Contacts of the strand formed by residues 39 - 52 (chain J) in PDB entry 4M7A
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 39 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3I PHE* 3.7 2.5 - - - -
8J LEU* 5.7 0.4 - - + -
18J ILE* 3.7 22.4 - - + -
30J LEU* 4.0 11.0 - - + -
32J ALA 3.2 12.1 - - - +
33J PHE* 3.8 8.1 - - + -
37J SER 3.5 13.0 - - - +
38J ASN* 1.3 84.9 - - - +
40J VAL* 1.3 69.3 + - - +
41J LEU* 3.7 29.2 - - + -
67J PHE* 3.2 3.3 - - - -
68J ILE* 2.5 54.8 + - + +
73J VAL* 4.5 8.3 - - + -
76J ILE* 3.7 24.0 - - + -
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Residues in contact with VAL 40 (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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3I PHE* 3.6 22.0 - - + -
6I PHE* 3.9 29.8 - - + -
72I LEU* 4.9 1.6 - - + -
82I LEU* 4.6 5.2 - - + -
31J GLN* 2.9 27.7 + - + -
32J ALA* 2.9 27.1 + - + +
39J ILE* 1.3 79.8 - - - +
41J LEU* 1.3 67.0 + - - +
65J MET* 3.5 31.6 - - + -
66J VAL 3.4 11.0 - - - +
67J PHE* 4.3 8.5 - - + -
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Residues in contact with LEU 41 (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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16J VAL* 3.8 11.4 - - + -
18J ILE* 3.9 24.0 - - + -
26J LEU* 4.8 6.1 - - + -
27J VAL 4.8 1.3 - - - -
28J GLY* 4.0 21.5 - - - +
29J THR 2.9 36.3 - - - +
30J LEU* 3.1 19.1 - - + +
39J ILE* 3.7 13.0 - - + +
40J VAL* 1.3 73.9 - - - +
42J SER* 1.3 61.1 + - - +
44J ALA* 4.2 9.4 - - + -
65J MET* 3.3 9.4 - - - +
66J VAL* 2.8 46.7 + - + +
68J ILE* 4.4 7.4 - - + -
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Residues in contact with SER 42 (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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74I LYS* 4.2 14.6 - - - -
28J GLY* 3.8 0.2 - - - -
29J THR* 3.0 34.6 + - - +
31J GLN* 2.9 23.9 + - - -
41J LEU* 1.3 74.3 - - - +
43J ASP* 1.3 77.2 + - - +
44J ALA 3.2 2.3 + - - -
64J GLU 2.8 9.4 - - - -
65J MET* 3.5 20.2 - - - -
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Residues in contact with ASP 43 (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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74I LYS* 2.6 35.2 + - - -
15J ARG* 5.4 4.9 + - - -
27J VAL 4.0 1.6 - - - +
28J GLY* 4.0 7.3 - - - -
29J THR* 4.1 15.4 - - + +
42J SER* 1.3 75.7 + - - +
44J ALA* 1.3 55.5 + - - +
45J VAL* 4.1 4.9 + - - +
62J ARG* 6.0 2.9 - - - -
63J SER 3.9 4.5 - - - -
64J GLU* 2.6 21.2 + - - +
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Residues in contact with ALA 44 (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 LEU* 4.2 11.7 - - + +
27J VAL 3.0 15.0 - - - +
28J GLY* 3.7 11.4 - - - -
41J LEU* 4.2 16.8 - - + -
42J SER 4.2 2.9 - - - +
43J ASP* 1.3 77.6 - - - +
45J VAL* 1.3 60.6 + - - +
46J GLU 4.2 0.2 + - - -
61J ARG 3.8 0.9 - - - +
62J ARG* 3.8 2.7 - - - -
63J SER* 3.1 33.7 + - - +
66J VAL* 4.2 15.5 - - + -
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Residues in contact with VAL 45 (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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15J ARG* 5.6 6.5 - - - +
25J THR 3.9 0.5 - - - +
26J LEU* 3.5 3.5 - - - -
27J VAL* 3.0 38.0 + - + +
43J ASP 4.9 4.5 - - - +
44J ALA* 1.3 74.6 - - - +
46J GLU* 1.3 64.5 + - - +
47J THR* 3.9 22.1 + - + +
60J GLU* 4.0 20.2 - - + +
61J ARG 3.4 8.1 - - - +
62J ARG* 4.2 27.4 - - + +
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Residues in contact with GLU 46 (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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18I GLU* 5.0 0.7 - - - +
69I TYR* 2.7 46.1 + - + +
71I TYR* 4.4 1.6 + - - -
24J ARG* 3.3 18.3 + - + +
25J THR 3.2 14.1 - - - +
26J LEU* 3.7 16.6 - - + -
44J ALA 4.2 0.6 + - - -
45J VAL* 1.3 73.2 - - - +
47J THR* 1.3 64.6 + - - +
48J ILE* 3.5 23.1 - - + +
60J GLU* 3.2 7.3 - - - +
61J ARG* 2.9 57.3 + - + +
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Residues in contact with THR 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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23J ALA 3.8 2.3 - - - +
24J ARG* 3.6 1.0 - - - -
25J THR* 2.8 47.7 + - + +
45J VAL* 3.9 13.0 - - + +
46J GLU* 1.3 78.4 - - - +
48J ILE* 1.3 60.9 + - - +
49J TYR* 4.1 16.5 + - - -
58J GLU* 4.4 13.7 - - - +
59J SER 3.1 11.2 - - - -
60J GLU* 3.8 19.1 - - + +
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Residues in contact with ILE 48 (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 GLY 4.2 4.3 - - - +
23J ALA 3.6 1.8 - - - -
24J ARG* 3.9 33.9 - - + +
46J GLU* 3.5 39.9 - - + +
47J THR* 1.3 77.3 - - - +
49J TYR* 1.3 74.0 + - - +
50J GLN* 3.7 14.9 + - + +
58J GLU* 3.3 4.6 - - - -
59J SER* 2.9 57.0 + - - +
60J GLU* 4.5 2.0 - - - +
61J ARG* 4.9 5.2 - - + -
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Residues in contact with TYR 49 (chain J).
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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51C LEU* 4.3 8.6 - - + +
56C LEU* 3.8 33.4 - - + -
22J GLY 4.2 1.9 - - - +
23J ALA* 2.9 44.3 + - + +
25J THR* 5.3 8.3 - - - -
47J THR* 4.1 15.3 + - - -
48J ILE* 1.3 78.4 - - - +
50J GLN* 1.3 60.8 + - - +
56J LEU* 4.4 14.6 - - + -
57J SER 3.5 4.3 - - - +
58J GLU* 2.8 44.9 + - + -
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Residues in contact with GLN 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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51C LEU* 5.1 1.3 - - - -
56D TYR* 5.1 4.7 - - - -
22I ASP* 5.6 4.2 + - - -
48J ILE* 3.7 14.8 + - + +
49J TYR* 1.3 75.9 - - - +
51J LEU* 1.3 61.6 + - - +
52J ASN* 3.0 25.8 + - - +
55J GLU 3.8 0.9 - - - +
56J LEU* 3.6 5.0 - - - +
57J SER* 2.8 44.1 + - - +
59J SER* 6.1 3.2 - - - -
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Residues in contact with LEU 51 (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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23C ALA* 4.6 8.3 - - + -
49C TYR* 4.8 8.7 - - + +
50C GLN* 5.2 0.2 - - - -
51C LEU* 3.9 46.7 - - + +
56C LEU* 6.0 0.4 - - + -
50J GLN* 1.3 72.1 - - - +
52J ASN* 1.3 61.7 + - - +
54J GLU* 5.0 12.1 - - - +
55J GLU* 3.0 27.4 - - - +
56J LEU* 3.2 30.7 - - + +
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Residues in contact with ASN 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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30D SER 4.3 2.6 - - - +
56D TYR* 3.3 40.1 + - - +
50J GLN* 3.0 38.9 + - - +
51J LEU* 1.3 75.3 - - - +
53J ASN* 1.3 76.2 + - - +
54J GLU 3.1 2.3 + - - -
55J GLU* 3.1 19.9 + - - +
57J SER* 3.9 10.1 + - - -
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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