Contacts of the helix formed by residues 46 - 65 (chain O) 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 TRP 46 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3214A C 3.9 32.8 - - - -
3215A C 4.0 28.0 - - - -
16O ARG* 4.5 16.4 - - - -
44O ALA 3.3 2.4 + - - -
45O PRO* 1.3 70.5 - - - +
47O ALA* 1.3 68.0 + - + +
49O VAL* 3.5 10.1 + - - +
50O ASP* 3.5 15.4 + - + +
107O MET* 3.7 25.6 - - + +
109O GLN* 4.3 13.9 - - + +
119O LYS* 2.8 59.0 + - + +
120O MET 3.7 7.9 - - - +
121O ALA* 3.6 26.9 - - + -
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Residues in contact with ALA 47 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2455A U 3.3 50.1 - - - +
2456A U 3.9 4.9 - - - +
16O ARG* 3.1 31.7 - - + +
45O PRO 3.0 1.2 + - - -
46O TRP* 1.3 83.4 - - + +
48O ARG* 1.3 57.5 + - + +
50O ASP* 2.5 23.6 - - - +
51O GLU* 3.9 0.5 - - - +
119O LYS 4.9 0.2 + - - -
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Residues in contact with ARG 48 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2318A A 4.1 28.3 + - - -
2452A A 5.1 3.8 + - - -
2454A G 3.2 29.9 + - - -
2455A U 3.1 35.6 + - - +
18O MET* 3.6 44.7 + - + +
28O LEU* 4.7 21.0 - - - +
29O LEU* 4.1 1.4 - - - +
32O LEU* 4.1 20.1 - - + +
45O PRO* 3.1 26.0 + - + +
47O ALA* 1.3 75.7 - - + +
49O VAL* 1.3 59.5 + - - +
50O ASP 3.2 0.9 - - - -
51O GLU* 3.2 5.7 + - - +
52O MET* 2.9 28.5 + - - +
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Residues in contact with VAL 49 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32O LEU* 5.3 0.7 - - - -
44O ALA* 3.3 43.5 - - + +
45O PRO 3.3 10.9 + - - +
46O TRP 3.7 8.5 - - - +
47O ALA 3.4 0.4 - - - -
48O ARG* 1.3 76.9 - - - +
50O ASP* 1.3 55.8 + - - +
52O MET* 3.2 9.3 + - - +
53O ARG* 2.9 26.7 + - - +
107O MET* 3.4 32.5 - - + -
121O ALA* 3.9 12.8 - - + +
123O ILE* 3.4 24.6 - - + +
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Residues in contact with ASP 50 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3215A C 5.0 1.6 + - - -
16O ARG* 2.6 34.2 + - - -
46O TRP* 3.5 11.5 + - + +
47O ALA 2.5 29.8 - - - +
49O VAL* 1.3 78.8 - - - +
51O GLU* 1.3 66.0 + - - +
53O ARG* 3.2 8.1 + - - +
54O GLY* 2.9 25.8 + - - -
107O MET* 3.8 24.5 - - + -
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Residues in contact with GLU 51 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15O PHE* 3.4 12.4 - - - -
16O ARG* 2.6 50.4 + - - +
18O MET* 3.3 30.2 - - + +
25O ARG* 2.8 28.1 + - - -
29O LEU* 3.6 7.2 - - + -
47O ALA 3.9 0.4 - - - +
48O ARG 3.2 2.0 + - - +
50O ASP* 1.3 94.7 + - - +
52O MET* 1.3 55.5 + - - +
54O GLY* 3.2 2.8 + - - -
55O TYR* 2.9 39.8 + - - -
270Q MET* 5.3 1.4 - - - +
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Residues in contact with MET 52 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29O LEU* 3.8 12.0 - - + +
32O LEU* 3.4 35.7 - - + +
33O LEU* 3.8 25.8 - - + +
36O LEU* 3.2 33.4 - - + -
48O ARG 2.9 13.1 + - - +
49O VAL* 3.2 11.0 + - - +
51O GLU* 1.3 76.7 - - - +
53O ARG* 1.3 56.7 + - - +
55O TYR* 3.2 5.8 + - - +
56O ALA* 2.6 43.8 + - + +
105O THR* 5.6 0.4 - - + -
123O ILE* 3.4 31.4 - - + -
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Residues in contact with ARG 53 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49O VAL 2.9 13.0 + - - +
50O ASP* 3.2 11.9 + - - +
52O MET* 1.3 82.0 - - - +
54O GLY* 1.3 56.1 + - - +
56O ALA* 3.4 7.3 - - - +
57O GLU* 2.9 52.0 + - - +
103O GLY 5.7 0.8 + - - -
104O TYR 4.5 1.4 + - - -
105O THR* 2.6 48.5 + - - +
107O MET* 3.6 38.8 - - - +
123O ILE* 4.4 5.8 - - + -
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Residues in contact with GLY 54 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50O ASP 2.9 13.4 + - - -
51O GLU* 3.2 4.0 + - - -
53O ARG* 1.3 77.6 - - - +
55O TYR* 1.3 63.5 + - - +
57O GLU* 3.6 11.3 + - - +
58O LYS* 3.4 24.3 + - - +
270Q MET* 3.5 26.6 - - - +
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Residues in contact with TYR 55 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15O PHE* 3.9 2.4 - - - -
25O ARG* 2.9 40.7 + - - -
26O ILE* 4.9 1.3 - - + -
29O LEU* 3.8 12.1 - - + -
33O LEU* 4.4 13.7 - - + -
51O GLU* 2.9 33.3 + - - +
52O MET* 3.6 8.7 - - - +
54O GLY* 1.3 75.8 - - - +
56O ALA* 1.3 57.7 + - - +
58O LYS* 3.2 7.4 + - - +
59O LEU* 2.9 28.2 + - - +
79O TRP* 3.1 42.4 - + + -
268Q ASP* 2.6 32.3 + - - -
269Q MET* 4.0 11.8 - - + +
270Q MET* 3.6 29.6 - - + +
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Residues in contact with ALA 56 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33O LEU* 4.4 5.1 - - - +
52O MET* 2.6 35.0 + - + +
53O ARG* 3.4 10.1 - - - +
55O TYR* 1.3 73.1 - - - +
57O GLU* 1.3 57.4 + - - +
59O LEU* 3.2 8.7 + - - +
60O ILE* 2.9 28.6 + - - +
105O THR* 3.9 2.9 - - + -
125O TYR* 3.2 37.0 + - + +
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Residues in contact with GLU 57 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53O ARG* 2.9 44.3 + - - +
54O GLY* 3.7 10.7 - - - +
56O ALA* 1.3 75.7 - - - +
58O LYS* 1.3 60.0 + - + +
60O ILE* 3.2 4.4 + - - +
61O ASP* 2.9 29.2 + - - +
102O GLY* 3.6 19.3 - - - +
104O TYR* 3.7 31.2 - - + +
105O THR* 3.5 25.5 + - + +
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Residues in contact with LYS 58 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54O GLY 3.4 13.2 + - - +
55O TYR 3.2 9.7 + - - +
57O GLU* 1.3 81.4 - - + +
59O LEU* 1.3 55.9 + - - +
61O ASP* 3.2 14.3 + - - +
62O TYR* 2.9 36.6 + - - -
269Q MET* 3.4 46.1 + - + +
270Q MET* 4.2 14.8 - - - -
272Q GLU* 3.6 29.2 + - - +
274Q ASP* 5.3 9.3 - - - +
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Residues in contact with LEU 59 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33O LEU* 3.9 35.0 - - + -
37O VAL* 4.8 2.9 - - + -
55O TYR 2.9 11.9 + - - +
56O ALA 3.3 10.8 - - - +
58O LYS* 1.3 74.6 - - - +
60O ILE* 1.3 62.3 + - + +
62O TYR* 3.2 10.0 + - + +
63O GLY* 2.9 25.3 + - - -
75O MET* 5.0 2.5 - - + +
76O ALA* 4.7 11.7 - - - +
79O TRP* 4.5 17.7 - - + -
80O LEU* 4.7 6.1 - - + -
89O LEU* 3.5 40.1 - - + +
93O LEU* 5.6 0.2 - - + -
125O TYR* 4.6 4.3 - - - +
269Q MET* 3.6 16.7 - - + -
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Residues in contact with ILE 60 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56O ALA 2.9 13.1 + - - +
57O GLU 3.2 6.7 + - - +
59O LEU* 1.3 77.3 - - + +
61O ASP* 1.3 56.5 + - - +
63O GLY* 3.2 2.4 + - - -
64O LYS* 2.9 31.9 + - + +
89O LEU* 4.4 12.1 - - + +
93O LEU* 4.1 25.1 - - + +
94O ALA* 5.2 2.2 - - - +
97O TYR* 3.6 30.7 - - + -
104O TYR* 3.5 34.1 - - + +
125O TYR* 3.3 42.2 - - + +
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Residues in contact with ASP 61 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57O GLU 2.9 13.8 + - - +
58O LYS* 3.3 18.3 - - - +
60O ILE* 1.3 77.4 - - - +
62O TYR* 1.3 63.7 + - + +
64O LYS* 3.1 25.8 - - - +
65O LEU* 3.4 9.1 + - - +
101O THR 3.7 7.0 - - - +
104O TYR* 2.5 34.0 + - - -
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Residues in contact with TYR 62 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58O LYS* 2.9 26.9 + - + +
59O LEU* 3.3 15.5 - - + +
61O ASP* 1.3 76.1 - - + +
63O GLY* 1.3 63.3 - - - +
65O LEU* 3.1 36.2 + - + +
71O ARG* 3.3 32.1 + - + -
72O ALA* 3.6 30.8 - - + +
75O MET* 3.5 36.6 - - + -
269Q MET* 3.8 29.0 - - + +
272Q GLU* 2.9 38.1 + - - -
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Residues in contact with GLY 63 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59O LEU 2.9 13.6 + - - -
60O ILE 3.2 4.2 + - - -
62O TYR* 1.3 76.9 - - - +
64O LYS* 1.3 62.4 + - - +
66O GLY* 3.0 13.9 + - - -
89O LEU* 4.1 19.2 - - - +
90O PHE* 3.3 29.9 - - - -
94O ALA* 4.3 9.5 - - - +
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Residues in contact with LYS 64 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60O ILE* 2.9 15.7 + - + +
61O ASP* 3.1 19.9 + - - +
63O GLY* 1.3 75.4 - - - +
65O LEU* 1.3 60.4 + - + +
66O GLY* 3.0 3.5 + - - -
94O ALA* 4.0 25.4 - - + +
97O TYR* 2.9 31.0 + - - -
98O LYS* 4.1 9.4 + - - +
100O GLN 2.7 29.5 + - - -
101O THR* 4.2 3.2 + - - +
104O TYR* 3.3 24.6 + - + +
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Residues in contact with LEU 65 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61O ASP 3.4 7.4 + - - +
62O TYR* 3.1 36.9 + - + +
64O LYS* 1.3 76.0 - - + +
66O GLY* 1.3 58.1 + - - +
68O THR* 5.1 2.6 + - - -
69O ASN* 3.5 35.1 - - + +
71O ARG* 6.0 1.3 - - - -
72O ALA* 4.6 0.4 - - + -
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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