Contacts of the helix formed by residues 49 - 70 (chain B) in PDB entry 3JRC
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 49 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A MET 3.4 1.6 + - - -
82A GLY* 4.5 7.1 - - - +
47B VAL* 3.8 4.4 - - + +
48B ASN* 1.3 90.9 + - - +
50B LEU* 1.3 68.4 + - - +
51B TYR 3.0 4.8 + - - -
52B GLU* 3.2 22.9 + - - +
53B LEU* 3.1 24.0 + - + +
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Residues in contact with LEU 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A LEU* 5.3 1.1 - - + -
62A LEU* 4.1 11.4 - - + -
66A VAL* 3.4 33.4 - - + -
80A MET* 3.4 25.8 + - + +
81A MET* 3.8 7.4 - - + +
35B LEU* 4.0 14.4 - - + -
38B TYR* 3.6 26.5 - - + -
39B PHE* 4.2 19.3 - - + -
47B VAL* 4.0 8.2 - - + +
49B ASP* 1.3 76.3 - - - +
51B TYR* 1.3 60.6 + - - +
53B LEU* 3.7 15.9 - - + +
54B VAL* 3.2 26.5 + - + +
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Residues in contact with TYR 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A LEU* 4.3 5.5 - - - +
59A GLU* 2.6 37.3 + - + +
62A LEU* 4.0 17.9 - - + -
81A MET* 3.6 34.0 - - + +
82A GLY* 3.9 16.2 - - - +
83A ILE* 4.0 19.1 - - + -
91A LYS* 3.9 15.0 + - + -
49B ASP 3.0 0.8 + - - -
50B LEU* 1.3 75.9 - - - +
52B GLU* 1.3 65.9 + - + +
54B VAL* 3.0 6.1 + - - +
55B LEU* 2.8 63.2 + - + +
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Residues in contact with GLU 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A GLY* 5.3 1.7 - - - +
49B ASP* 3.2 22.0 + - - +
51B TYR* 1.3 81.8 - - + +
53B LEU* 1.3 57.1 + - - +
55B LEU* 3.7 19.1 - - - +
56B ALA* 2.8 44.8 + - + +
94B LYS* 2.8 37.8 + - - -
95B TYR* 4.4 0.3 + - - -
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Residues in contact with LEU 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A VAL* 4.4 12.3 - - + -
11A LEU* 3.6 27.0 - - + +
38B TYR* 4.1 24.9 - - + +
47B VAL* 5.9 0.2 - - + -
49B ASP* 3.1 23.1 + - + +
50B LEU* 3.7 24.7 - - + +
52B GLU* 1.3 78.6 - - - +
54B VAL* 1.3 61.1 + - - +
56B ALA* 3.7 5.2 - - + +
57B GLU* 3.3 18.6 + - - +
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Residues in contact with VAL 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 3.8 20.0 - - + -
27A LEU* 5.4 4.0 - - + -
58A VAL* 3.5 32.1 - - + -
62A LEU* 4.3 24.2 - - + -
31B VAL* 5.2 4.9 - - + -
35B LEU* 4.5 9.0 - - + -
50B LEU* 3.2 26.4 + - + +
51B TYR 3.0 7.0 + - - +
53B LEU* 1.3 73.7 - - - +
55B LEU* 1.3 69.3 + - - +
57B GLU* 2.8 14.4 + - - +
58B VAL* 2.9 16.1 + - + +
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Residues in contact with LEU 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A TYR* 4.3 9.9 - - + +
55A LEU* 4.5 11.2 - - + -
51B TYR* 2.8 52.0 + - + +
52B GLU* 3.7 24.0 - - - +
54B VAL* 1.3 73.6 - - - +
56B ALA* 1.3 54.5 + - - +
58B VAL* 3.1 5.9 + - + +
59B GLU* 2.7 69.2 + - + +
91B LYS* 6.0 0.7 - - - +
94B LYS* 4.9 3.1 - - - +
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Residues in contact with ALA 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B GLU* 2.8 27.5 + - + +
53B LEU* 3.7 6.1 - - - +
55B LEU* 1.3 78.7 - - - +
57B GLU* 1.3 63.4 + - - +
58B VAL 3.1 0.3 + - - -
60B GLN* 3.0 37.0 + - - +
95B TYR* 3.5 23.0 + - + +
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Residues in contact with GLU 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A ASP* 4.2 1.9 - - - +
11A LEU* 3.5 34.6 - - + +
26A PRO* 3.8 1.6 - - - +
27A LEU* 4.1 14.8 - - + -
28A ARG* 3.0 69.9 + - - +
53B LEU* 3.3 13.5 + - - +
54B VAL* 2.8 14.6 + - - +
56B ALA* 1.3 76.7 - - - +
58B VAL* 1.3 57.5 + - + +
60B GLN* 4.1 6.8 - - - +
61B PRO* 3.1 24.1 - - - +
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Residues in contact with VAL 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A LEU* 4.6 11.0 - - + -
31A VAL* 4.2 22.9 - - + +
54A VAL* 3.5 32.3 - - + -
55A LEU* 6.3 0.4 - - - -
58A VAL* 3.8 32.5 - - + -
31B VAL* 5.5 0.4 - - + -
54B VAL* 2.9 19.0 + - + +
55B LEU* 3.8 5.2 - - + +
57B GLU* 1.3 80.2 - - - +
59B GLU* 1.3 67.5 + - + +
61B PRO* 3.3 11.8 - - - +
62B LEU* 3.5 13.3 + - + +
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Residues in contact with GLU 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A TYR* 2.9 34.2 + - + +
55B LEU* 2.7 43.2 + - + +
58B VAL* 1.3 72.2 - - + +
60B GLN* 1.3 66.1 + - - +
62B LEU* 3.2 7.5 + - + +
63B LEU* 3.0 34.6 + - + +
91B LYS* 3.4 29.5 + - + +
94B LYS* 4.3 7.4 + - - +
95B TYR* 2.5 42.2 + - + +
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Residues in contact with GLN 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ARG* 4.5 19.5 + - - +
56B ALA* 3.0 29.0 + - - +
57B GLU* 4.0 9.2 + - - +
59B GLU* 1.3 76.7 - - - +
61B PRO* 1.4 65.6 - - + +
63B LEU* 3.7 1.9 - - - +
64B ASP* 2.9 30.4 + - - +
95B TYR* 3.4 37.7 - - + +
97B MET* 3.9 8.3 - - - +
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Residues in contact with PRO 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ARG* 3.4 36.6 - - + +
31A VAL* 3.8 17.3 - - + -
32A LYS* 3.9 16.0 - - + +
35A LEU* 4.5 1.3 - - - -
57B GLU 3.1 26.2 - - - +
58B VAL 3.3 6.3 - - - +
60B GLN* 1.4 92.1 - - + +
62B LEU* 1.3 55.7 + - - +
64B ASP* 3.2 8.1 + - + +
65B MET* 2.6 39.0 + - - +
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Residues in contact with LEU 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A VAL* 5.4 1.3 - - + -
35A LEU* 3.7 25.7 - - + +
50A LEU* 4.1 20.9 - - + +
51A TYR* 4.2 16.2 - - + -
54A VAL* 4.0 28.3 - - + -
58B VAL* 3.5 12.1 + - + +
59B GLU* 3.2 11.1 + - + +
61B PRO* 1.3 74.4 - - - +
63B LEU* 1.3 69.1 + - + +
65B MET* 3.1 1.9 + - - +
66B VAL* 2.9 42.4 + - + +
81B MET* 4.0 26.5 - - + -
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Residues in contact with LEU 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A TYR* 6.2 0.7 - - + -
59B GLU* 3.0 19.6 + - + +
60B GLN 3.7 3.1 - - - +
62B LEU* 1.3 79.4 - - + +
64B ASP* 1.3 65.3 + - - +
66B VAL* 3.9 3.7 - - - +
67B MET* 2.9 29.7 + - - +
81B MET* 4.0 22.7 - - + -
83B ILE* 5.4 0.2 - - + -
88B LEU* 3.9 26.2 - - + -
91B LYS* 3.9 29.4 - - + +
92B LEU* 4.1 11.0 - - + -
95B TYR* 3.5 35.0 - - + -
97B MET* 3.7 15.5 - - + -
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Residues in contact with ASP 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A LYS* 3.5 20.6 + - + +
60B GLN 2.9 20.1 + - - +
61B PRO* 3.3 9.5 - - + +
63B LEU* 1.3 77.7 - - - +
65B MET* 1.3 64.8 + - - +
67B MET* 3.3 2.1 + - - +
68B GLN* 3.1 38.2 + - - +
97B MET* 3.2 19.0 - - + +
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Residues in contact with MET 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A LYS* 3.5 35.0 - - + +
35A LEU* 4.1 22.9 - - + -
36A LYS* 3.7 37.9 - - + +
39A PHE* 4.3 18.7 - - + -
61B PRO 2.6 19.6 + - - +
62B LEU 3.9 2.0 - - - +
64B ASP* 1.3 73.7 - - - +
66B VAL* 1.3 63.6 + - - +
68B GLN* 3.3 32.9 + - + +
69B TYR* 3.1 20.8 + - - +
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Residues in contact with VAL 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A PHE* 4.0 10.1 - - + -
50A LEU* 3.9 18.6 - - + -
62B LEU* 2.9 38.8 + - + +
63B LEU* 4.0 2.7 - - - +
65B MET* 1.3 72.6 - - - +
67B MET* 1.3 61.1 + - + +
69B TYR* 3.1 7.2 + - - +
70B THR* 2.8 31.4 + - + -
77B ALA* 3.7 34.8 - - + +
80B MET* 4.0 16.4 - - + -
81B MET* 4.4 13.0 - - + -
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Residues in contact with MET 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B LEU* 2.9 21.7 + - - +
64B ASP* 3.8 5.2 - - - +
66B VAL* 1.3 77.4 - - + +
68B GLN* 1.3 57.6 + - - +
70B THR* 3.6 3.4 - - - -
71B ARG* 2.9 6.1 + - - -
72B GLY* 2.8 67.0 + - - +
74B GLN* 4.2 15.7 - - + +
77B ALA* 4.0 24.7 - - + -
88B LEU* 4.9 2.5 - - + -
92B LEU* 4.0 35.2 - - + -
97B MET* 4.7 7.9 - - + +
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Residues in contact with GLN 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A LYS* 3.7 17.7 + - - -
64B ASP* 3.1 31.0 + - - +
65B MET* 3.4 32.1 - - + +
67B MET* 1.3 77.7 - - - +
69B TYR* 1.3 60.3 + - - +
71B ARG* 3.3 20.2 + - - +
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Residues in contact with TYR 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A PHE* 3.7 39.7 + + + -
42A LEU* 5.1 8.7 + - - +
44A GLY* 4.2 21.5 + - - -
45A GLN 5.5 1.0 + - - -
46A ASP* 6.1 0.9 - - - -
47A VAL* 5.4 3.4 - - + +
65B MET 3.1 12.2 + - - +
66B VAL* 3.1 11.4 + - - +
68B GLN* 1.3 74.5 - - - +
70B THR* 1.3 65.3 + - + +
71B ARG* 3.1 21.3 + - - +
80B MET* 3.8 33.9 - - + -
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Residues in contact with THR 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B VAL 2.8 23.5 + - - +
67B MET* 3.6 9.9 + - - -
69B TYR* 1.3 75.0 - - + +
71B ARG* 1.3 72.8 + - - +
72B GLY 3.4 0.2 - - - -
73B ASN* 3.2 41.0 + - - +
76B ARG* 4.0 13.7 - - + +
77B ALA* 3.7 29.3 - - - +
80B MET* 3.9 20.2 - - - -
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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