Contacts of the helix formed by residues 46 - 60 (chain J) 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 ILE 46 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30J MET* 3.6 30.5 - - + -
35J LEU* 4.1 26.3 - - + +
36J GLY* 4.3 25.4 - - - +
39J LEU* 5.7 2.2 - - + -
40J GLY* 5.8 2.7 - - - -
44J VAL* 3.9 19.3 - - + +
45J SER* 1.3 73.7 - - - +
47J ASN* 1.3 65.6 + - - +
48J GLN 3.2 1.1 - - - -
49J PHE* 3.2 7.1 + - + +
50J CYS* 2.9 27.2 + - - +
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Residues in contact with ASN 47 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30J MET* 4.2 19.5 - - + -
45J SER* 5.7 2.4 - - - -
46J ILE* 1.3 82.4 - - - +
48J GLN* 1.3 85.6 + - - +
50J CYS* 3.1 10.3 - - - -
51J LYS* 2.9 31.8 + - - +
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Residues in contact with GLN 48 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45J SER* 4.3 21.3 - - - +
46J ILE 3.2 0.4 - - - +
47J ASN* 1.3 94.0 + - - +
49J PHE* 1.3 57.3 + - - +
51J LYS* 3.2 25.4 + - - +
52J GLU* 2.9 37.5 + - + +
78J PHE* 5.1 7.6 - - + -
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Residues in contact with PHE 49 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20J ILE* 6.4 0.4 - - + -
22J ALA* 5.3 7.2 - - + -
24J VAL* 5.6 3.1 - - + -
29J ALA* 6.4 0.2 - - + -
35J LEU* 4.8 10.3 - - + -
39J LEU* 3.5 39.9 - - + -
44J VAL* 4.9 13.2 - - + -
45J SER 3.5 16.9 + - - +
46J ILE* 3.2 11.6 + - - +
48J GLN* 1.3 78.4 - - - +
50J CYS* 1.3 62.9 + - - +
52J GLU* 3.2 9.4 + - - +
53J PHE* 2.9 46.3 + + + +
68J THR* 5.4 2.2 - - + -
70J ILE* 3.8 47.1 - - + -
78J PHE* 4.7 11.6 - + + -
80J ILE* 4.3 9.5 - - + +
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Residues in contact with CYS 50 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28J LEU* 6.5 1.1 - - - -
29J ALA* 4.1 11.4 - - + -
30J MET* 3.8 34.8 - - + -
35J LEU* 3.9 7.0 - - + -
46J ILE 2.9 12.9 + - - +
47J ASN* 3.1 19.0 + - - +
49J PHE* 1.3 81.1 - - - +
51J LYS* 1.3 59.9 + - - +
53J PHE* 3.2 3.5 + - - +
54J ASN* 2.7 45.1 + - - +
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Residues in contact with LYS 51 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47J ASN* 2.9 15.2 + - - +
48J GLN* 3.3 28.9 - - - +
50J CYS* 1.3 82.4 - - - +
52J GLU* 1.3 58.9 + - + +
54J ASN* 3.2 11.2 + - + +
55J GLU* 2.9 29.5 + - + +
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Residues in contact with GLU 52 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48J GLN* 2.9 22.5 + - + +
49J PHE* 3.4 6.7 - - - +
51J LYS* 1.3 77.6 - - + +
53J PHE* 1.3 57.2 + - - +
55J GLU* 3.2 16.1 + - - +
56J ARG* 2.9 35.2 + - + +
78J PHE* 6.0 5.6 - - + -
80J ILE* 3.4 31.9 + - + +
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Residues in contact with PHE 53 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22J ALA* 5.7 0.2 - - + -
24J VAL* 3.2 35.2 - - + -
25J ARG 3.1 26.5 - - - -
26J ALA* 4.8 1.3 - - - -
29J ALA* 3.9 18.2 - - + -
49J PHE* 2.9 31.0 + + + +
50J CYS* 3.2 9.6 + - - +
52J GLU* 1.3 77.3 - - - +
54J ASN* 1.3 57.6 + - - +
56J ARG* 3.2 8.6 + - + +
57J THR* 2.9 42.6 + - - -
66J LEU* 3.5 20.2 - - + -
68J THR* 3.8 28.7 - - + -
80J ILE* 4.5 9.4 - - + +
82J ILE* 4.8 7.9 - - + -
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Residues in contact with ASN 54 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26J ALA 5.3 2.5 - - - +
27J GLY 4.7 8.4 + - - +
28J LEU* 4.3 20.4 - - - +
29J ALA* 3.1 24.2 + - - +
50J CYS* 2.7 28.6 + - - +
51J LYS* 3.4 11.2 - - + +
53J PHE* 1.3 74.1 - - - +
55J GLU* 1.3 57.9 + - - +
57J THR* 3.2 10.3 + - - -
58J LYS* 2.9 29.7 + - - +
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Residues in contact with GLU 55 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51J LYS* 2.9 13.9 + - + +
52J GLU* 3.3 20.9 - - - +
54J ASN* 1.3 76.4 - - - +
56J ARG* 1.3 57.6 + - + +
58J LYS* 3.2 14.6 + - - +
59J ASP* 2.9 48.7 + - - +
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Residues in contact with ARG 56 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52J GLU* 2.9 19.9 + - + +
53J PHE* 3.2 11.9 + - + +
55J GLU* 1.3 78.9 - - + +
57J THR* 1.3 60.8 + - - +
59J ASP* 3.2 28.5 + - - +
60J ILE* 3.0 25.3 + - - +
80J ILE* 3.3 48.7 + - + +
81J LYS* 5.4 0.6 - - - +
82J ILE* 3.9 43.0 - - + +
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Residues in contact with THR 57 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26J ALA* 3.2 47.0 + - + +
53J PHE* 2.9 31.8 + - - -
54J ASN* 3.2 9.4 + - - -
56J ARG* 1.3 77.1 - - - +
58J LYS* 1.3 59.1 + - - +
60J ILE* 3.0 16.0 - - - +
61J LYS 2.8 27.4 - - - +
62J GLU* 3.8 21.1 - - + +
66J LEU* 4.3 9.2 - - + +
82J ILE* 5.2 0.2 - - - +
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Residues in contact with LYS 58 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54J ASN 2.9 13.2 + - - +
55J GLU* 3.4 20.6 - - - +
57J THR* 1.3 77.8 - - - +
59J ASP* 1.3 57.1 + - - +
60J ILE 2.7 16.7 + - - +
61J LYS 5.1 2.0 + - - -
62J GLU* 3.6 28.0 + - - +
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Residues in contact with ASP 59 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55J GLU* 2.9 35.1 + - - +
56J ARG* 3.2 25.4 + - - +
58J LYS* 1.3 74.0 - - - +
60J ILE* 1.3 66.3 + - - +
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Residues in contact with ILE 60 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56J ARG 3.0 15.7 + - - +
57J THR* 3.0 13.6 - - - +
58J LYS* 2.7 19.2 + - - +
59J ASP* 1.3 76.6 - - - +
61J LYS* 1.3 78.6 + - + +
66J LEU* 3.6 35.9 - - + -
82J ILE* 5.3 7.0 - - + -
84J GLN* 6.4 2.0 - - + -
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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
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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