Contacts of the helix formed by residues 60 - 74 (chain O) in PDB entry 4B2Q
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 ALA 60 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56O ALA 3.5 9.4 + - - +
57O LEU* 3.5 15.5 - - - +
58O SER 3.1 0.2 - - - -
59O GLU* 1.3 77.2 - - - +
61O THR* 1.3 60.9 + - + +
63O LEU* 2.9 26.6 + - - +
64O PHE* 3.0 41.8 + - + -
59P GLU* 5.1 9.4 - - - +
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Residues in contact with THR 61 (chain O).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18O GLY 3.8 8.1 - - - +
19O LEU* 3.6 2.4 - - - +
21O GLY 4.8 1.1 - - - -
22O ALA* 3.7 10.2 + - - -
57O LEU 5.4 1.3 - - - +
58O SER 3.1 17.4 + - - +
60O ALA* 1.3 77.2 - - + +
62O GLY* 1.3 56.9 + - - +
63O LEU 3.3 0.9 - - - -
64O PHE* 4.4 7.2 - - + -
65O CYS* 3.4 30.5 + - - +
19P LEU* 3.2 35.0 - - + +
22P ALA* 3.5 16.2 - - + +
23P GLY* 3.3 26.1 - - - +
26P ILE* 6.0 0.2 - - + -
62P GLY* 5.7 0.9 - - - -
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Residues in contact with GLY 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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61N THR* 5.6 0.7 - - - -
64N PHE* 4.9 4.5 - - - -
19O LEU* 3.6 17.6 - - - +
22O ALA* 3.8 18.7 - - - +
59O GLU* 3.0 19.1 + - - +
61O THR* 1.3 81.2 + - - +
63O LEU* 1.3 61.2 + - - +
66O LEU* 3.2 23.6 - - - +
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Residues in contact with LEU 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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64N PHE* 6.0 1.8 - - + -
56O ALA 5.9 0.7 - - - +
59O GLU* 3.1 41.7 - - + +
60O ALA* 2.9 10.2 + - - +
62O GLY* 1.3 82.3 - - - +
64O PHE* 1.3 63.0 + - + +
65O CYS 3.4 0.4 - - - -
66O LEU* 3.1 15.4 + - + +
67O MET* 2.9 45.4 + - + +
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Residues in contact with PHE 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 ALA* 3.0 44.4 + - + +
61O THR* 4.3 4.0 - - + +
63O LEU* 1.3 77.9 - - + +
65O CYS* 1.3 61.6 - - - +
67O MET* 3.1 35.2 + - + +
68O VAL* 3.1 19.2 + - - +
19P LEU* 4.2 11.2 - - + -
59P GLU* 5.0 7.6 - - - -
62P GLY 4.9 7.4 - - - -
63P LEU* 6.1 1.8 - - + -
66P LEU* 3.5 51.1 - - + +
70P PHE* 5.6 3.8 - + - -
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Residues in contact with CYS 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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15O SER* 3.4 26.1 + - - +
16O THR* 5.2 0.2 - - - -
18O GLY 3.5 13.0 - - - -
19O LEU* 3.5 21.8 - - + +
61O THR 3.4 13.3 + - - +
63O LEU 3.4 0.2 - - - -
64O PHE* 1.3 77.9 - - - +
66O LEU* 1.3 60.5 + - - +
68O VAL* 3.7 17.0 + - - +
69O SER* 3.8 9.5 + - - -
16P THR* 3.4 23.1 - - - -
19P LEU* 3.3 31.2 - - - -
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Residues in contact with LEU 66 (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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64N PHE* 3.5 62.4 - - + +
68N VAL* 5.8 3.1 - - + -
19O LEU* 3.7 10.8 - - + +
62O GLY 3.2 24.0 - - - +
63O LEU* 3.1 17.6 + - + +
64O PHE 3.0 0.6 - - - -
65O CYS* 1.3 79.6 - - - +
67O MET* 1.3 61.6 + - + +
69O SER* 2.7 27.7 + - - +
70O PHE* 3.1 32.5 - - + -
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Residues in contact with MET 67 (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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63O LEU* 2.9 31.4 + - + +
64O PHE* 3.1 37.4 + - + +
66O LEU* 1.3 75.9 - - + +
68O VAL* 1.3 66.5 + - - +
70O PHE* 3.2 13.3 + - + +
71O LEU* 3.1 35.2 + - + +
70P PHE* 6.3 2.7 - - + -
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Residues in contact with VAL 68 (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 SER* 3.7 16.8 - - - -
64O PHE* 3.1 17.7 - - + +
65O CYS 3.8 7.6 - - - +
66O LEU 3.3 0.2 - - - -
67O MET* 1.3 77.7 - - + +
69O SER* 1.3 59.6 + - - +
71O LEU* 3.4 15.2 + - + +
72O LEU* 3.2 28.0 - - + +
12P ALA 3.9 11.9 - - - +
16P THR* 3.6 25.8 - - + -
19P LEU* 6.1 0.7 - - + -
66P LEU* 5.9 2.9 - - + -
69P SER* 4.5 15.0 - - - +
73P LEU* 4.6 13.7 - - + -
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Residues in contact with SER 69 (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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68N VAL* 4.5 17.7 - - - +
12O ALA* 4.1 16.2 - - - -
15O SER* 3.6 18.0 + - - -
16O THR* 4.9 2.9 - - - -
65O CYS 3.8 5.2 + - - -
66O LEU* 2.7 27.4 + - - +
68O VAL* 1.3 80.7 - - - +
70O PHE* 1.3 68.8 + - - +
72O LEU* 3.3 2.8 + - - +
73O LEU* 3.2 33.5 + - - +
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Residues in contact with PHE 70 (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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64N PHE* 5.7 3.8 - + - -
67N MET* 6.3 1.8 - - + -
68N VAL* 6.5 0.9 - - + -
71N LEU* 5.1 8.5 - - + -
66O LEU* 3.1 51.1 - - + -
67O MET* 3.2 12.6 + - + +
69O SER* 1.3 76.9 + - - +
71O LEU* 1.3 54.7 + - + +
72O LEU 3.0 5.3 + - - -
73O LEU* 3.8 1.8 - - + -
74O PHE* 2.9 44.7 + + + +
75O GLY* 2.7 31.8 + - - -
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Residues in contact with LEU 71 (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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67O MET* 3.1 29.1 + - + +
68O VAL* 3.8 9.0 - - + +
69O SER 3.3 1.0 - - - -
70O PHE* 1.3 79.5 - - + +
72O LEU* 1.3 67.1 + - - +
75O GLY* 4.8 7.6 - - - -
76O VAL* 3.0 28.3 + - - +
70P PHE* 5.1 9.0 - - + -
73P LEU* 4.1 23.1 - - + +
74P PHE* 3.7 39.0 - - + -
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Residues in contact with LEU 72 (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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8O LYS* 3.3 38.0 - - - +
9O TYR* 5.2 1.0 - - - -
11O GLY* 3.4 38.4 - - - +
12O ALA* 3.6 5.8 - - + +
68O VAL* 3.2 28.0 - - + +
69O SER 3.3 6.7 + - - +
70O PHE 3.0 0.2 - - - -
71O LEU* 1.3 87.6 - - - +
73O LEU* 1.3 64.3 + - - +
76O VAL* 3.7 12.5 - - - +
9P TYR* 3.4 43.7 - - + +
12P ALA* 5.3 0.7 - - + -
13P GLY* 4.8 1.3 - - - +
73P LEU* 3.8 13.9 - - + -
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Residues in contact with LEU 73 (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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68N VAL* 4.6 14.8 - - + -
71N LEU* 4.3 33.4 - - + +
72N LEU* 3.8 9.2 - - + -
76N VAL* 5.5 2.8 - - - +
8O LYS 4.2 0.2 - - - +
9O TYR* 3.6 34.6 - - + -
12O ALA* 3.8 22.2 - - + -
69O SER* 3.2 21.2 + - - +
70O PHE* 5.5 1.8 - - + -
71O LEU 3.8 0.2 - - - -
72O LEU* 1.3 87.6 - - - +
74O PHE* 1.3 80.9 + - + +
75O GLY 3.5 1.1 - - - -
76O VAL* 5.2 2.2 - - - +
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Residues in contact with PHE 74 (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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71N LEU* 3.7 43.1 - - + -
76N VAL* 5.4 10.3 - - - -
70O PHE* 2.9 37.6 + + + +
73O LEU* 1.3 90.6 - - + +
75O GLY* 1.3 58.6 + - - +
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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