Contacts of the strand formed by residues 68 - 73 (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 ILE 68 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A CYS* 4.0 24.0 - - - -
21A GLU 3.8 7.9 - - - +
22A THR* 5.3 0.4 - - + -
23A ASN* 4.7 1.7 - - - +
39A MET* 3.6 33.7 - - + +
41A CYS* 4.3 9.6 - - - -
63A ILE* 4.2 13.0 - - + -
64A ARG 3.5 16.2 - - - +
65A GLY* 3.0 10.8 + - - +
66A SER 3.5 1.3 - - - +
67A LYS* 1.3 80.3 - - - +
69A ARG* 1.3 66.2 + - - +
70A PHE* 3.5 25.1 - - - +
71A LEU* 4.1 12.8 - - + -
73B ARG* 3.4 18.0 - - + -
76B ASN* 3.2 11.4 - - - +
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Residues in contact with ARG 69 (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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21A GLU* 2.9 24.2 + - + +
22A THR 3.0 26.6 + - - +
23A ASN* 3.1 38.8 + - - +
24A THR 5.0 0.6 - - - -
25A GLY* 3.9 5.3 - - - +
67A LYS 4.1 0.8 + - - -
68A ILE* 1.3 72.7 - - - +
70A PHE* 1.3 74.0 + - + +
21B LEU* 5.3 4.0 - - - -
23B ASP* 4.0 25.7 + - - +
25B ARG* 3.1 32.4 - - - +
72B LEU* 3.6 7.1 - - + +
73B ARG 3.1 22.1 + - - -
76B ASN* 3.5 26.8 - - + +
26K GLU* 5.9 1.0 + - - +
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Residues in contact with PHE 70 (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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19A THR* 5.8 1.6 - - + -
20A CYS* 3.7 1.4 - - - -
21A GLU* 3.1 66.9 + - + +
68A ILE* 3.5 4.8 - - - +
69A ARG* 1.3 92.1 - - + +
71A LEU* 1.3 76.5 + - - +
72A ILE* 3.9 22.9 - - + -
21B LEU* 5.2 1.1 - - + -
25B ARG* 3.7 15.5 - - - -
27B PHE* 3.7 20.0 - + - -
47B GLU* 4.5 2.5 - - - -
65B ARG* 4.8 3.6 - - - -
67B LEU* 4.1 15.3 - - + -
70B VAL* 4.0 12.6 - - + -
71B LEU 3.2 14.8 - - - +
72B LEU* 4.0 13.5 - - + -
73B ARG* 4.5 0.9 - - - +
19K ILE* 5.2 4.9 - - + -
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Residues in contact with LEU 71 (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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10A LEU* 4.3 21.8 - - + -
18A VAL* 4.5 12.6 - - + -
19A THR 3.3 6.5 - - - +
20A CYS* 3.7 25.6 - - + -
32A LEU* 6.0 0.2 - - + -
39A MET* 4.6 8.5 - - + -
41A CYS* 4.2 20.0 - - - -
43A MET* 5.8 0.4 - - - -
68A ILE* 4.1 19.5 - - + -
70A PHE* 1.3 78.8 - - - +
72A ILE* 1.3 64.5 + - - +
73A LEU* 3.9 13.9 - - + -
70B VAL* 3.3 8.1 - - - +
71B LEU* 2.8 56.5 + - + +
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Residues in contact with ILE 72 (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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17A ILE 4.2 0.7 - - - +
18A VAL* 3.4 9.0 - - - -
19A THR* 2.7 46.1 + - - +
70A PHE* 3.9 15.3 - - + -
71A LEU* 1.3 75.5 - - - +
73A LEU* 1.3 71.4 + - - +
75A ASP* 6.0 0.2 - - - +
67B LEU* 3.0 44.6 - - + +
69B LEU 3.4 9.0 - - - +
70B VAL* 4.6 1.8 - - + -
16K ARG* 5.7 5.8 - - + -
19K ILE* 3.8 42.8 - - + -
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Residues in contact with LEU 73 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A VAL* 3.8 39.0 - - + +
10A LEU* 4.0 18.4 - - + -
13A ALA* 4.0 7.4 - - + -
17A ILE 4.9 0.4 - - - -
18A VAL* 3.7 21.5 - - + -
71A LEU* 4.0 19.5 - - + -
72A ILE* 1.3 87.8 - - - +
74A PRO* 1.4 76.1 - - + +
75A ASP* 3.6 2.8 + - - +
77A LEU* 3.7 8.1 - - + -
41B ILE* 5.3 0.9 - - + -
69B LEU* 2.8 36.0 + - + +
71B LEU* 4.1 18.8 - - + +
16K ARG* 6.2 0.2 - - - +
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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