Contacts of the strand formed by residues 56 - 62 (chain g) 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 ASN 56 (chain g).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44g GLU 5.7 3.0 + - - -
45g CYS 3.4 5.5 + - - +
46g VAL* 4.0 22.3 - - - +
54g GLN* 4.6 2.6 - - - +
55g ASN* 1.3 82.5 + - - +
57g ILE* 1.3 60.9 + - - +
58g GLY 3.7 2.2 - - - +
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Residues in contact with ILE 57 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34e TRP* 4.0 27.1 - - + -
86e LEU* 4.9 0.7 - - + -
88e GLN* 2.8 55.0 - - + +
89e SER* 4.2 10.4 + - - +
45g CYS* 2.9 32.7 + - - +
47g GLU* 4.3 16.6 - - + +
55g ASN* 4.1 7.6 - - + +
56g ASN* 1.3 77.0 - - - +
58g GLY* 1.3 64.3 + - - +
59g MET 3.5 7.3 + - - +
60g VAL* 4.2 12.8 - - + -
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Residues in contact with GLY 58 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42g ILE 3.5 1.7 - - - +
43g ASP* 4.9 0.7 - - - -
44g GLU* 3.5 17.2 + - - +
45g CYS* 3.3 34.7 + - - +
56g ASN* 3.7 4.2 - - - +
57g ILE* 1.3 76.3 - - - +
59g MET* 1.3 62.9 + - - -
60g VAL* 3.6 0.9 + - - +
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Residues in contact with MET 59 (chain g).
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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15e VAL* 4.8 10.5 - - + -
20e LEU* 3.6 26.5 - - + -
23e ARG* 4.6 15.7 - - - +
24e TYR* 3.2 14.1 + - + +
87e LEU 4.7 0.2 - - - +
89e SER* 4.9 7.3 + - - -
32g ARG* 4.7 3.6 - - + -
41g VAL* 3.8 19.5 - - + -
42g ILE 3.3 7.2 - - - +
43g ASP* 2.8 57.3 + - + +
57g ILE* 3.5 8.9 + - - +
58g GLY* 1.3 72.6 - - - -
60g VAL* 1.3 62.6 + - - +
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Residues in contact with VAL 60 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20e LEU* 3.5 3.7 - - - +
24e TYR* 3.4 6.7 - - - -
86e LEU* 3.6 22.4 - - + -
87e LEU 2.5 25.8 - - - +
88e GLN* 4.1 6.5 - - - -
41g VAL* 3.4 6.1 - - - -
42g ILE* 2.9 51.4 + - + +
45g CYS* 4.0 16.4 - - + -
57g ILE* 4.2 10.1 - - + -
58g GLY 3.8 5.2 - - - +
59g MET* 1.3 77.2 - - - +
61g VAL* 1.3 61.5 + - - +
62g ILE* 4.5 9.9 - - + -
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Residues in contact with VAL 61 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17e PRO* 3.9 27.6 - - + +
20e LEU* 3.5 25.4 - - + -
21e ILE* 4.0 20.4 - - + -
24e TYR* 3.8 6.6 + - + -
54e MET* 4.6 11.0 - - + -
84e ILE* 5.7 0.6 - - + +
86e LEU* 3.3 4.0 - - - +
87e LEU* 2.7 60.3 + - + +
39g ASN* 5.2 0.2 - - + -
40g LEU 3.4 9.0 - - - +
41g VAL* 4.9 0.2 - - + -
60g VAL* 1.3 72.0 - - - +
62g ILE* 1.3 72.4 + - - +
63g ARG 4.6 0.2 - - - +
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Residues in contact with ILE 62 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85e THR 3.5 12.3 - - - +
86e LEU* 3.8 22.9 - - + -
19g LEU* 4.1 18.2 - - + -
21g LEU* 4.6 10.5 - - + -
27g VAL* 4.4 11.9 - - + -
39g ASN* 3.2 5.0 - - - +
40g LEU* 2.8 42.8 + - + +
42g ILE* 3.8 29.2 - - + -
60g VAL* 4.5 3.1 - - + -
61g VAL* 1.3 80.3 - - - +
63g ARG* 1.3 70.8 + - - +
66g SER* 4.4 3.4 - - - +
67g ILE* 3.2 26.9 - - + -
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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