Contacts of the strand formed by residues 17 - 22 (chain o) 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 17 (chain o).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15n PRO* 3.5 47.3 - - + +
16o HIS* 1.3 77.1 - - - +
18o VAL* 1.3 65.6 + - - +
19o THR* 5.5 0.2 - - - +
29o ARG* 3.9 32.8 - - + +
30o GLY* 3.3 25.4 - - - +
31o LYS* 3.6 15.0 - - + +
72o ILE 4.2 1.4 - - - +
73o LEU 4.8 0.2 - - - -
74o PRO* 3.5 19.4 - - - +
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Residues in contact with VAL 18 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13o ALA* 4.2 22.9 - - + -
16o HIS 4.1 1.6 - - - +
17o ILE* 1.3 81.4 - - - +
19o THR* 1.3 66.4 + - - +
20o CYS* 5.0 2.7 - - + -
29o ARG* 3.5 2.5 - - - -
30o GLY 2.9 29.7 + - - +
32o LEU* 3.9 35.4 - - + -
41o CYS* 6.4 0.2 - - - -
43o MET* 3.4 27.6 - - + +
71o LEU* 5.2 7.2 - - + -
72o ILE 3.4 12.8 - - - +
73o LEU* 4.4 8.7 - - + -
74o PRO* 4.3 2.7 - - + -
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Residues in contact with THR 19 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18n PRO* 5.4 3.7 - - + +
19n ILE* 4.4 11.4 + - + +
17o ILE* 5.5 0.3 - - - +
18o VAL* 1.3 75.3 - - - +
20o CYS* 1.3 65.6 + - - +
27o VAL* 3.3 28.9 - - + -
28o TYR 3.4 5.8 - - - +
29o ARG* 3.5 27.5 + - + +
70o PHE* 6.2 1.3 - - + -
71o LEU* 3.2 5.2 - - - +
72o ILE* 2.7 61.0 + - + +
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Residues in contact with CYS 20 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18o VAL* 5.0 2.5 - - + -
19o THR* 1.3 77.6 - - - +
21o GLU* 1.3 63.8 + - - +
22o THR* 3.9 4.0 + - - -
27o VAL* 3.4 4.5 - - - -
28o TYR* 2.9 39.8 + - + +
41o CYS* 6.0 2.0 - - + -
43o MET* 4.5 13.7 - - + -
63o ILE* 3.9 24.2 - - - -
68o ILE* 4.0 34.5 - - - -
70o PHE* 3.6 6.1 - - - -
71o LEU* 4.3 9.0 - - + -
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Residues in contact with GLU 21 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19n ILE* 6.0 1.2 - - - +
24n PRO* 6.0 1.9 - - - +
20o CYS* 1.3 74.1 - - - +
22o THR* 1.3 70.0 + - - +
25o GLY* 3.5 15.6 - - - +
26o GLU 3.5 8.1 - - - +
27o VAL* 4.2 19.3 - - + +
68o ILE* 3.8 3.8 - - - +
69o ARG* 2.9 42.7 + - + +
70o PHE* 3.1 39.7 + - + +
25p ARG* 3.0 35.5 + - - -
65p ARG* 5.0 3.8 + - - -
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Residues in contact with THR 22 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20o CYS* 4.7 3.8 - - - -
21o GLU* 1.3 76.3 - - - +
23o ASN* 1.3 58.6 + - - +
24o THR* 3.6 10.2 + - - -
25o GLY 2.9 17.3 + - - -
26o GLU* 3.1 35.9 + - - +
28o TYR* 3.6 26.5 - - + -
63o ILE* 3.9 25.8 - - + -
67o LYS 3.3 10.3 - - - +
68o ILE* 4.4 0.4 - - - +
69o ARG* 3.1 14.6 + - - -
68u ILE* 4.3 11.0 - - + -
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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