Contacts of the helix formed by residues 50 - 64 (chain I) in PDB entry 4QOC
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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23I GLU 3.8 16.4 - - - +
24I GLN 3.2 10.4 + - - +
26I THR* 3.2 19.5 + - - +
28I VAL* 3.8 10.8 - - + -
49I THR* 1.3 71.3 - - - +
51I LYS* 1.3 57.3 + - - +
53I VAL* 3.1 6.1 + - - +
54I LEU* 2.9 40.6 + - + +
100I TYR* 3.6 43.3 - - + +
103I ILE* 3.8 25.6 - - + -
104I TYR* 3.6 20.0 - - + -
107I LEU* 3.7 24.9 - - - -
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Residues in contact with LYS 51 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21I ALA* 5.7 2.6 + - - +
24I GLN* 3.0 47.8 + - + +
25I GLU* 3.3 27.3 + - - +
49I THR* 3.2 5.8 - - - +
50I MET* 1.3 75.1 - - - +
52I GLU* 1.3 62.0 + - - +
54I LEU* 3.4 7.1 + - - +
55I PHE* 3.0 21.9 + - + +
100I TYR* 4.7 4.5 - - - -
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Residues in contact with GLU 52 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25G GLU* 5.4 2.3 - - - +
45I LYS* 2.5 38.9 + - - -
48I TYR* 3.1 13.2 - - + -
49I THR* 2.9 44.9 + - - +
51I LYS* 1.3 76.2 - - - +
53I VAL* 1.3 67.9 + - - +
55I PHE* 3.0 16.2 + - - +
56I TYR* 3.0 32.8 + - + -
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Residues in contact with VAL 53 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28I VAL* 4.0 16.6 - - + -
30I PRO* 4.6 4.5 - - + -
34I LEU* 4.4 10.3 - - + -
38I LEU* 4.0 22.2 - - + +
48I TYR* 3.9 16.8 - - + -
49I THR 3.0 14.0 + - - +
50I MET* 3.4 10.1 - - - +
52I GLU* 1.3 80.3 - - - +
54I LEU* 1.3 59.1 + - + +
56I TYR* 3.3 2.8 + - - +
57I LEU* 2.8 48.5 + - + +
103I ILE* 4.1 21.3 - - + -
107I LEU* 5.4 0.9 - - + -
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Residues in contact with LEU 54 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50I MET* 2.9 33.7 + - + +
51I LYS* 3.8 7.2 - - - +
53I VAL* 1.3 77.8 - - + +
55I PHE* 1.3 62.3 + - - +
57I LEU* 4.5 1.3 - - + -
58I GLY* 2.9 21.8 + - - -
99I ILE* 3.9 12.8 - - + -
100I TYR* 3.7 22.4 - - + +
103I ILE* 3.6 32.5 - - + -
201I 35T 3.5 67.8 + - + -
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Residues in contact with PHE 55 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51I LYS* 3.0 12.6 + - + +
52I GLU* 3.0 11.3 + - - +
54I LEU* 1.3 79.0 - - - +
56I TYR* 1.3 99.9 + + - +
58I GLY* 3.1 1.6 + - - -
59I GLN* 3.1 52.0 + - + +
201I 35T 4.6 4.7 + - - -
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Residues in contact with TYR 56 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38I LEU* 3.3 23.3 - - + -
41I VAL* 3.7 30.3 - - + +
42I GLY 4.9 1.7 + - - -
43I ALA* 4.4 27.4 - - + -
45I LYS* 5.8 1.4 - - - -
48I TYR* 4.3 22.2 - + - -
52I GLU* 3.0 36.5 + - + -
53I VAL 3.9 0.7 - - - +
55I PHE* 1.3 103.0 - + - +
57I LEU* 1.3 60.7 + - - +
59I GLN* 3.2 6.3 + - + +
60I TYR* 2.8 29.3 + - - +
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Residues in contact with LEU 57 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34I LEU* 4.3 23.8 - - + -
37I LEU* 4.9 9.4 - - + -
38I LEU* 4.0 4.7 - - + +
53I VAL* 2.8 30.5 + - + +
54I LEU* 4.0 3.6 - - + +
56I TYR* 1.3 73.2 - - - +
58I GLY* 1.3 58.2 + - - +
60I TYR* 3.5 16.5 - - + +
61I ILE* 2.9 36.5 + - - +
82I LEU* 4.2 23.3 - - + -
85I LEU* 5.1 0.2 - - + -
86I PHE* 4.2 6.1 - - + -
103I ILE* 3.6 35.7 - - + -
201I 35T 4.0 19.5 - - + -
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Residues in contact with GLY 58 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54I LEU 2.9 15.0 + - - -
55I PHE 3.1 3.1 + - - -
57I LEU* 1.3 79.3 - - - +
59I GLN* 1.3 59.3 + - - +
61I ILE* 3.6 3.1 + - - +
62I MET* 3.2 27.3 + - - +
201I 35T 3.3 43.3 + - - -
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Residues in contact with GLN 59 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41I VAL* 4.0 12.1 - - + -
55I PHE* 3.1 50.1 + - + +
56I TYR* 3.6 8.5 - - + +
58I GLY* 1.3 73.0 - - - +
60I TYR* 1.3 65.4 + - - +
62I MET* 3.2 9.5 + - - +
63I THR* 2.8 36.8 + - + +
201I 35T 3.9 26.7 + - - -
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Residues in contact with TYR 60 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37I LEU* 3.7 35.0 - - + +
40I SER* 3.3 28.9 - - - -
41I VAL* 3.5 16.5 - - + +
56I TYR 2.8 17.2 + - - +
57I LEU* 3.5 18.2 - - + +
59I GLN* 1.3 76.9 - - - +
61I ILE* 1.3 72.7 + - + +
63I THR* 2.8 20.8 + - - -
64I LYS* 3.1 36.9 + - + +
66I LEU* 4.4 4.0 - - + -
80I ASP* 2.6 37.7 + - - -
81I LEU* 4.3 6.2 - - - +
82I LEU* 4.2 13.2 - - + -
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Residues in contact with ILE 61 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57I LEU* 2.9 23.5 + - + +
58I GLY 3.7 4.5 - - - +
60I TYR* 1.3 81.8 - - + +
62I MET* 1.3 59.2 + - - +
64I LYS 3.4 1.2 + - - -
65I ARG 3.3 3.1 + - - -
66I LEU* 3.0 42.7 + - + +
67I TYR* 3.7 17.5 - - + -
75I VAL* 4.1 4.7 - - + -
82I LEU* 3.6 30.7 - - + -
91I PHE* 4.3 7.2 - - + -
201I 35T 3.5 61.7 - - + -
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Residues in contact with MET 62 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58I GLY 3.2 13.6 + - - +
59I GLN* 3.2 15.5 + - - +
61I ILE* 1.3 76.7 - - - +
63I THR* 1.3 58.2 + - + +
65I ARG* 3.0 31.5 + - - +
67I TYR* 3.7 32.1 - - + +
68I ASP* 4.6 9.0 - - + -
201I 35T 3.8 50.7 - - + -
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Residues in contact with THR 63 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41I VAL* 4.2 14.3 - - + +
59I GLN* 2.8 29.3 + - + +
60I TYR* 2.8 20.8 + - - -
62I MET* 1.3 74.0 - - + +
64I LYS* 1.3 75.5 + - - +
65I ARG* 3.1 24.9 + - - +
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Residues in contact with LYS 64 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40I SER* 5.9 1.6 - - - -
60I TYR* 3.1 46.0 + - + +
63I THR* 1.3 91.2 + - - +
65I ARG* 1.3 71.7 + - - +
66I LEU* 3.2 29.9 + - + +
80I ASP* 3.9 10.8 - - - +
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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