Contacts of the strand formed by residues 26 - 34 (chain b) 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 ILE 26 (chain b).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18b ARG* 3.4 47.1 - - + +
19b CYS 3.2 5.2 - - - +
20b ILE* 3.8 26.9 - - + -
24b GLY 4.3 6.7 - - - +
25b ARG* 1.3 77.2 - - - +
27b PHE* 1.3 65.8 + - - +
28b ILE* 3.8 17.9 - - + -
46b ASP 3.8 0.3 - - - +
47b GLU* 3.3 4.3 - - - -
48b PHE* 2.8 49.1 + - + +
49b ARG* 5.6 1.3 - - - -
50b LYS* 6.1 5.6 - - + -
47c LEU* 6.4 1.6 - - + -
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Residues in contact with PHE 27 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70a PHE* 3.7 24.7 - + - -
17b MET 3.3 3.1 - - - +
18b ARG* 3.5 0.2 - - - -
19b CYS* 2.7 44.4 + - + +
21b LEU* 3.7 32.3 - - + +
25b ARG* 4.2 5.1 - - + -
26b ILE* 1.3 81.7 - - - +
28b ILE* 1.3 59.4 - - - +
42b LEU* 4.0 14.8 - - + -
45b CYS* 3.8 18.2 - - - -
46b ASP 3.4 2.9 - - - -
47b GLU* 3.9 21.3 - - + -
67b LEU* 3.6 25.8 - - + -
70b VAL* 3.8 23.6 - - + -
72b LEU* 4.0 15.7 - - + -
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Residues in contact with ILE 28 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16b ARG* 3.6 23.8 + - - +
17b MET 3.5 8.7 - - - +
18b ARG* 3.9 20.2 - - + +
26b ILE* 3.8 14.1 - - + -
27b PHE* 1.3 76.0 - - - +
29b GLY* 1.3 62.0 + - - +
45b CYS* 3.2 2.8 - - - -
46b ASP 2.7 38.8 + - - -
48b PHE* 3.7 29.8 - - + -
83b GLU* 3.6 45.3 - - + +
101b K 4.3 6.3 - - - -
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Residues in contact with GLY 29 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16b ARG* 3.6 10.8 - - - -
17b MET* 2.9 28.9 + - - +
27b PHE 4.2 0.4 - - - -
28b ILE* 1.3 80.2 - - - +
30b THR* 1.3 65.3 + - - -
31b PHE 3.4 1.4 + - - -
42b LEU* 4.0 16.9 - - - +
43b CYS 3.6 11.0 - - - -
45b CYS* 4.0 5.2 - - - -
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Residues in contact with THR 30 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14b ASP* 3.8 20.2 - - - +
15b TYR 3.3 11.2 - - - +
16b ARG* 3.1 24.2 + - - +
29b GLY* 1.3 69.6 - - - -
31b PHE* 1.3 63.6 + - - +
32b LYS* 3.1 25.3 + - + +
42b LEU* 3.2 3.2 - - - -
43b CYS* 2.8 46.6 + - + -
44b ASP* 4.2 6.1 + - - -
87b PRO* 4.3 15.8 - - + +
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Residues in contact with PHE 31 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9b MET* 3.5 35.9 - - + -
12b HIS* 3.7 21.5 - - + +
13b ILE* 3.4 13.3 - - + -
14b ASP* 2.7 27.0 + - - -
15b TYR 2.9 17.0 + - - +
17b MET* 3.8 23.3 - - + -
29b GLY 3.4 0.4 + - - -
30b THR* 1.3 70.9 - - - +
32b LYS* 1.3 61.4 + - - +
33b ALA 3.6 27.1 - - - -
34b PHE* 3.4 25.4 - + + -
40b LEU* 3.8 15.9 - - + -
41b ILE 3.8 5.8 - - - -
42b LEU* 3.8 11.4 - - + -
80b MET* 4.3 15.7 - - + -
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Residues in contact with LYS 32 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78a LYS* 5.2 6.5 + - - -
83a LEU* 4.3 32.2 - - + +
84a LYS 5.5 5.8 + - - +
13b ILE* 3.8 17.8 - - - +
14b ASP* 2.9 29.3 + - - +
30b THR* 3.6 19.5 - - + +
31b PHE* 1.3 75.0 - - - +
33b ALA* 1.3 64.3 + - - +
41b ILE* 2.9 24.0 + - + +
43b CYS* 3.5 31.9 - - + +
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Residues in contact with ALA 33 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5a VAL* 3.8 22.0 - - + -
6a PRO* 4.2 2.7 - - + -
83a LEU* 3.8 22.4 - - + -
13b ILE* 4.3 9.2 - - + -
31b PHE* 3.6 9.5 - - - -
32b LYS* 1.3 80.3 - - - +
34b PHE* 1.3 64.2 + - - +
40b LEU* 3.4 4.0 - - - -
41b ILE* 2.9 36.0 + - + +
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Residues in contact with PHE 34 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5a VAL* 4.4 9.9 + - - +
6a PRO* 3.4 12.5 - - - +
6b SER* 3.5 21.3 - - - -
9b MET* 3.4 42.2 - - + -
10b LEU* 4.1 15.5 - - + -
13b ILE* 3.8 22.2 - - + +
31b PHE* 3.4 26.2 - + + -
33b ALA* 1.3 75.5 - - - +
35b ASP* 1.3 79.5 - - - +
38b MET* 5.0 5.4 - - + -
39b ASN 3.3 13.2 - - - +
40b LEU* 4.1 4.9 - - + -
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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