Contacts of the helix formed by residues 49 - 70 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A VAL* 4.4 1.5 - - - +
48A ASN* 1.3 91.3 - - + +
50A LEU* 1.3 62.5 - - - +
51A TYR 3.2 3.4 - - - -
52A GLU* 3.6 15.4 + - + +
53A LEU* 3.2 22.3 + - - +
81B MET 3.8 4.5 - - - +
82B GLY* 3.9 17.0 - - - +
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Residues in contact with LEU 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A LEU* 4.1 15.9 - - + -
38A TYR* 3.9 15.0 - - + -
39A PHE* 3.9 18.6 - - + -
47A VAL* 3.7 10.2 - - + +
49A ASP* 1.3 73.2 - - - +
51A TYR* 1.3 63.5 + - - +
53A LEU* 3.7 26.2 - - + -
54A VAL* 3.2 21.9 + - + +
62B LEU* 4.1 13.0 - - + +
66B VAL* 3.9 28.3 - - + -
80B MET* 3.3 27.7 + - + +
81B MET* 3.4 7.3 + - + -
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Residues in contact with TYR 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A LEU* 1.3 74.6 - - - +
52A GLU* 1.3 71.3 + - - +
53A LEU 3.0 1.7 + - - -
54A VAL* 3.1 2.3 + - - +
55A LEU* 2.9 57.5 + - + +
55B LEU* 4.3 6.2 - - - +
59B GLU* 2.9 34.8 + - + +
62B LEU* 4.2 13.7 - - + -
63B LEU* 6.2 0.7 - - + -
81B MET* 3.0 44.7 + - + +
83B ILE* 3.9 20.2 - - + -
91B LYS* 4.0 18.9 + - + -
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Residues in contact with GLU 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A ASP* 3.6 20.1 + - + +
51A TYR* 1.3 81.6 - - + +
53A LEU* 1.3 61.5 + - - +
55A LEU* 3.3 22.7 - - - +
56A ALA* 3.1 28.1 + - + +
94A LYS* 4.0 16.9 + - - +
95A TYR* 4.0 15.8 + - - -
81B MET 4.5 0.6 + - - -
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Residues in contact with LEU 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A TYR* 4.3 9.0 - - + +
47A VAL* 6.2 0.2 - - + -
49A ASP 3.2 18.6 + - - +
50A LEU* 3.6 28.7 - - + +
51A TYR 3.0 0.6 - - - -
52A GLU* 1.3 76.5 - - - +
54A VAL* 1.3 66.1 + - - +
56A ALA* 3.3 4.7 + - - +
57A GLU* 3.1 25.1 + - + +
7B ASN* 5.2 12.1 - - + +
10B VAL* 4.3 24.5 - - + +
11B LEU* 3.9 27.6 - - + -
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Residues in contact with VAL 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A VAL* 5.2 8.1 - - + -
35A LEU* 4.4 10.1 - - + -
50A LEU* 3.2 25.3 + - + +
51A TYR 3.1 4.3 + - - +
53A LEU* 1.3 77.3 - - - +
55A LEU* 1.3 68.5 + - - +
57A GLU* 3.0 12.6 + - - +
58A VAL* 3.1 16.8 + - + +
11B LEU* 3.9 24.7 - - + -
27B LEU* 5.5 4.0 - - + -
58B VAL* 3.5 31.0 - - + -
62B LEU* 4.0 22.0 - - + -
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Residues in contact with LEU 55 (chain A).
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 50.0 + - + +
52A GLU* 3.3 27.4 - - - +
54A VAL* 1.3 77.4 - - - +
56A ALA* 1.3 53.0 + - - +
58A VAL* 3.0 7.4 + - - +
59A GLU* 2.7 61.9 + - + +
91A LYS* 4.9 2.7 - - - +
94A LYS* 3.8 9.9 - - - +
95A TYR* 4.3 0.9 - - - +
51B TYR* 4.3 15.7 - - - +
55B LEU* 4.5 11.4 - - + -
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Residues in contact with ALA 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A GLU* 3.1 23.0 + - + +
53A LEU* 3.6 5.4 - - - +
55A LEU* 1.3 78.8 - - - +
57A GLU* 1.3 63.2 + - - +
58A VAL 3.5 0.3 + - - -
59A GLU 4.2 0.2 - - - -
60A GLN* 3.4 33.6 + - - +
95A TYR* 3.3 30.7 + - + +
28B ARG* 6.2 0.7 - - - +
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Residues in contact with GLU 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A LEU* 3.1 15.2 + - - +
54A VAL* 3.0 13.4 + - - +
56A ALA* 1.3 78.5 - - - +
58A VAL* 1.3 60.8 + - + +
61A PRO* 3.2 21.7 - - - +
7B ASN* 3.5 12.2 - - - +
8B SER* 3.0 34.0 - - - +
11B LEU* 4.3 17.5 - - + +
27B LEU* 4.3 13.2 - - + +
28B ARG* 3.2 56.6 + - + +
31B VAL* 4.5 1.9 - - - +
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Residues in contact with VAL 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A VAL* 3.3 16.6 - - + +
55A LEU* 3.0 7.2 + - - +
57A GLU* 1.3 82.5 - - + +
59A GLU* 1.3 66.7 + - + +
60A GLN 3.2 2.2 - - - -
61A PRO* 3.2 5.6 - - - +
62A LEU* 3.1 22.2 + - + +
27B LEU* 5.3 7.2 - - + -
31B VAL* 4.1 22.2 - - + +
54B VAL* 3.5 32.1 - - + -
58B VAL* 3.8 33.0 - - + -
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Residues in contact with GLU 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A LEU* 2.7 36.3 + - + +
58A VAL* 1.3 74.0 - - + +
60A GLN* 1.3 56.9 + - - +
62A LEU* 3.8 6.9 - - + +
63A LEU* 2.9 41.0 + - + +
91A LYS* 2.7 30.3 + - - +
94A LYS* 3.3 11.8 + - - -
95A TYR* 2.8 41.3 + - + +
51B TYR* 2.6 36.9 + - + +
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Residues in contact with GLN 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A ALA* 3.4 18.5 + - - +
59A GLU* 1.3 75.1 - - - +
61A PRO* 1.3 69.4 - - + +
63A LEU* 3.9 1.1 - - - +
64A ASP* 2.8 33.3 + - - +
95A TYR* 3.6 49.7 + - + +
97A MET* 4.1 19.2 - - + +
28B ARG* 3.3 34.3 + - - +
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Residues in contact with PRO 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A GLU 3.2 27.6 - - - +
58A VAL 3.2 6.3 - - - +
60A GLN* 1.3 94.3 - - + +
62A LEU* 1.3 61.6 + - - +
64A ASP* 3.6 5.9 - - + +
65A MET* 3.0 31.1 + - - +
28B ARG* 3.5 38.4 - - + +
31B VAL* 3.8 15.0 - - + -
32B LYS* 3.9 17.7 - - + +
35B LEU* 4.3 1.3 - - - -
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Residues in contact with LEU 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A VAL* 3.1 19.3 + - + +
59A GLU* 3.8 7.4 - - + +
61A PRO* 1.3 79.9 - - - +
63A LEU* 1.3 64.2 + - + +
65A MET* 3.7 1.0 - - - +
66A VAL* 3.1 38.6 + - + +
81A MET* 4.0 13.9 - - + -
31B VAL* 4.4 2.0 - - + +
35B LEU* 3.7 30.7 - - + +
50B LEU* 4.1 11.2 - - + -
51B TYR* 4.0 36.3 - - + +
54B VAL* 4.3 22.2 - - + -
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Residues in contact with LEU 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A GLU* 2.9 28.8 + - + +
60A GLN 3.9 2.2 - - - +
62A LEU* 1.3 70.9 - - + +
64A ASP* 1.3 68.4 + - - +
65A MET 2.9 3.2 + - - -
66A VAL* 4.4 5.2 - - + -
67A MET* 2.9 30.7 + - + +
81A MET* 4.2 22.0 - - + -
83A ILE* 5.4 0.9 - - + -
88A LEU* 3.6 30.7 - - + -
91A LYS* 4.0 31.9 - - + +
92A LEU* 4.5 10.1 - - + +
95A TYR* 4.1 20.9 - - + -
97A MET* 4.1 16.2 - - - -
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Residues in contact with ASP 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A GLN 2.8 23.1 + - - +
61A PRO* 3.6 9.4 - - + +
63A LEU* 1.3 72.2 - - - +
65A MET* 1.3 63.1 + - - +
67A MET* 4.2 3.4 - - - +
68A GLN* 3.2 28.9 + - - +
97A MET* 3.4 25.2 - - + +
32B LYS* 3.2 29.4 + - - -
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Residues in contact with MET 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A PRO 3.0 25.5 + - - +
62A LEU 3.7 3.6 - - - +
63A LEU 2.9 2.2 + - - -
64A ASP* 1.3 90.0 - - - +
66A VAL* 1.3 55.2 + - + +
67A MET 3.2 1.3 - - - -
68A GLN* 3.1 38.7 + - - +
69A TYR* 2.7 34.4 + - - +
32B LYS* 4.0 41.5 - - + +
35B LEU* 4.1 17.5 - - + -
36B LYS* 4.8 11.4 - - - -
39B PHE* 4.2 18.0 - - + -
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Residues in contact with VAL 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A LEU* 3.1 24.8 + - + +
63A LEU* 3.9 8.3 - - + +
65A MET* 1.3 71.6 - - + +
67A MET* 1.3 64.3 + - + +
69A TYR* 3.9 8.1 - - + -
70A THR* 2.7 42.1 + - + +
77A ALA* 4.0 15.7 - - + +
80A MET* 5.1 6.3 - - - -
81A MET* 3.7 28.0 - - + -
88A LEU* 6.1 0.7 - - + -
39B PHE* 4.1 8.7 - - + -
50B LEU* 3.4 34.1 - - + -
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Residues in contact with MET 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A LEU* 2.9 21.6 + - + +
64A ASP* 4.2 3.4 - - - +
66A VAL* 1.3 81.7 - - + +
68A GLN* 1.3 55.2 + - - +
70A THR* 3.6 6.9 + - - -
71A ARG 3.2 2.9 + - - -
72A GLY* 2.7 68.5 + - - +
74A GLN* 3.2 37.5 - - + +
77A ALA* 4.5 7.2 - - - -
88A LEU* 5.1 4.9 - - - -
92A LEU* 4.6 24.0 - - + -
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Residues in contact with GLN 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A ASP* 3.2 21.2 + - - +
65A MET* 3.1 35.1 + - - +
67A MET* 1.3 78.1 - - - +
69A TYR* 1.3 64.1 + - - +
71A ARG* 3.4 17.2 + - - +
32B LYS* 5.4 0.3 + - - -
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Residues in contact with TYR 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A MET 2.7 19.5 + - - +
66A VAL* 3.1 8.3 + - - +
68A GLN* 1.3 75.7 - - - +
70A THR* 1.3 61.0 + - + +
71A ARG* 3.1 9.9 + - - +
76A ARG* 5.3 9.4 - - - -
80A MET* 3.4 41.1 - - + -
39B PHE* 4.0 39.0 - + + -
42B LEU* 4.6 17.8 + - + +
44B GLY* 6.0 0.7 - - - -
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Residues in contact with THR 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A VAL 2.7 27.1 + - - +
67A MET* 3.6 6.1 + - - -
69A TYR* 1.3 73.3 - - + +
71A ARG* 1.3 63.8 + - - +
73A ASN* 3.0 49.2 + - - +
76A ARG* 4.2 17.5 - - + +
77A ALA* 3.5 33.5 - - + +
80A MET* 4.2 19.3 - - - -
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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