Contacts of the strand formed by residues 41 - 49 (chain a) 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 CYS 41 (chain a).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10a LEU* 4.5 7.6 - - - -
20a CYS* 6.0 0.2 - - - -
32a LEU* 3.9 23.6 - - + -
34a GLU 3.6 3.1 - - - -
35a ALA* 4.1 10.1 - - - -
39a MET 3.3 17.3 - - - -
40a ASN* 1.3 77.7 - - - +
42a GLN* 1.3 60.6 + - - +
43a MET* 4.5 12.3 - - + -
62a TYR* 3.2 6.6 - - - -
63a ILE* 2.7 47.5 + - + +
68a ILE* 4.3 10.3 - - + -
71a LEU* 4.4 16.2 - - + -
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Residues in contact with GLN 42 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32a LEU* 3.5 5.0 - - - +
33a ILE* 3.0 55.6 + - + +
34a GLU* 2.9 14.7 + - - +
41a CYS* 1.3 74.7 - - - +
43a MET* 1.3 62.7 + - - +
60a GLN* 3.4 24.5 + - - +
61a VAL 3.3 14.4 - - - +
62a TYR* 3.8 12.0 - - + -
8g GLU* 3.2 29.3 + - - +
11g LYS* 4.1 15.9 - - - +
12g PHE* 4.0 22.2 - - + -
76g VAL* 5.7 1.4 - - - +
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Residues in contact with MET 43 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18a VAL* 3.4 41.5 - - + +
20a CYS* 4.5 7.0 - - + -
28a TYR* 3.7 13.7 - - - +
30a GLY 3.6 19.5 - - - +
31a LYS 3.2 10.1 - - - +
32a LEU* 4.2 11.4 - - + -
33a ILE* 4.3 2.5 - - - +
41a CYS* 4.5 9.4 - - + -
42a GLN* 1.3 80.3 - - - +
44a SER* 1.3 61.3 + - - +
46a ILE* 3.3 24.2 - - + -
60a GLN* 3.3 7.4 - - - +
61a VAL* 2.8 38.2 + - + +
63a ILE* 4.0 24.7 - - - -
71a LEU* 5.9 0.4 - - - -
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Residues in contact with SER 44 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31a LYS* 2.9 32.5 + - - -
33a ILE* 3.5 26.6 - - - +
43a MET* 1.3 70.1 - - - +
45a ASN* 1.3 84.8 + - - +
46a ILE* 3.5 4.1 - - - +
59a GLU 3.2 7.4 - - - -
60a GLN* 2.7 27.3 + - - -
75g ARG* 5.3 1.1 + - - -
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Residues in contact with ASN 45 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29a ARG 3.6 6.6 - - - +
30a GLY* 3.6 5.7 - - - -
31a LYS* 5.1 13.8 - - + +
44a SER* 1.3 87.0 + - - +
46a ILE* 1.3 62.1 - - - +
47a THR* 4.0 1.7 + - - -
57a GLN* 4.9 5.6 + - - +
58a LEU 3.5 5.4 - - - -
59a GLU* 3.0 16.2 + - - +
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Residues in contact with ILE 46 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28a TYR* 3.9 28.5 - - + -
29a ARG 3.1 4.7 - - - +
30a GLY* 3.8 4.0 - - - -
43a MET* 3.3 47.6 - - + +
44a SER 3.7 13.9 - - - +
45a ASN* 1.3 73.6 - - - +
47a THR* 1.3 64.2 + - - +
48a VAL* 3.5 15.5 - - + +
56a ALA 3.7 0.2 - - - +
57a GLN* 3.2 11.9 + - - -
58a LEU* 2.9 42.5 + - + +
59a GLU 5.0 0.2 - - - +
61a VAL* 3.7 22.4 - - + -
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Residues in contact with THR 47 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27a VAL 3.4 3.6 - - - +
29a ARG* 2.8 40.5 + - - +
45a ASN 4.8 1.9 + - - -
46a ILE* 1.3 73.5 - - - +
48a VAL* 1.3 71.2 + - - +
49a THR* 3.8 6.1 + - - +
55a VAL* 4.2 17.7 - - + -
56a ALA 3.4 8.5 - - - +
57a GLN* 3.5 22.5 + - - +
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Residues in contact with VAL 48 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26a GLU* 4.3 3.4 - - + -
27a VAL 3.3 6.5 - - - +
28a TYR* 3.6 37.9 - - + +
46a ILE* 3.5 7.4 + - - +
47a THR* 1.3 76.8 - - - +
49a THR* 1.3 64.9 + - - +
50a TYR* 3.6 35.9 - - + +
55a VAL* 3.2 6.9 - - - +
56a ALA* 3.2 49.8 + - + +
58a LEU* 4.1 14.1 - - + +
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Residues in contact with THR 49 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25a GLY 4.3 1.6 - - - +
26a GLU* 3.5 2.8 - - - -
27a VAL* 2.9 43.8 + - + +
47a THR* 3.8 9.0 + - - +
48a VAL* 1.3 77.0 + - - +
50a TYR* 1.3 74.3 + - - +
53a GLY 3.9 19.5 - - - +
54a ARG 3.5 3.4 - - - +
55a VAL* 4.0 12.0 - - + +
21k TYR* 4.0 23.1 - - + -
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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