Contacts of the helix formed by residues 50 - 64 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23G GLU* 3.4 45.1 - - - +
24G GLN* 3.2 8.4 + - - +
26G THR* 2.8 23.2 + - - +
28G VAL* 4.2 8.3 - - + -
49G THR* 1.3 71.5 - - - +
51G LYS* 1.3 66.2 + - - +
53G VAL* 3.4 12.8 + - - +
54G LEU* 3.1 33.4 + - - +
100G TYR* 3.9 21.5 - - + -
103G ILE* 4.1 26.7 - - + -
104G TYR* 3.9 17.9 - - + +
107G LEU* 4.1 13.5 - - + -
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Residues in contact with LYS 51 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24G GLN* 3.0 39.2 + - + +
49G THR* 3.1 5.8 - - - +
50G MET* 1.3 77.3 - - - +
52G GLU* 1.3 65.0 + - + +
54G LEU* 3.2 8.7 + - + +
55G PHE* 3.0 23.5 + - + +
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Residues in contact with GLU 52 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45G LYS* 3.6 22.9 + - - -
47G THR 4.5 0.2 - - - +
48G TYR* 3.3 24.2 - - + +
49G THR* 2.8 45.5 + - + +
51G LYS* 1.3 77.9 - - + +
53G VAL* 1.3 63.3 + - - +
55G PHE* 3.1 7.3 + - - +
56G TYR* 3.0 41.2 + - + -
25I GLU* 4.4 9.4 - - - +
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Residues in contact with VAL 53 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28G VAL* 3.8 23.8 - - + -
30G PRO* 4.7 9.4 - - + -
34G LEU* 4.7 9.0 - - + -
38G LEU* 4.2 12.1 - - + +
48G TYR* 4.0 12.5 - - + +
49G THR 3.1 13.1 + - - +
50G MET* 3.7 12.1 - - - +
51G LYS 3.3 0.2 - - - -
52G GLU* 1.3 76.6 - - - +
54G LEU* 1.3 59.3 + - - +
56G TYR* 3.3 6.6 + - - +
57G LEU* 2.9 47.2 + - + +
103G ILE* 4.4 19.5 - - + -
107G LEU* 5.2 1.6 - - + -
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Residues in contact with LEU 54 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24G GLN* 3.3 31.9 - - - +
50G MET* 3.1 18.9 + - - +
51G LYS* 3.7 7.0 - - + +
53G VAL* 1.3 79.7 - - - +
55G PHE* 1.3 63.5 + - - +
57G LEU* 3.4 4.1 + - + +
58G GLY* 3.0 20.1 + - - -
99G ILE* 4.9 0.2 - - + -
100G TYR* 3.6 17.3 - - + +
103G ILE* 3.6 28.5 - - + -
201G 35T 3.8 60.6 + - + -
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Residues in contact with PHE 55 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51G LYS* 3.0 13.2 + - + +
52G GLU* 3.5 10.3 - - - +
54G LEU* 1.3 77.8 - - - +
56G TYR* 1.3 83.7 + + - +
58G GLY* 3.2 2.3 + - - -
59G GLN* 2.8 64.1 + - + +
201G 35T 5.3 1.7 + - - -
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Residues in contact with TYR 56 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37G LEU* 4.7 0.2 - - - +
38G LEU* 3.5 26.9 - - + -
41G VAL* 3.7 27.7 - - + +
42G GLY* 3.8 24.3 - - - -
43G ALA* 4.6 5.9 + - - +
45G LYS* 5.9 3.5 - - - -
48G TYR* 3.8 32.1 - + - -
52G GLU* 3.0 37.7 + - + +
53G VAL 4.5 0.2 - - - -
55G PHE* 1.3 96.1 - + - +
57G LEU* 1.3 60.7 + - - +
59G GLN* 3.6 5.4 - - + +
60G TYR* 2.9 28.9 + - - +
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Residues in contact with LEU 57 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34G LEU* 4.0 23.1 - - + -
37G LEU* 4.0 14.4 - - + -
38G LEU* 4.5 3.4 - - + -
53G VAL* 2.9 31.1 + - + +
54G LEU* 3.9 5.6 - - + +
56G TYR* 1.3 73.0 - - - +
58G GLY* 1.3 60.2 + - - +
60G TYR* 3.4 4.5 + - + +
61G ILE* 2.9 37.5 + - + +
82G LEU* 3.9 27.1 - - + -
86G PHE* 4.4 5.2 - - + -
103G ILE* 3.8 34.8 - - + -
201G 35T 4.1 17.9 - - + -
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Residues in contact with GLY 58 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54G LEU 3.0 12.6 + - - -
55G PHE 3.7 2.5 - - - -
57G LEU* 1.3 76.2 - - - +
59G GLN* 1.3 57.4 + - - +
61G ILE* 3.3 5.9 + - - +
62G MET* 2.8 36.3 + - - +
201G 35T 3.6 36.9 - - - -
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Residues in contact with GLN 59 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41G VAL* 4.8 15.0 + - + +
55G PHE* 2.8 54.8 + - + +
56G TYR* 3.6 8.5 - - + +
57G LEU 3.3 0.2 - - - -
58G GLY* 1.3 77.6 - - - +
60G TYR* 1.3 51.2 + - - +
62G MET* 4.4 5.9 - - - +
63G THR* 2.4 62.9 + - + +
201G 35T 6.1 0.9 - - - -
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Residues in contact with TYR 60 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37G LEU* 3.5 43.5 - - + -
40G SER* 3.6 26.5 - - - -
41G VAL* 4.3 8.5 - - + +
56G TYR 2.9 18.4 + - - +
57G LEU 3.6 4.5 - - - +
59G GLN* 1.3 77.6 - - - +
61G ILE* 1.3 63.0 + - + +
63G THR* 3.5 4.9 + - - -
64G LYS* 2.7 64.2 + - + +
80G ASP* 2.6 37.7 + - - -
81G LEU* 3.7 13.4 - - + +
82G LEU* 4.2 8.5 - - + -
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Residues in contact with ILE 61 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57G LEU* 2.9 26.6 + - + +
58G GLY 3.8 4.0 - - - +
60G TYR* 1.3 80.0 - - + +
62G MET* 1.3 57.5 + - - +
64G LYS* 4.6 2.2 - - - -
65G ARG* 3.0 4.7 + - - -
66G LEU* 2.8 33.6 + - + +
67G TYR* 3.6 33.2 + - + +
75G VAL* 3.9 10.8 - - + -
82G LEU* 3.6 31.2 - - + -
91G PHE* 4.1 9.0 - - + -
201G 35T 3.6 48.5 - - + -
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Residues in contact with MET 62 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58G GLY 2.8 20.1 + - - +
59G GLN* 3.7 7.4 - - - +
61G ILE* 1.3 76.6 - - - +
63G THR* 1.3 57.8 + - + +
64G LYS 2.6 6.3 + - - -
65G ARG* 2.5 36.9 + - - +
67G TYR* 3.7 45.5 - - + +
68G ASP* 6.1 0.2 - - - -
69G GLU* 6.0 2.2 - - + +
201G 35T 4.0 44.0 - - + -
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Residues in contact with THR 63 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41G VAL* 4.4 10.3 - - + +
59G GLN* 2.4 55.6 + - + +
60G TYR* 3.5 8.3 + - - -
62G MET* 1.3 73.7 - - + +
64G LYS* 1.3 57.3 + - - +
65G ARG* 4.6 8.0 + - - +
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Residues in contact with LYS 64 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60G TYR* 2.7 51.6 + - + +
61G ILE* 4.9 0.2 - - - -
62G MET 2.6 4.8 + - - -
63G THR* 1.3 77.1 + - - +
65G ARG* 1.3 64.2 + - - +
66G LEU* 3.4 27.6 - - + +
80G ASP* 3.0 25.4 + - - +
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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