIS* 1.3 65.3 + + - +
78S GLU* 3.2 20.1 + - + +
79S VAL* 2.9 47.5 + - + +
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Residues in contact with HIS 76 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122R ARG* 4.2 3.4 - - - -
141R ILE* 3.7 21.8 - - + +
142R PHE* 3.5 35.6 - + - -
72S GLU* 2.9 46.8 + - + +
73S THR* 3.3 10.3 - - + +
75S HIS* 1.3 83.1 - + + +
77S ALA* 1.3 58.2 + - - +
79S VAL* 3.2 10.1 + - - +
80S VAL* 2.9 36.7 + - + +
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Residues in contact with ALA 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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73S THR 2.9 13.0 + - - +
74S ARG* 3.2 12.5 + - + +
76S HIS* 1.3 76.9 - - - +
78S GLU* 1.3 57.5 + - + +
80S VAL* 3.2 9.9 + - - +
81S LYS* 2.9 28.6 + - - +
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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
----------------------------------------------------------
74S ARG* 2.9 42.4 + - + +
75S HIS* 3.3 22.4 + - - +
77S ALA* 1.3 76.7 - - + +
79S VAL* 1.3 57.7 + - - +
81S LYS* 3.2 10.1 + - - +
82S LYS* 2.9 37.9 + - - +
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Residues in contact with VAL 79 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75S HIS* 2.9 42.3 + - + +
76S HIS* 3.4 12.3 - - - +
78S GLU* 1.3 76.0 - - + +
80S VAL* 1.3 65.8 + - + +
82S LYS* 3.2 15.9 + - + +
83S VAL* 3.0 32.1 + - + +
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Residues in contact with VAL 80 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76S HIS* 2.9 22.8 + - + +
77S ALA* 3.2 11.4 + - - +
79S VAL* 1.3 79.6 - - + +
81S LYS* 1.3 56.5 + - - +
83S VAL* 3.2 10.1 + - - +
84S ASN* 2.9 27.2 + - - +
204S LEU* 4.0 47.3 - - + +
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Residues in contact with LYS 81 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77S ALA 2.9 13.2 + - - +
78S GLU* 3.4 12.6 - - - +
80S VAL* 1.3 77.8 - - - +
82S LYS* 1.3 56.6 + - + +
84S ASN* 3.2 9.6 + - + +
85S GLU* 2.9 52.9 + - + +
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Residues in contact with LYS 82 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78S GLU* 2.9 22.3 + - - +
79S VAL* 3.3 17.2 - - + +
81S LYS* 1.3 75.9 - - + +
83S VAL* 1.3 59.3 + - + +
85S GLU* 3.2 19.0 + - - +
86S MET* 2.9 38.6 + - + +
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Residues in contact with VAL 83 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79S VAL* 3.0 28.7 + - + +
80S VAL* 3.2 10.3 + - - +
82S LYS* 1.3 77.0 - - + +
84S ASN* 1.3 58.1 + - - +
86S MET* 3.2 14.0 + - - +
87S ILE* 2.9 40.9 + - + +
141S PHE* 3.8 40.2 - - + -
143S LEU* 4.2 7.4 - - + -
204S LEU* 3.9 14.1 - - + -
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Residues in contact with ASN 84 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80S VAL* 2.9 12.6 + - - +
81S LYS* 3.2 13.2 + - + +
83S VAL* 1.3 76.0 - - - +
85S GLU* 1.3 58.3 + - + +
87S ILE* 3.2 9.5 + - - +
88S VAL* 2.9 38.0 + - - +
202S PRO* 2.7 45.0 + - - +
204S LEU* 3.1 32.0 - - + +
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Residues in contact with GLU 85 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81S LYS* 2.9 48.2 + - + +
82S LYS* 3.4 18.7 - - - +
84S ASN* 1.3 78.8 - - + +
86S MET* 1.3 57.3 + - + +
88S VAL* 3.2 8.4 + - - +
89S THR* 2.9 36.4 + - + +
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Residues in contact with MET 86 (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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82S LYS* 2.9 23.0 + - + +
83S VAL* 3.2 18.8 + - - +
85S GLU* 1.3 76.7 - - + +
87S ILE* 1.3 62.1 + - + +
89S THR* 2.7 21.1 + - - -
90S GLY 3.2 9.2 + - - -
91S GLN* 3.2 39.4 + - + +
92S TYR* 4.6 5.2 + - - +
140S ASN* 3.7 29.8 - - + +
141S PHE* 3.6 33.9 - - + -
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Residues in contact with ILE 87 (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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83S VAL* 2.9 36.1 + - + +
84S ASN* 3.2 8.9 + - - +
86S MET* 1.3 75.5 - - - +
88S VAL* 1.3 63.9 + - - +
90S GLY* 3.3 12.1 + - - -
92S TYR* 4.4 18.8 + - + -
141S PHE* 4.0 25.4 - - + -
143S LEU* 4.8 1.3 - - + -
200S ILE* 4.3 20.9 - - + +
201S ALA 3.5 37.0 - - - +
202S PRO* 3.9 8.5 - - + -
204S LEU* 4.1 15.5 - - + -
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Residues in contact with VAL 88 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84S ASN* 2.9 23.0 + - - +
85S GLU* 3.4 11.0 - - - +
87S ILE* 1.3 75.9 - - - +
89S THR* 1.3 66.4 + - + +
90S GLY* 3.3 1.6 + - - -
202S PRO* 3.9 26.2 - - + -
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Residues in contact with THR 89 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85S GLU* 2.9 19.2 + - + +
86S MET* 2.7 25.3 + - - -
88S VAL* 1.3 81.0 - - + +
90S GLY* 1.3 60.6 + - - +
91S GLN* 3.4 22.7 + - + +
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Residues in contact with GLY 90 (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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86S MET 3.2 3.6 + - - -
87S ILE 3.3 9.0 + - - -
88S VAL 3.2 5.8 + - - -
89S THR* 1.3 77.8 - - - +
91S GLN* 1.3 62.7 + - - +
92S TYR* 3.2 27.7 - - - +
312c ARG* 5.3 7.0 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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