Contacts of the strand formed by residues 41 - 50 (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 MET 41 (chain e).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35e LEU* 3.6 25.3 + - + +
38e GLN* 3.3 48.8 - - + +
39e VAL 4.4 1.4 - - - -
40e ASN* 1.3 82.6 + - + +
42e ARG* 1.3 82.5 + - - +
43e ILE* 4.6 4.7 - - + -
63e GLU* 3.5 40.2 - - + +
64e ILE 3.4 8.3 - - - +
65e HIS* 4.0 15.5 - - + +
22f LYS* 4.8 8.3 - - - -
70f LEU* 4.2 17.7 - - + -
25g ARG* 5.6 0.2 + - - -
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Residues in contact with ARG 42 (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* 3.0 31.1 + - + +
33e VAL 3.3 13.7 - - - +
34e TRP* 3.2 57.1 - - - +
35e LEU* 4.2 3.4 - - - +
39e VAL 5.8 3.4 + - - +
40e ASN 4.1 0.2 + - - -
41e MET* 1.3 82.1 - - - +
43e ILE* 1.3 72.6 + - - +
64e ILE* 2.8 45.0 + - + +
66e SER* 5.7 4.1 + - - +
88e GLN* 3.6 4.2 + - - +
25g ARG* 5.4 8.4 - - - +
47g GLU* 3.4 29.0 + - - -
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Residues in contact with ILE 43 (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* 3.5 0.9 - - - +
33e VAL* 2.6 48.1 + - + +
35e LEU* 4.5 16.3 - - + +
41e MET* 4.6 2.7 - - + -
42e ARG* 1.3 83.7 - - - +
44e GLU* 1.3 63.6 - - - +
58e LEU* 3.9 26.5 - - + -
61e ALA* 4.8 0.7 - - + -
62e GLU 3.4 12.8 - - - +
63e GLU* 4.1 10.1 - - + -
64e ILE* 4.6 2.0 - - - -
74e LEU* 4.9 0.9 - - + -
77e ILE* 4.2 10.3 - - + -
79e LEU* 3.7 26.5 - - + -
70f LEU* 4.9 4.9 - - + -
71f TYR* 3.8 27.6 - - + -
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Residues in contact with GLU 44 (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 35.7 + - - +
31e ILE 3.0 10.3 - - - +
32e GLN* 3.7 20.3 + - + +
33e VAL* 5.4 0.2 - - - -
43e ILE* 1.3 78.2 - - - +
45e GLY* 1.3 58.0 + - - +
58e LEU* 5.1 0.7 - - - -
61e ALA* 3.1 4.7 - - - +
62e GLU* 2.9 45.5 + - - +
64e ILE* 4.0 8.6 - - + +
71e ARG* 3.0 30.2 + - - -
90e VAL 3.2 24.1 - - - +
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Residues in contact with GLY 45 (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* 3.5 19.0 - - - -
31e ILE* 2.7 42.1 + - - +
44e GLU* 1.3 76.5 - - - +
46e CYS* 1.3 58.2 + - - -
58e LEU* 4.0 14.9 - - - +
60e ASP 3.9 7.4 - - - -
61e ALA* 4.2 4.9 - - - -
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Residues in contact with CYS 46 (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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28e ARG* 3.6 22.7 - - + +
29e SER 3.6 17.0 - - - +
30e ARG* 3.9 24.6 - - - +
45e GLY* 1.3 70.9 - - - -
47e ILE* 1.3 61.2 + - - +
48e ILE* 2.9 7.8 + - + +
58e LEU* 3.3 2.9 - - - -
59e ASP* 2.7 44.3 + - + +
60e ASP* 4.1 3.8 - - - +
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Residues in contact with ILE 47 (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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21e ILE* 4.3 18.2 - - + -
24e TYR* 4.4 12.6 + - + +
25e LEU* 3.2 35.4 - - + +
28e ARG* 5.7 2.3 - - - +
29e SER 4.1 5.5 + - - -
31e ILE* 3.8 33.9 - - + -
45e GLY 3.9 0.2 + - - -
46e CYS* 1.3 67.6 - - - +
48e ILE* 1.3 61.6 + - - +
49e GLY* 3.5 26.0 - - - +
50e PHE* 4.2 15.5 - - + -
56e LEU* 4.4 17.7 - - + -
57e VAL 3.5 5.8 - - - +
58e LEU* 3.7 16.8 - - + -
87e LEU* 4.8 3.4 - - + -
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Residues in contact with ILE 48 (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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25e LEU* 3.4 20.7 - - - +
46e CYS* 2.9 4.1 + - + +
47e ILE* 1.3 73.1 - - - +
49e GLY* 1.3 56.3 + - - +
57e VAL* 3.1 8.3 + - + +
58e LEU 3.9 4.3 - - - -
59e ASP* 2.7 60.1 - - + +
76e ARG* 3.4 18.6 - - + +
3f LEU* 3.4 26.9 - - + +
5f LEU* 3.4 39.9 + - + +
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Residues in contact with GLY 49 (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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25e LEU* 4.4 7.0 - - - -
47e ILE* 3.4 10.6 - - - +
48e ILE* 1.3 81.7 - - - +
50e PHE* 1.3 66.8 + - - +
56e LEU* 3.7 0.2 - - - -
57e VAL* 2.8 27.0 + - - +
5f LEU 3.1 17.3 + - - -
6f ASN* 3.3 8.3 - - - -
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Residues in contact with PHE 50 (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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18e ILE* 4.1 37.2 - - + -
21e ILE* 3.3 34.3 - - + -
22e PHE* 4.0 22.4 - + + -
25e LEU* 4.4 13.0 - - + -
47e ILE* 4.2 7.6 - - + -
49e GLY* 1.3 80.4 - - - +
51e ASP* 1.3 87.3 + - - +
54e MET* 5.3 2.0 - - + -
55e ASN 3.1 16.8 - - - +
56e LEU* 3.8 12.3 - - + -
6f ASN* 3.0 21.6 + - - +
7f PRO* 3.2 17.0 - - - +
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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