Contacts of the strand formed by residues 40 - 48 (chain P) in PDB entry 4PJO
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 LEU 40 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6O PRO* 4.8 0.4 - - - -
19P CYS* 3.8 28.0 - - - -
31P PHE* 3.7 24.9 - - + -
33P ALA 3.4 2.5 - - - -
34P PHE* 4.1 6.3 - - + -
38P MET* 3.5 17.9 - - + +
39P ASN* 1.3 82.7 - - - +
41P ILE* 1.3 66.9 + - - +
42P LEU* 4.1 16.6 - - + -
71P LEU* 3.3 8.8 - - - +
72P LEU* 3.0 49.1 + - + -
77P LEU* 3.7 20.6 - - + -
80P MET* 3.9 14.8 - - - -
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Residues in contact with ILE 41 (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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6O PRO* 3.8 17.5 - - + -
9O VAL* 3.4 34.1 - - + -
73O LEU* 5.4 1.1 - - + -
83O LEU* 4.9 9.2 - - + -
31P PHE* 3.7 0.9 - - - -
32P LYS* 2.8 40.2 + - + -
33P ALA* 2.9 27.7 + - + +
40P LEU* 1.3 80.3 - - - +
42P LEU* 1.3 68.3 + - - +
69P LEU* 3.8 26.9 - - + -
70P VAL 3.4 3.4 - - - +
71P LEU* 3.8 24.5 - - + -
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Residues in contact with LEU 42 (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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17P MET* 5.1 0.9 - - + +
19P CYS* 4.0 20.9 - - + -
27P PHE* 4.0 33.4 - - + +
29P GLY* 4.0 16.8 - - - +
30P THR 3.2 2.2 - - - +
31P PHE* 3.8 28.7 - - + -
40P LEU* 4.3 18.8 - - + -
41P ILE* 1.3 83.0 - - - +
43P CYS* 1.3 59.4 + - - +
45P CYS* 3.8 20.4 - - + -
68P GLY 3.5 2.1 - - - +
69P LEU* 3.5 7.8 - - - +
70P VAL* 2.9 36.2 + - + +
72P LEU* 5.2 3.1 - - + -
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Residues in contact with CYS 43 (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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78O LYS* 3.7 31.2 - - - +
16P ARG* 3.3 0.7 + - - -
29P GLY* 3.5 0.9 - - - -
30P THR* 2.8 41.4 + - - +
32P LYS* 3.5 25.8 - - + -
42P LEU* 1.3 70.6 - - - +
44P ASP* 1.3 85.4 + - - +
45P CYS 2.9 4.8 + - - -
68P GLY 4.1 0.4 - - - -
69P LEU* 3.5 20.9 - - - -
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Residues in contact with ASP 44 (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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16N ARG* 4.8 11.4 + - - +
78O LYS* 3.4 27.8 + - - +
16P ARG* 2.8 22.9 + - - +
30P THR* 4.2 6.6 + - - -
43P CYS* 1.3 78.8 - - - +
45P CYS* 1.3 60.6 + - - +
46P ASP* 3.0 15.7 - - - +
66P VAL* 5.6 1.1 - - - -
68P GLY* 3.2 16.7 + - - -
69P LEU* 4.5 0.6 - - - +
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Residues in contact with CYS 45 (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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27P PHE* 3.8 32.1 - - - -
28P ILE 3.2 12.6 - - - -
42P LEU* 3.8 26.2 - - + -
43P CYS 2.9 2.7 + - - -
44P ASP* 1.3 72.8 - - - +
46P ASP* 1.3 71.6 + - - +
66P VAL* 4.1 0.2 - - - +
67P LEU* 3.0 28.0 + - - +
68P GLY 2.7 22.7 + - - +
70P VAL* 3.5 22.9 - - + -
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Residues in contact with ASP 46 (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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16P ARG* 4.3 9.2 + - - +
27P PHE* 3.4 3.5 - - - -
28P ILE 2.7 33.4 + - - +
44P ASP 3.0 17.2 - - - +
45P CYS* 1.3 81.1 - - - +
47P GLU* 1.3 60.6 + - - +
48P PHE* 3.6 24.4 - - + -
64P LYS* 3.5 30.6 + - + +
65P ARG 3.9 3.6 - - - -
66P VAL* 4.0 18.3 - - - +
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Residues in contact with GLU 47 (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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22N LEU* 3.8 1.7 - - - +
70O PHE* 4.6 1.0 - - - -
25P ARG* 3.4 23.9 + - - -
26P ILE 3.3 5.6 - - - +
27P PHE* 3.6 16.6 - - + -
45P CYS 4.3 0.4 + - - -
46P ASP* 1.3 73.2 - - - +
48P PHE* 1.3 73.0 + - - +
49P ARG* 2.7 33.5 + - - +
63P GLU 3.5 0.9 - - - +
64P LYS* 3.3 4.9 - - - +
65P ARG* 2.9 70.4 + - + +
67P LEU* 3.8 20.5 - - + +
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Residues in contact with PHE 48 (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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16P ARG* 6.0 0.4 - - - -
25P ARG* 3.6 2.8 - - - -
26P ILE* 2.9 45.7 + - + +
28P ILE* 3.6 35.2 - - + -
46P ASP* 3.6 28.9 - - + -
47P GLU* 1.3 78.5 - - - +
49P ARG* 1.3 67.0 + - - +
50P LYS* 6.1 0.7 - - + -
62P GLU* 3.7 34.5 - - + +
63P GLU 3.5 3.8 - - - -
64P LYS* 3.6 42.6 - - + -
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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