Contacts of the strand formed by residues 40 - 46 (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 LEU 40 (chain g).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17e PRO* 4.1 1.8 - - - -
9g LEU* 3.9 16.6 - - + -
17g LEU* 5.3 0.2 - - + -
19g LEU* 3.6 29.4 - - + -
31g LEU* 4.1 12.8 - - + -
33g GLY 3.4 3.4 - - - +
34g PHE* 3.6 18.6 - - + -
38g MET* 3.5 17.3 - - + +
39g ASN* 1.3 86.1 - - - +
41g VAL* 1.3 63.6 + - - +
42g ILE* 4.1 12.3 - - + -
61g VAL* 3.4 8.0 - - - +
62g ILE* 2.8 41.2 + - + +
67g ILE* 4.2 12.6 - - + -
70g LEU* 4.0 17.9 - - + -
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Residues in contact with VAL 41 (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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15e VAL* 3.7 17.0 - - + +
16e GLN 3.9 2.2 - - - -
17e PRO* 3.6 37.9 - - + -
20e LEU* 3.4 29.6 - - + -
31g LEU* 3.4 3.3 - - - +
32g ARG* 2.9 35.8 + - + -
33g GLY 2.8 17.5 + - - +
40g LEU* 1.3 71.8 - - - +
42g ILE* 1.3 70.6 + - - +
59g MET* 3.8 18.8 - - - -
60g VAL 3.4 3.1 - - - +
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Residues in contact with ILE 42 (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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17g LEU* 4.8 2.9 - - + -
19g LEU* 4.4 14.1 - - + -
28g GLN 4.7 0.7 - - - -
29g GLY* 3.5 35.7 - - - +
30g ILE 3.5 2.0 - - - +
31g LEU* 3.7 25.8 - - + -
40g LEU* 4.0 14.3 - - + -
41g VAL* 1.3 90.8 - - - +
43g ASP* 1.3 63.8 + - - +
45g CYS* 3.7 13.7 - - + -
58g GLY 3.5 1.6 - - - +
59g MET* 3.3 2.3 - - - -
60g VAL* 2.9 44.9 + - + +
62g ILE* 3.8 27.4 - - + -
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Residues in contact with ASP 43 (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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29g GLY* 3.7 0.9 - - - -
30g ILE* 2.8 38.3 + - + +
32g ARG* 2.4 41.0 + - + +
42g ILE* 1.3 73.0 - - - +
44g GLU* 1.3 102.7 + - - +
45g CYS 3.2 2.0 - - - -
58g GLY* 3.9 1.6 - - - -
59g MET* 2.8 35.2 + - + +
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Residues in contact with GLU 44 (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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16g LYS* 4.8 4.9 + - - -
28g GLN 4.0 0.5 - - - +
29g GLY* 3.8 9.0 - - - -
30g ILE* 3.5 23.2 - - + +
32g ARG* 4.1 15.2 + - - -
43g ASP* 1.3 94.4 + - - +
45g CYS* 1.3 61.7 + - - +
46g VAL* 4.0 8.1 - - - +
56g ASN* 5.8 3.4 - - - -
58g GLY* 3.5 14.9 + - - -
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Residues in contact with CYS 45 (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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86e LEU* 5.1 0.7 - - - -
27g VAL* 3.4 31.4 - - - -
28g GLN 3.2 6.1 - - - -
42g ILE* 3.7 18.4 - - + -
43g ASP 3.9 0.9 - - - -
44g GLU* 1.3 75.6 - - - +
46g VAL* 1.3 63.8 + - - +
56g ASN* 3.4 4.5 - - - +
57g ILE* 2.9 49.0 + - + -
58g GLY 3.3 20.5 + - - +
60g VAL* 4.0 16.2 - - + -
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Residues in contact with VAL 46 (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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16g LYS* 4.4 15.5 - - - +
27g VAL* 3.5 2.1 - - - -
28g GLN* 2.7 41.4 + - + +
44g GLU 4.0 8.3 - - - +
45g CYS* 1.3 82.1 - - - +
47g GLU* 1.3 62.7 + - - +
48g MET* 3.3 14.2 - - + +
54g GLN* 3.7 20.9 - - + +
55g ASN 3.0 31.0 - - - +
56g ASN* 4.0 20.0 - - - +
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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