Contacts of the helix formed by residues 60 - 74 (chain p) 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 p).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56p ALA 3.5 10.0 + - - +
57p LEU* 3.5 16.2 - - - +
58p SER 3.1 0.2 - - - -
59p GLU* 1.3 77.6 - - - +
61p THR* 1.3 61.1 + - + +
63p LEU* 2.9 26.4 + - - +
64p PHE* 3.0 41.8 + - + -
59q GLU* 5.2 9.4 - - - +
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Residues in contact with THR 61 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18p GLY 3.8 9.6 - - - +
19p LEU* 3.6 2.3 - - - +
21p GLY 4.8 0.4 - - - -
22p ALA* 3.7 10.5 + - - -
57p LEU 5.4 1.6 - - - +
58p SER 3.1 17.0 + - - +
60p ALA* 1.3 78.1 - - + +
62p GLY* 1.3 56.2 + - - +
63p LEU 3.3 1.1 + - - -
64p PHE* 4.4 7.9 - - + -
65p CYS* 3.4 30.3 + - - +
19q LEU* 3.3 32.5 - - + +
22q ALA* 3.6 15.0 - - + +
23q GLY* 3.4 27.5 - - - +
26q ILE* 6.0 0.2 - - + -
62q GLY* 5.7 1.1 - - - -
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Residues in contact with GLY 62 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61o THR* 5.7 0.4 - - - -
64o PHE* 4.9 5.0 - - - -
19p LEU* 3.6 16.6 - - - +
22p ALA* 3.8 18.8 - - - +
59p GLU* 3.0 18.8 + - - +
61p THR* 1.3 81.4 + - - +
63p LEU* 1.3 61.2 + - - +
66p LEU* 3.2 23.9 - - - +
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Residues in contact with LEU 63 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64o PHE* 6.1 1.8 - - + -
56p ALA 5.9 0.9 - - - +
59p GLU* 3.1 41.3 - - + +
60p ALA* 2.9 10.2 + - - +
62p GLY* 1.3 82.4 - - - +
64p PHE* 1.3 63.4 + - + +
66p LEU* 3.1 15.6 + - + +
67p MET* 2.8 46.1 + - + +
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Residues in contact with PHE 64 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60p ALA* 3.0 48.0 + - + +
61p THR* 4.3 4.5 - - + +
63p LEU* 1.3 77.3 - - + +
65p CYS* 1.3 61.5 + - - +
67p MET* 3.1 35.3 + - + +
68p VAL* 3.1 19.4 + - - +
19q LEU* 4.4 9.9 - - + -
59q GLU* 5.0 9.6 - - - -
62q GLY 5.0 4.7 - - - -
63q LEU* 6.1 1.6 - - + -
66q LEU* 3.6 50.0 - - + +
70q PHE* 5.7 3.4 - + - -
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Residues in contact with CYS 65 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15p SER* 3.4 26.0 + - - +
16p THR* 5.2 0.2 - - - -
18p GLY* 3.5 18.2 - - - -
19p LEU* 3.5 21.6 - - + +
61p THR 3.4 13.8 + - - +
63p LEU 3.4 0.4 - - - -
64p PHE* 1.3 78.4 - - - +
66p LEU* 1.3 59.2 - - - +
68p VAL* 3.7 16.4 + - - +
69p SER* 3.8 9.5 + - - -
16q THR* 3.6 17.0 - - - -
19q LEU* 3.3 31.6 - - - -
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Residues in contact with LEU 66 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64o PHE* 3.5 61.9 - - + +
68o VAL* 5.9 2.9 - - + -
19p LEU* 3.7 11.9 - - + +
62p GLY 3.2 25.4 - - - +
63p LEU* 3.1 16.9 + - + +
64p PHE 3.0 0.4 - - - -
65p CYS* 1.3 78.5 - - - +
67p MET* 1.3 61.9 + - + +
69p SER* 2.7 28.0 + - - +
70p PHE* 3.1 34.2 - - + -
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Residues in contact with MET 67 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63p LEU* 2.8 31.4 + - + +
64p PHE* 3.1 37.7 + - + +
66p LEU* 1.3 77.0 - - + +
68p VAL* 1.3 65.2 + - + +
70p PHE* 3.2 14.0 + - + +
71p LEU* 3.1 36.2 + - + +
70q PHE* 6.4 1.8 - - + -
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Residues in contact with VAL 68 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15p SER* 3.7 19.5 - - - -
64p PHE* 3.1 18.4 + - + +
65p CYS* 3.8 7.6 - - - +
66p LEU 3.3 0.2 - - - -
67p MET* 1.3 79.6 - - + +
69p SER* 1.3 60.3 + - - +
71p LEU* 3.4 15.8 + - + +
72p LEU* 3.2 28.9 - - + +
12q ALA 4.1 9.9 - - - +
16q THR* 3.8 22.4 - - + -
19q LEU* 6.2 0.7 - - + -
66q LEU* 5.8 3.6 - - + -
69q SER* 4.6 15.3 - - - +
70q PHE* 6.5 1.8 - - + -
73q LEU* 4.5 14.6 - - + -
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Residues in contact with SER 69 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68o VAL* 4.5 18.9 - - - +
12p ALA* 4.1 15.3 - - - -
15p SER* 3.6 18.5 + - - -
16p THR* 4.9 3.1 - - - -
65p CYS 3.8 4.4 + - - -
66p LEU* 2.7 27.8 + - - +
68p VAL* 1.3 80.5 - - - +
70p PHE* 1.3 68.7 + - - +
72p LEU* 3.3 3.1 + - - +
73p LEU* 3.2 33.4 + - - +
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Residues in contact with PHE 70 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64o PHE* 5.6 3.1 - + - -
67o MET* 6.3 2.2 - - + -
71o LEU* 5.1 8.5 - - + -
66p LEU* 3.1 52.3 - - + -
67p MET* 3.2 12.4 + - + +
69p SER* 1.3 78.2 + - - +
71p LEU* 1.3 53.3 + - + +
72p LEU 3.0 6.1 - - - -
73p LEU* 4.8 1.8 - - + -
74p PHE* 2.9 43.2 + + + +
75p GLY* 2.7 32.3 + - - -
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Residues in contact with LEU 71 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67p MET* 3.1 29.0 + - + +
68p VAL* 3.8 9.6 - - + +
69p SER 3.3 0.8 - - - -
70p PHE* 1.3 76.9 - - + +
72p LEU* 1.3 67.6 - - - +
75p GLY* 4.8 7.4 - - - -
76p VAL* 3.0 28.9 + - - +
70q PHE* 5.1 9.4 - - + -
73q LEU* 4.4 20.1 - - + +
74q PHE* 3.6 39.5 - - + -
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Residues in contact with LEU 72 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8p LYS* 3.3 38.6 - - - +
9p TYR* 5.2 0.9 - - - -
11p GLY* 3.4 37.0 - - - +
12p ALA* 3.6 5.6 - - + +
68p VAL* 3.2 28.0 - - + +
69p SER 3.3 6.5 + - - +
70p PHE 3.0 0.2 - - - -
71p LEU* 1.3 86.7 - - - +
73p LEU* 1.3 64.3 + - - +
76p VAL* 3.7 12.4 - - + +
9q TYR* 3.4 42.2 - - + +
12q ALA* 5.4 0.7 - - + -
13q GLY* 5.0 1.6 - - - +
73q LEU* 3.7 15.3 - - + -
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Residues in contact with LEU 73 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68o VAL* 4.6 13.9 - - + -
71o LEU* 4.1 34.1 - - + +
72o LEU* 3.8 8.3 - - + -
76o VAL* 5.4 3.1 - - - +
8p LYS 4.2 0.4 - - - +
9p TYR* 3.6 35.1 - - + -
12p ALA* 3.8 21.8 - - + -
69p SER* 3.2 22.1 + - - +
70p PHE* 5.8 1.6 - - + -
72p LEU* 1.3 86.5 - - - +
74p PHE* 1.3 82.1 + - + +
75p GLY 3.5 1.3 + - - -
76p VAL* 5.2 2.4 - - - +
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Residues in contact with PHE 74 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71o LEU* 3.7 43.5 - - + -
76o VAL* 5.5 8.7 - - - -
70p PHE* 2.9 36.5 + + + +
73p LEU* 1.3 89.9 - - + +
75p GLY* 1.3 57.8 + - - +
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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