Contacts of the strand formed by residues 26 - 34 (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 ILE 26 (chain p).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18p ARG* 4.0 30.3 - - + +
19p CYS 3.2 8.5 - - - +
20p ILE* 3.8 28.0 - - + -
24p GLY 4.3 7.4 - - - +
25p ARG* 1.3 78.2 - - - +
27p PHE* 1.3 66.0 + - - +
28p ILE* 3.8 25.6 - - + -
46p ASP 3.8 0.2 - - - +
47p GLU* 3.3 4.7 - - - +
48p PHE* 2.8 48.6 + - + +
49p ARG* 5.5 1.3 - - - -
50p LYS* 6.1 5.4 - - + -
47q LEU* 6.2 3.4 - - + -
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Residues in contact with PHE 27 (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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70o PHE* 3.8 22.9 - + - -
17p MET 3.3 2.9 - - - +
18p ARG* 3.4 0.2 - - - -
19p CYS* 2.7 44.0 + - + +
21p LEU* 3.6 36.3 - - + +
25p ARG* 4.2 5.4 - - + -
26p ILE* 1.3 81.1 - - - +
28p ILE* 1.3 60.6 + - - +
29p GLY 4.2 0.2 - - - -
42p LEU* 4.0 15.0 - - + -
45p CYS* 3.8 18.8 - - - -
46p ASP 3.4 2.9 - - - -
47p GLU* 3.9 22.2 - - + -
67p LEU* 3.7 23.6 - - + -
70p VAL* 3.8 23.1 - - + -
72p LEU* 4.0 15.9 - - + -
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Residues in contact with ILE 28 (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* 3.7 23.5 + - - +
17p MET 3.5 9.4 - - - +
18p ARG* 3.7 27.4 - - + +
26p ILE* 3.8 7.2 - - + -
27p PHE* 1.3 75.8 - - - +
29p GLY* 1.3 59.1 - - - +
45p CYS* 3.2 3.5 - - - -
46p ASP 2.7 38.6 + - - -
48p PHE* 3.6 31.9 - - + -
83p GLU* 3.7 46.2 - - + +
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Residues in contact with GLY 29 (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* 3.8 10.8 - - - -
17p MET* 2.9 29.5 + - - +
27p PHE 4.2 0.4 - - - -
28p ILE* 1.3 80.0 - - - +
30p THR* 1.3 64.5 + - - -
31p PHE 3.4 1.0 + - - -
42p LEU* 4.0 17.2 - - - +
43p CYS 3.6 10.5 - - - -
45p CYS* 4.0 5.2 - - - -
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Residues in contact with THR 30 (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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14p ASP* 3.6 27.6 - - + +
15p TYR 3.3 6.3 - - - +
16p ARG* 3.0 25.0 + - - +
29p GLY* 1.3 69.0 - - - -
31p PHE* 1.3 61.9 + - - +
32p LYS* 3.1 22.7 + - + +
42p LEU* 3.2 3.1 - - - -
43p CYS* 2.8 45.3 + - + -
44p ASP* 4.2 5.9 + - - -
87p PRO* 4.2 15.2 - - + +
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Residues in contact with PHE 31 (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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9p MET* 3.5 28.3 - - + -
12p HIS* 3.3 22.0 - - + +
13p ILE* 3.4 14.3 - - + +
14p ASP* 2.5 29.8 + - - -
15p TYR 2.9 16.6 + - - +
17p MET* 3.9 20.6 - - + -
29p GLY 3.4 0.2 + - - -
30p THR* 1.3 72.1 - - - +
32p LYS* 1.3 58.3 + - - +
33p ALA 3.6 26.0 - - - -
34p PHE* 3.4 24.7 - + + -
40p LEU* 3.8 17.0 - - + -
41p ILE 3.8 5.6 - - - -
42p LEU* 3.9 15.7 - - + -
80p MET* 3.7 22.2 - - + -
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Residues in contact with LYS 32 (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* 5.2 3.4 - - - -
83o LEU* 3.9 44.1 - - + +
13p ILE* 3.6 14.6 - - - +
14p ASP* 4.6 14.9 - - + +
30p THR* 3.6 24.1 - - + +
31p PHE* 1.3 75.5 - - - +
33p ALA* 1.3 64.2 + - - +
41p ILE* 2.8 25.7 + - + +
43p CYS* 3.5 33.0 - - - +
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Residues in contact with ALA 33 (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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5o VAL* 3.9 32.3 - - + -
6o PRO* 4.4 2.2 - - + -
83o LEU* 5.1 4.5 - - + -
13p ILE* 4.2 8.1 - - - -
31p PHE* 3.6 9.3 - - - -
32p LYS* 1.3 82.7 - - + +
34p PHE* 1.3 64.0 + - - +
40p LEU* 3.4 3.8 - - - -
41p ILE* 2.9 42.2 + - + +
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Residues in contact with PHE 34 (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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5o VAL* 4.5 9.9 - - - +
6o PRO* 3.6 12.1 - - - +
6p SER* 3.5 22.4 - - - -
9p MET* 3.4 39.5 - - + -
10p LEU* 4.0 29.2 - - + -
13p ILE* 4.3 7.4 - - + -
31p PHE* 3.4 27.8 - + + -
33p ALA* 1.3 77.2 - - - +
35p ASP* 1.3 79.7 + - - +
38p MET* 5.0 5.2 - - - -
39p ASN 3.3 13.7 - - - +
40p LEU* 4.1 5.2 - - + -
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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