Contacts of the helix formed by residues 60 - 74 (chain j) 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 j).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56j ALA 3.5 9.3 + - - +
57j LEU* 3.5 16.2 - - - +
58j SER 3.1 0.6 - - - -
59j GLU* 1.3 77.2 - - - +
61j THR* 1.3 60.7 + - + +
63j LEU* 2.9 26.8 + - - +
64j PHE* 3.0 39.9 + - + -
59k GLU* 5.4 7.6 - - - +
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Residues in contact with THR 61 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18j GLY 3.8 9.5 - - - +
19j LEU* 3.6 2.4 - - - +
21j GLY* 4.8 0.7 - - - -
22j ALA* 3.7 10.2 + - - -
57j LEU 5.4 0.9 - - - +
58j SER 3.1 16.7 + - - +
60j ALA* 1.3 78.7 - - + +
62j GLY* 1.3 59.1 + - - +
63j LEU 3.3 0.8 + - - -
64j PHE* 4.4 6.7 - - + -
65j CYS* 3.4 30.1 + - - +
19k LEU* 3.2 23.1 - - + +
22k ALA* 3.6 15.5 - - + +
23k GLY* 3.2 38.0 - - - +
26k ILE* 6.0 0.2 - - + -
62k GLY* 5.9 0.4 - - - -
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Residues in contact with GLY 62 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19j LEU* 3.6 17.0 - - - +
22j ALA* 3.8 19.0 - - - +
59j GLU* 3.0 17.4 + - - +
60j ALA 3.0 1.4 - - - -
61j THR* 1.3 80.4 + - - +
63j LEU* 1.3 62.3 + - - +
66j LEU* 3.2 24.3 - - - +
61s THR* 5.8 0.7 - - - -
64s PHE* 5.0 4.9 - - - -
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Residues in contact with LEU 63 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56j ALA 5.9 0.7 - - - +
59j GLU* 3.1 41.5 - - + +
60j ALA* 2.9 9.5 + - - +
62j GLY* 1.3 82.7 - - - +
64j PHE* 1.3 63.2 + - + +
65j CYS 3.4 0.2 - - - -
66j LEU* 3.1 14.8 + - + +
67j MET* 2.9 44.7 + - + +
64s PHE* 6.2 1.1 - - + -
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Residues in contact with PHE 64 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60j ALA* 3.0 45.3 + - + +
61j THR* 4.3 4.5 - - + +
63j LEU* 1.3 77.7 - - + +
65j CYS* 1.3 61.0 + - - +
67j MET* 3.1 36.5 + - + +
68j VAL* 3.1 18.0 + - - +
19k LEU* 4.3 11.7 - - + -
59k GLU* 5.1 9.2 - - - -
62k GLY 5.2 4.5 - - - -
63k LEU* 6.4 0.9 - - + -
66k LEU* 3.9 47.6 - - + -
70k PHE* 6.0 1.8 - + - -
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Residues in contact with CYS 65 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15j SER* 3.4 25.0 + - - +
16j THR* 5.2 0.2 - - - -
18j GLY* 3.5 18.6 - - - -
19j LEU* 3.5 21.4 - - + +
61j THR 3.4 14.2 + - - -
63j LEU 3.4 0.4 - - - -
64j PHE* 1.3 79.0 - - - +
66j LEU* 1.3 59.4 + - - +
68j VAL* 3.7 16.8 + - - +
69j SER* 3.8 9.2 + - - -
16k THR* 3.5 18.8 - - - -
19k LEU* 3.5 28.9 - - - -
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Residues in contact with LEU 66 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19j LEU* 3.7 11.5 - - + +
62j GLY 3.2 24.5 - - - +
63j LEU* 3.1 18.0 + - + +
64j PHE 3.0 0.6 - - - -
65j CYS* 1.3 78.5 - - - +
67j MET* 1.3 61.3 + - + +
69j SER* 2.7 27.6 + - - +
70j PHE* 3.1 34.4 - - + -
64s PHE* 3.6 61.2 - - + -
68s VAL* 6.0 2.7 - - + -
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Residues in contact with MET 67 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63j LEU* 2.9 32.1 + - + +
64j PHE* 3.1 37.9 + - + +
66j LEU* 1.3 76.5 - - + +
68j VAL* 1.3 64.6 + - + +
70j PHE* 3.2 13.7 + - + +
71j LEU* 3.1 36.3 + - + +
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Residues in contact with VAL 68 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15j SER* 3.7 17.0 - - - -
64j PHE* 3.1 19.2 + - + +
65j CYS 3.8 7.4 - - - +
66j LEU 3.3 0.6 - - - -
67j MET* 1.3 78.3 - - + +
69j SER* 1.3 61.2 + - - +
71j LEU* 3.4 16.2 + - + +
72j LEU* 3.2 29.3 - - + +
12k ALA 4.2 10.1 - - - +
16k THR* 3.6 26.9 - - + -
19k LEU* 6.1 0.7 - - + -
66k LEU* 5.9 3.6 - - + -
69k SER* 4.8 12.6 - - - +
73k LEU* 4.8 12.3 - - + -
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Residues in contact with SER 69 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12j ALA* 4.1 16.6 - - - +
15j SER* 3.6 18.2 + - - -
16j THR* 4.9 3.4 - - - -
65j CYS 3.8 4.8 + - - -
66j LEU* 2.7 28.0 + - - +
68j VAL* 1.3 79.3 - - - +
70j PHE* 1.3 68.2 + - - +
72j LEU* 3.3 2.8 + - - +
73j LEU* 3.2 32.5 + - - +
68s VAL* 4.7 16.7 - - - +
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Residues in contact with PHE 70 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66j LEU* 3.1 50.9 - - + -
67j MET* 3.2 12.4 + - + +
69j SER* 1.3 78.0 + - - +
71j LEU* 1.3 53.5 - - + +
72j LEU 3.0 5.2 - - - -
73j LEU* 3.8 2.5 - - + -
74j PHE* 2.9 43.5 + + + +
75j GLY* 2.7 32.2 + - - -
64s PHE* 5.7 3.1 - + - -
67s MET* 6.4 1.1 - - + -
71s LEU* 5.3 7.4 - - + -
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Residues in contact with LEU 71 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67j MET* 3.1 30.1 + - + +
68j VAL* 3.8 11.9 - - + +
69j SER 3.3 0.4 - - - -
70j PHE* 1.3 79.5 - - + +
72j LEU* 1.3 68.4 + - - +
75j GLY* 4.8 7.4 - - - -
76j VAL* 3.0 28.2 + - - +
9k TYR* 5.4 0.2 - - - -
70k PHE* 5.4 7.9 - - + -
73k LEU* 4.5 17.8 - - + +
74k PHE* 4.1 33.7 - - + -
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Residues in contact with LEU 72 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8j LYS* 3.3 39.6 - - - +
9j TYR* 5.2 1.4 - - - -
11j GLY* 3.4 39.0 - - - +
12j ALA* 3.6 5.6 - - + +
68j VAL* 3.2 27.4 - - + +
69j SER 3.3 6.2 + - - +
70j PHE 3.0 0.4 - - - -
71j LEU* 1.3 86.7 - - - +
73j LEU* 1.3 64.3 + - - +
76j VAL* 3.7 12.0 - - + +
9k TYR* 3.7 41.1 - - + +
12k ALA* 5.6 0.4 - - + -
13k GLY* 4.9 2.0 - - - +
73k LEU* 4.1 14.6 - - + -
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Residues in contact with LEU 73 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8j LYS 4.2 0.2 - - - +
9j TYR* 3.6 35.3 - - + -
12j ALA* 3.8 22.7 - - + -
69j SER* 3.2 22.8 + - - +
70j PHE* 5.5 1.8 - - + -
72j LEU* 1.3 86.9 - - - +
74j PHE* 1.3 80.9 + - + +
75j GLY 3.5 0.9 - - - -
76j VAL* 5.2 2.4 - - - +
68s VAL* 4.8 12.8 - - + -
71s LEU* 4.2 33.2 - - + +
72s LEU* 4.1 8.1 - - + -
76s VAL* 5.7 0.9 - - - +
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Residues in contact with PHE 74 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70j PHE* 2.9 39.4 + + + +
73j LEU* 1.3 90.8 - - + +
75j GLY* 1.3 59.3 + - - +
71s LEU* 3.9 39.0 - - + -
76s VAL* 5.7 5.8 - - - -
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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