Contacts of the helix formed by residues 50 - 64 (chain D) in PDB entry 5J7F
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 MET 50 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23D GLU 4.1 7.6 - - - +
24D GLN 3.4 10.3 + - - +
26D THR* 2.9 23.1 + - - +
28D VAL* 3.9 23.5 - - + +
48D TYR 3.9 0.2 + - - -
49D THR* 1.3 71.2 - - - +
51D LYS* 1.3 56.3 + - - +
53D VAL* 3.4 5.0 + - - +
54D LEU* 2.9 37.4 + - + +
100D TYR* 3.2 50.7 - - + +
103D ILE* 3.8 40.4 - - + -
104D TYR* 3.7 26.2 - - + -
107D LEU* 4.9 0.7 - - - -
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Residues in contact with LYS 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D ALA* 4.6 5.8 - - + -
14D VAL* 2.7 32.7 + - - +
15D THR* 3.0 31.6 - - + -
24D GLN* 2.9 30.7 + - + +
25D GLU* 3.9 8.5 - - - +
49D THR* 3.1 12.3 - - + -
50D MET* 1.3 76.4 - - - +
52D GLU* 1.3 57.7 + - - +
54D LEU* 4.5 3.4 - - - -
55D PHE 3.0 22.3 + - - -
100D TYR* 4.4 2.0 + - - +
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Residues in contact with GLU 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D GLY 3.1 27.9 + - - +
13D ALA* 4.2 7.4 - - + +
27D LEU* 5.5 0.5 - - - +
45D LYS* 4.9 8.1 - - - +
47D THR 4.8 0.5 - - - +
48D TYR* 3.5 26.0 - - + -
49D THR* 2.8 45.3 + - + +
51D LYS* 1.3 76.2 - - - +
53D VAL* 1.3 68.4 + - - +
55D PHE* 3.2 3.5 + - - +
56D TYR* 3.0 32.0 + - + -
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Residues in contact with VAL 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D VAL* 3.9 18.8 - - + -
30D PRO* 4.4 7.6 - - + -
34D LEU* 4.8 9.4 - - + -
38D LEU* 4.1 20.8 - - + +
48D TYR* 3.5 23.8 - - + -
49D THR 3.0 18.3 + - - +
50D MET* 3.7 7.4 - - - +
52D GLU* 1.3 77.0 - - - +
54D LEU* 1.3 57.8 + - - +
56D TYR* 3.1 4.4 + - - +
57D LEU* 2.9 44.1 + - + +
103D ILE* 4.3 19.3 - - + -
107D LEU* 6.1 0.4 - - + -
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Residues in contact with LEU 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D VAL* 3.7 10.5 - - + +
16D THR* 5.9 0.4 - - + -
50D MET* 2.9 30.1 + - + +
51D LYS* 3.6 6.5 - - - +
53D VAL* 1.3 76.3 - - - +
55D PHE* 1.3 55.6 + - - +
57D LEU* 3.4 2.6 + - - -
58D GLY 2.9 15.2 + - - -
99D ILE* 3.7 7.2 - - + -
100D TYR* 3.4 35.2 - - + +
103D ILE* 3.6 28.0 - - + -
201D 6GG 2.7 77.3 + - + +
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Residues in contact with PHE 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A MET* 3.4 38.6 - - + +
63A THR* 4.3 6.1 - - - -
65A ARG* 4.0 14.1 - - + -
67A TYR* 3.7 17.3 - - - -
12D GLY* 3.6 21.5 - - - -
13D ALA* 3.9 9.2 - - - -
14D VAL* 3.3 17.9 - - + +
51D LYS 3.0 15.3 + - - +
52D GLU 3.4 7.4 - - - +
53D VAL 3.2 0.4 - - - -
54D LEU* 1.3 77.1 - - - +
56D TYR* 1.3 92.2 + + - +
58D GLY* 3.3 1.2 + - - -
59D GLN* 3.1 40.5 + - + +
201D 6GG 3.7 5.8 - - - -
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Residues in contact with TYR 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D GLY 3.2 23.8 + - - -
38D LEU* 3.6 26.0 - - + -
41D VAL* 3.6 16.9 - - + +
42D GLY 4.6 3.3 + - - -
43D ALA* 3.4 43.2 - - + -
44D GLN 5.1 0.7 + - - -
48D TYR* 3.7 21.7 - + - -
52D GLU* 3.0 30.0 + - + -
53D VAL 3.8 0.9 - - - +
55D PHE* 1.3 92.0 - + - +
57D LEU* 1.3 61.9 + - - +
59D GLN* 3.4 18.4 + - - +
60D TYR* 3.0 26.7 + - - +
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Residues in contact with LEU 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D LEU* 4.0 16.8 - - + -
37D LEU* 3.4 28.7 - - + -
38D LEU* 4.2 5.2 - - + -
53D VAL* 2.9 25.0 + - + +
54D LEU* 3.7 4.3 - - - +
56D TYR* 1.3 76.3 - - - +
58D GLY* 1.3 57.4 + - - +
60D TYR* 3.2 6.3 + - + +
61D ILE* 3.0 36.4 + - + +
82D LEU* 4.2 17.3 - - + -
86D PHE* 4.0 7.6 - - + -
103D ILE* 3.5 37.0 - - + -
201D 6GG 3.8 22.4 - - + -
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Residues in contact with GLY 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A MET* 3.6 7.9 - - - -
54D LEU 2.9 11.9 + - - -
55D PHE 3.8 1.6 - - - -
57D LEU* 1.3 75.8 - - - +
59D GLN* 1.3 57.6 + - - +
61D ILE* 3.5 2.0 + - - -
62D MET* 2.9 29.8 + - - +
201D 6GG 3.4 43.6 + - - -
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Residues in contact with GLN 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A GLN 5.1 0.8 + - - -
62A MET* 3.7 23.2 - - + +
63A THR* 3.1 38.4 + - - +
41D VAL* 3.4 27.9 + - + +
55D PHE* 3.1 24.8 + - + +
56D TYR* 3.5 25.0 - - - +
57D LEU 3.2 0.2 - - - -
58D GLY* 1.3 76.1 - - - +
60D TYR* 1.3 60.2 + - - +
62D MET* 3.8 4.7 - - - +
63D THR* 2.7 41.4 + - - +
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Residues in contact with TYR 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D LEU* 4.0 32.1 - - + -
40D SER* 3.9 21.3 - - - -
41D VAL* 3.8 16.5 - - + +
56D TYR 3.0 13.9 + - - +
57D LEU* 3.3 11.4 - - + +
59D GLN* 1.3 76.0 - - - +
61D ILE* 1.3 64.6 + - + +
63D THR* 3.4 1.1 + - - -
64D LYS* 3.0 62.6 + - + +
66D LEU* 3.8 17.7 - - + -
80D ASP* 2.6 38.0 + - - -
81D LEU* 4.4 6.9 - - - +
82D LEU* 4.0 13.4 + - + -
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Residues in contact with ILE 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57D LEU* 3.0 17.9 + - + +
58D GLY* 3.7 5.6 - - - +
60D TYR* 1.3 82.9 - - + +
62D MET* 1.3 60.2 + - - +
64D LYS 3.6 0.2 + - - -
65D ARG* 2.9 22.9 + - - -
66D LEU* 3.0 28.1 + - + -
67D TYR* 3.9 3.2 - - - +
75D VAL* 3.8 26.5 - - + -
82D LEU* 4.0 26.0 - - + -
91D PHE* 4.6 1.3 - - + -
201D 6GG 3.2 62.4 - - + -
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Residues in contact with MET 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A PHE* 3.6 15.6 - - - -
58A GLY 4.7 3.6 - - - +
59A GLN* 3.8 13.9 - - - +
62A MET* 3.3 39.0 - - + -
201A 6GG 3.6 54.7 - - + +
58D GLY 2.9 14.4 + - - +
59D GLN* 3.8 4.9 - - - +
61D ILE* 1.3 74.3 - - - +
63D THR* 1.3 65.1 + - - +
65D ARG* 3.1 12.8 + - - +
67D TYR* 4.0 5.3 - - - -
201D 6GG 3.6 51.6 - - + -
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Residues in contact with THR 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A PHE* 4.0 5.6 - - + -
59A GLN* 2.9 31.8 + - - +
41D VAL* 4.8 9.9 - - + +
59D GLN* 2.7 27.1 + - - +
60D TYR* 4.0 4.7 - - - -
62D MET* 1.3 76.3 - - - +
64D LYS* 1.3 64.2 + - + +
65D ARG* 3.2 20.4 + - - -
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Residues in contact with LYS 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D TYR* 3.0 55.8 + - + +
63D THR* 1.3 81.3 - - + +
65D ARG* 1.3 79.1 + - - +
66D LEU* 3.9 21.6 - - + +
80D ASP* 3.4 18.3 + - - +
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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