Contacts of the helix formed by residues 50 - 64 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23E GLU 3.3 27.1 - - - +
24E GLN* 3.3 7.0 + - - +
26E THR* 2.8 17.0 + - - +
28E VAL* 4.3 6.3 - - + -
49E THR* 1.3 72.2 - - - +
51E LYS* 1.3 63.1 + - - +
53E VAL* 3.3 12.2 + - + +
54E LEU* 3.0 34.3 + - + +
100E TYR* 3.5 33.9 - - + -
103E ILE* 4.0 25.1 - - + -
104E TYR* 3.8 21.5 - - + +
107E LEU* 4.0 25.6 - - - -
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Residues in contact with LYS 51 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C ILE 3.9 16.7 + - - +
20C PRO* 3.8 32.9 - - + +
24E GLN* 2.9 42.9 + - + +
49E THR* 3.1 6.9 - - - +
50E MET* 1.3 79.2 - - - +
52E GLU* 1.3 61.5 + - - +
54E LEU* 3.5 2.4 + - - +
55E PHE* 3.1 22.2 + - + +
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Residues in contact with GLU 52 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C PRO* 3.5 28.2 - - + +
22C SER* 2.7 20.2 + - - +
45E LYS* 2.4 35.9 + - - -
48E TYR* 3.3 14.8 - - + +
49E THR* 3.0 39.7 + - - +
51E LYS* 1.3 75.1 - - - +
53E VAL* 1.3 65.7 + - - +
55E PHE* 3.2 1.7 + - - +
56E TYR* 2.9 41.2 + - + -
25K GLU* 4.3 2.3 - - - +
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Residues in contact with VAL 53 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28E VAL* 3.8 23.6 - - + -
30E PRO* 4.7 3.4 - - + -
34E LEU* 4.7 9.2 - - + -
38E LEU* 4.2 21.8 - - + +
48E TYR* 4.0 13.0 - - + -
49E THR 3.5 13.2 - - - +
50E MET* 3.3 12.5 + - - +
52E GLU* 1.3 77.5 - - - +
54E LEU* 1.3 58.5 + - - +
56E TYR* 3.4 1.5 + - - +
57E LEU* 2.8 50.7 + - + +
103E ILE* 4.3 21.3 - - + -
107E LEU* 5.2 0.9 - - + -
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Residues in contact with LEU 54 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E GLN* 3.7 22.4 - - + +
50E MET* 3.0 24.3 + - + +
51E LYS 3.9 3.1 - - - +
53E VAL* 1.3 76.4 - - - +
55E PHE* 1.3 58.0 + - - +
57E LEU* 3.4 3.5 + - - -
58E GLY* 2.9 25.3 + - - -
99E ILE* 4.6 0.7 - - + -
100E TYR* 3.3 30.5 - - + +
103E ILE* 3.7 26.9 - - + -
201E 35T 3.4 61.9 + - + -
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Residues in contact with PHE 55 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C ILE* 4.3 16.4 - - + -
20C PRO* 3.4 29.4 - - + -
23C GLU* 3.7 43.3 - - + -
97C ARG* 4.0 26.5 - - + +
100C TYR* 4.4 9.6 - + - -
104C TYR* 5.0 0.2 - - - -
51E LYS 3.1 13.0 + - - +
52E GLU 3.6 6.5 - - - +
54E LEU* 1.3 79.9 - - - +
56E TYR* 1.3 77.6 + + - +
58E GLY* 3.1 3.2 + - - -
59E GLN* 3.0 58.6 + - + +
201E 35T 4.8 2.8 + - - -
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Residues in contact with TYR 56 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C PRO* 4.9 0.7 - - + -
22C SER* 2.9 31.9 + - - -
23C GLU* 3.4 37.5 + - + -
26C THR* 4.2 2.5 + - - -
104C TYR* 5.1 0.9 - - - -
38E LEU* 3.6 21.1 - - + +
41E VAL* 3.6 24.2 - - + +
42E GLY 4.4 0.8 + - - -
43E ALA* 3.9 42.1 - - + -
48E TYR* 4.4 10.8 - + - -
52E GLU* 2.9 40.5 + - + +
53E VAL* 4.8 1.1 - - - -
55E PHE* 1.3 88.8 - + - +
57E LEU* 1.3 57.8 + - - +
59E GLN* 3.4 3.6 + - + +
60E TYR* 2.9 28.8 + - - +
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Residues in contact with LEU 57 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E LEU* 4.5 23.3 - - + -
37E LEU* 5.3 3.8 - - + -
38E LEU* 4.6 4.9 - - + -
53E VAL* 2.8 27.4 + - + +
54E LEU* 3.7 4.3 - - - +
56E TYR* 1.3 76.4 - - - +
58E GLY* 1.3 63.4 + - - +
60E TYR* 3.2 12.0 + - + +
61E ILE* 3.0 27.8 + - - +
82E LEU* 3.7 30.5 - - + -
86E PHE* 4.1 5.6 - - + -
103E ILE* 3.7 29.4 - - + -
201E 35T 3.7 28.0 - - + -
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Residues in contact with GLY 58 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54E LEU 2.9 14.7 + - - -
55E PHE 3.1 2.6 + - - -
57E LEU* 1.3 78.1 - - - +
59E GLN* 1.3 60.3 + - - +
61E ILE* 3.4 3.6 + - - +
62E MET* 3.2 27.5 + - - +
201E 35T 3.4 43.0 - - - -
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Residues in contact with GLN 59 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C ARG* 3.4 23.4 + - - +
100C TYR* 3.9 11.1 - - - +
101C THR* 3.1 28.6 + - - +
104C TYR* 4.1 18.1 - - + +
41E VAL* 4.4 11.0 - - + -
55E PHE* 3.0 54.3 + - + +
56E TYR* 3.8 6.7 - - + +
58E GLY* 1.3 73.2 - - - +
60E TYR* 1.3 65.9 + - - +
62E MET* 3.4 3.6 + - - +
63E THR* 3.0 31.8 + - + +
201E 35T 3.7 16.4 + - - -
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Residues in contact with TYR 60 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E LEU* 3.4 52.0 - - + +
40E SER* 3.6 22.4 - - - -
41E VAL* 3.8 16.1 - - + +
56E TYR 2.9 14.1 + - - +
57E LEU* 3.4 14.4 - - + +
58E GLY 3.2 0.2 - - - -
59E GLN* 1.3 77.4 - - - +
61E ILE* 1.3 73.6 + - + +
63E THR* 3.2 6.4 + - - -
64E LYS* 3.0 56.7 + - + +
66E LEU* 4.5 2.2 - - + -
80E ASP* 2.8 35.7 + - - -
81E LEU* 4.2 3.1 - - - +
82E LEU* 4.2 11.4 - - + -
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Residues in contact with ILE 61 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57E LEU* 3.0 14.6 + - + +
58E GLY 3.7 6.1 - - - +
59E GLN 3.4 0.2 - - - -
60E TYR* 1.3 84.2 - - + +
62E MET* 1.3 61.5 + - - +
64E LYS 3.5 2.8 + - - -
66E LEU* 3.0 41.6 + - + +
67E TYR* 3.3 34.5 - - + +
75E VAL* 4.2 5.4 - - + -
82E LEU* 3.5 31.9 - - + -
91E PHE* 4.3 9.9 - - + -
201E 35T 3.4 45.8 - - + -
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Residues in contact with MET 62 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C THR* 3.7 36.6 - - + +
105C ARG* 2.7 24.5 + - - +
58E GLY 3.2 14.9 + - - +
59E GLN* 3.7 6.3 - - - +
60E TYR 3.2 0.2 - - - -
61E ILE* 1.3 79.5 - - - +
63E THR* 1.3 58.0 + - + +
64E LYS 3.5 3.3 + - - -
66E LEU 4.8 1.6 + - - +
67E TYR* 4.0 44.7 - - + +
68E ASP* 5.8 0.9 - - - -
69E GLU 5.9 1.8 - - - +
201E 35T 3.8 33.4 - - + -
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Residues in contact with THR 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C THR* 5.9 1.6 - - + +
104C TYR* 4.3 33.7 - - + +
105C ARG* 4.0 19.2 + - - +
41E VAL* 4.3 10.1 - - + +
59E GLN* 3.0 19.8 + - - +
60E TYR* 3.2 12.2 + - - -
62E MET* 1.3 78.1 - - + +
64E LYS* 1.3 71.1 + - - +
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Residues in contact with LYS 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60E TYR* 3.0 52.1 + - + +
61E ILE 3.8 0.4 - - - -
62E MET 4.2 2.5 - - - -
63E THR* 1.3 86.2 - - - +
66E LEU* 3.3 57.4 + - + +
80E ASP* 2.7 24.1 + - - -
81E LEU* 6.2 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