Contacts of the strand formed by residues 128 - 134 (chain 3) in PDB entry 1QJX
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 LYS 128 (chain 3).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1273 LEU* 1.3 79.2 - - - +
1293 VAL* 1.3 63.8 + - - +
1543 VAL* 5.0 7.6 - - + -
1553 TRP 3.2 8.5 - - - +
1563 ASP* 2.6 44.5 + - + +
1933 TYR* 3.9 0.7 - - - -
1943 GLN* 2.8 36.0 + - + +
1953 THR* 3.1 37.1 + - + +
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Residues in contact with VAL 129 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723 LEU* 5.2 1.6 - - + -
823 ILE* 3.8 19.7 - - + -
1273 LEU* 3.9 27.5 - - + +
1283 LYS* 1.3 78.8 - - - +
1303 LEU* 1.3 66.5 + - - +
1313 LEU* 4.1 9.9 - - + -
1533 VAL 3.8 0.2 - - - +
1543 VAL* 3.4 4.2 - - - +
1553 TRP* 2.8 52.5 + - + +
1573 VAL* 6.5 0.2 - - + -
1913 CYS* 3.3 28.7 - - - -
1923 TRP 3.5 9.4 - - - +
1933 TYR* 4.5 1.6 - - - -
1943 GLN* 3.9 4.5 - - - +
2093 MET* 6.3 2.0 - - - -
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Residues in contact with LEU 130 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1293 VAL* 1.3 74.5 - - - +
1313 LEU* 1.3 63.6 + - - +
1323 ALA* 3.8 25.4 - - + -
1443 ARG* 4.4 9.9 - - + +
1483 MET* 4.3 24.7 - - + +
1523 HIS* 3.9 29.2 - - + +
1533 VAL 3.6 3.6 - - - +
1543 VAL* 4.1 8.7 - - + +
1903 THR 3.8 0.5 - - - +
1913 CYS* 3.4 4.2 - - - -
1923 TRP* 2.8 55.4 + - + +
1943 GLN* 3.4 28.0 - - - +
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Residues in contact with LEU 131 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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833 PHE* 4.3 4.7 - - + -
1173 PHE* 3.6 48.2 - - + -
1293 VAL* 4.1 5.6 - - + -
1303 LEU* 1.3 73.9 - - - +
1323 ALA* 1.3 60.0 + - - +
1523 HIS* 3.1 4.1 - - - +
1533 VAL* 2.8 40.5 + - + +
1553 TRP* 4.3 17.9 - - + -
1633 VAL* 3.9 18.4 - - + -
1653 LEU* 3.9 24.3 - - + +
1893 ILE* 5.3 1.6 - - + -
1903 THR 3.7 2.9 - - - +
1913 CYS* 3.6 28.5 - - + -
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Residues in contact with ALA 132 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1303 LEU* 3.8 12.7 + - + -
1313 LEU* 1.3 75.9 - - - +
1333 TYR* 1.3 62.7 + - - +
1343 THR* 5.0 1.5 + - - +
1473 ALA* 3.7 33.7 - - + +
1513 THR 3.2 9.6 - - - +
1523 HIS* 3.7 6.7 - - + -
1653 LEU* 4.7 4.6 - - - +
1883 TYR 3.8 0.3 - - - +
1893 ILE* 3.2 7.3 - - - +
1903 THR* 2.9 37.7 + - - +
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Residues in contact with TYR 133 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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873 VAL* 4.0 12.6 - - + -
1323 ALA* 1.3 74.6 - - - +
1343 THR* 1.3 69.9 + - - +
1353 PRO* 3.5 31.2 - - + +
1363 PRO* 3.8 3.8 - - - +
1473 ALA 5.6 0.2 - - - -
1503 GLY* 3.9 2.4 - - - -
1513 THR* 2.6 49.6 + - + +
1653 LEU* 4.9 5.3 - - + +
1673 VAL* 3.6 41.5 - - + +
1683 PRO* 3.9 30.2 + - + -
1703 ILE* 4.3 16.5 + - + +
1763 ARG* 4.8 1.6 + - - -
1863 ALA* 2.8 30.1 + - - +
1883 TYR 3.2 17.0 - - - -
1893 ILE* 4.5 2.0 - - + +
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Residues in contact with THR 134 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1323 ALA 5.0 0.7 + - - -
1333 TYR* 1.3 78.1 + - - +
1353 PRO* 1.3 72.0 - - + +
1383 ILE* 3.6 30.5 - - + -
1393 GLY 4.5 1.6 - - - +
1413 PRO* 3.4 37.2 - - + +
1463 GLU 6.0 1.1 - - - +
1473 ALA* 4.8 7.5 + - - -
1503 GLY* 5.4 2.7 - - - -
1873 GLY* 3.3 4.3 - - - -
1883 TYR* 2.8 40.3 + - + -
1903 THR* 4.9 2.6 + - - -
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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