Contacts of the strand formed by residues 56 - 65 (chain e) 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 56 (chain e).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21e ILE* 4.9 5.4 - - + -
33e VAL* 4.3 3.1 - - + -
47e ILE* 4.4 17.9 - - + -
49e GLY 3.7 2.9 - - - +
50e PHE* 3.8 15.3 - - + -
54e MET* 3.6 22.7 - - + +
55e ASN* 1.3 79.7 - - - +
57e VAL* 1.3 61.9 + - - +
58e LEU* 3.9 28.1 + - + -
77e ILE 3.6 0.9 - - - +
78e MET* 3.2 5.9 - - - +
79e LEU* 2.9 47.6 + - + +
84e ILE* 3.9 18.4 - - + -
87e LEU* 4.2 22.2 - - + -
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Residues in contact with VAL 57 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47e ILE* 3.5 5.9 - - - +
48e ILE* 3.1 36.3 + - + -
49e GLY 2.8 15.3 + - - +
56e LEU* 1.3 74.3 - - - +
58e LEU* 1.3 61.1 + - - +
76e ARG* 4.2 6.1 - - + -
77e ILE 3.3 9.0 - - - +
78e MET* 4.5 3.4 - - + -
5f LEU* 3.4 29.6 - - + +
6f ASN 3.6 21.3 - - - +
7f PRO* 3.6 13.0 - - + -
10f PHE* 4.0 27.6 - - + -
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Residues in contact with LEU 58 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31e ILE* 5.2 3.6 - - + +
33e VAL* 4.6 11.9 - - + -
43e ILE* 3.9 28.3 - - + -
45e GLY* 4.0 21.5 - - - +
46e CYS 3.3 1.6 - - - +
47e ILE* 3.7 30.5 - - + -
48e ILE* 3.9 2.2 - - - -
56e LEU* 4.1 17.3 - - + +
57e VAL* 1.3 75.9 - - - +
59e ASP* 1.3 63.3 + - - +
60e ASP 3.7 0.9 - - - -
61e ALA* 4.1 8.5 - - + +
75e GLY 3.7 2.4 - - - +
76e ARG* 3.4 2.8 - - - +
77e ILE* 2.8 49.6 + - + -
79e LEU* 4.4 12.3 - - + -
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Residues in contact with ASP 59 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46e CYS* 2.7 22.3 + - + +
48e ILE* 2.7 26.9 - - + +
58e LEU* 1.3 72.6 - - - +
60e ASP* 1.3 69.7 + - + +
61e ALA 3.6 0.7 - - - -
75e GLY 3.3 13.9 - - - +
76e ARG* 2.2 43.2 + - - +
3f LEU* 5.8 0.3 - - - +
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Residues in contact with ASP 60 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30e ARG* 2.7 42.8 + - - +
45e GLY* 4.3 1.8 - - - -
46e CYS* 4.1 8.3 - - + +
58e LEU 3.7 0.2 - - - -
59e ASP* 1.3 86.9 - - + +
61e ALA* 1.3 60.8 + - - +
62e GLU* 3.8 2.1 - - - +
73e GLN* 4.9 5.3 - - - +
75e GLY* 4.5 10.2 + - - -
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Residues in contact with ALA 61 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43e ILE* 4.8 0.7 - - + -
44e GLU 3.1 10.8 - - - +
45e GLY* 4.2 0.9 - - - -
58e LEU* 4.1 13.2 - - + -
60e ASP* 1.3 76.4 - - - +
62e GLU* 1.3 62.3 + - - +
73e GLN* 3.9 3.3 - - - +
74e LEU* 2.9 27.5 + - + +
75e GLY 3.0 19.1 + - - +
77e ILE* 3.6 37.9 - - + -
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Residues in contact with GLU 62 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30e ARG* 3.3 28.3 + - - +
43e ILE* 3.4 3.6 - - - +
44e GLU* 2.9 39.3 + - - +
60e ASP 3.8 0.4 - - - +
61e ALA* 1.3 78.8 - - - +
63e GLU* 1.3 64.9 + - - +
64e ILE* 4.0 2.7 + - - +
71e ARG* 3.0 37.5 + - + -
72e LYS 3.1 14.6 - - - +
73e GLN* 3.4 31.1 + - - +
74e LEU* 3.6 5.6 - - - -
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Residues in contact with GLU 63 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41e MET* 3.5 22.7 - - - +
42e ARG 3.5 5.6 - - - -
43e ILE* 4.1 7.0 - - + -
62e GLU* 1.3 73.7 - - - +
64e ILE* 1.3 58.7 + - - +
65e HIS* 3.2 32.9 + - - +
71e ARG* 3.6 2.8 - - - -
72e LYS* 2.9 51.6 + - + +
74e LEU* 3.7 12.1 - - + +
22f LYS* 4.1 14.2 + - - +
71f TYR* 2.8 35.6 + - - -
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Residues in contact with ILE 64 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32e GLN* 3.3 30.7 - - - +
40e ASN 3.8 0.5 - - - +
41e MET* 3.4 2.2 - - - -
42e ARG* 2.8 40.1 + - + +
43e ILE 4.6 2.5 - - - -
44e GLU* 4.0 22.9 - - + +
62e GLU* 4.1 8.3 - - - +
63e GLU* 1.3 75.7 - - - +
65e HIS* 1.3 64.1 + - - +
66e SER* 4.0 1.2 + - - -
69e LYS* 4.0 24.0 - - - +
70e SER 4.2 3.1 - - - +
71e ARG* 3.4 45.5 - - + +
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Residues in contact with HIS 65 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40e ASN* 3.6 5.9 - - - +
41e MET* 4.0 20.7 + - + +
63e GLU* 3.2 47.8 + - + +
64e ILE* 1.3 76.2 - - - +
66e SER* 1.3 57.2 + - - +
67e LYS* 3.3 15.5 + - + +
68e THR* 3.8 24.2 - - + +
69e LYS* 2.7 38.9 + - - -
70e SER 3.6 13.2 + - - -
72e LYS* 4.7 7.7 - - + +
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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