Contacts of the strand formed by residues 188 - 193 (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 TYR 188 (chain 3).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2851 VAL* 3.8 40.1 - - + +
853 ILE 3.4 8.7 - - - +
863 LYS* 4.0 16.3 - - + -
873 VAL* 4.2 1.8 - - - +
1323 ALA 3.8 0.2 - - - +
1333 TYR* 3.2 8.7 - - - -
1343 THR* 2.8 49.9 + - + -
1353 PRO 6.0 0.4 - - - -
1363 PRO* 6.2 0.4 - - + -
1383 ILE 3.8 16.1 + - - -
1393 GLY* 4.4 3.7 - - - -
1403 LYS* 3.4 42.4 + - + -
1873 GLY* 1.3 86.7 - - - -
1893 ILE* 1.3 67.8 + - - +
1903 THR* 4.2 7.0 - - + -
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Residues in contact with ILE 189 (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* 3.9 23.4 - - + -
843 ALA* 3.3 2.9 - - - -
853 ILE* 3.0 39.6 + - + +
873 VAL* 3.3 18.8 - - + +
1153 PHE* 3.4 51.6 - - + -
1173 PHE* 5.2 4.7 - - + -
1313 LEU* 5.3 1.6 - - + -
1323 ALA 3.2 10.5 - - - +
1333 TYR* 4.6 1.8 - - + -
1653 LEU* 4.0 15.0 - - + -
1673 VAL* 3.6 11.7 - - + -
1883 TYR* 1.3 75.5 - - - +
1903 THR* 1.3 66.4 + - - +
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Residues in contact with THR 190 (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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813 GLU* 4.5 1.8 - - - +
833 PHE* 3.4 7.4 - - - -
843 ALA* 3.7 19.1 - - + -
1303 LEU 3.8 0.5 - - - +
1313 LEU* 3.7 2.1 - - - +
1323 ALA* 2.9 34.6 + - - +
1343 THR* 4.9 0.6 + - - +
1403 LYS* 4.0 11.7 - - - -
1413 PRO* 3.7 23.4 - - + +
1473 ALA* 3.7 12.8 - - - +
1883 TYR* 4.7 4.7 - - + -
1893 ILE* 1.3 86.7 - - - +
1913 CYS* 1.3 61.6 + - - +
1923 TRP* 2.8 29.3 + - + -
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Residues in contact with CYS 191 (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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813 GLU* 3.6 2.1 - - - +
823 ILE* 2.7 48.2 + - + -
833 PHE* 3.0 43.0 + - + +
1293 VAL* 3.3 33.2 - - - -
1303 LEU 3.4 2.7 - - - -
1313 LEU* 3.6 15.0 - - + -
1903 THR* 1.3 75.1 - - - +
1923 TRP* 1.3 62.6 + - - +
2093 MET* 4.9 6.3 - - - -
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Residues in contact with TRP 192 (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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793 ALA 3.4 20.0 - - - +
803 GLU 3.4 5.8 - - - +
813 GLU* 3.5 39.9 - - + -
823 ILE* 4.0 6.3 - - - -
1293 VAL* 3.5 6.4 - - - +
1303 LEU* 2.8 46.6 + - + +
1413 PRO 3.8 14.8 - - - -
1423 ARG 3.7 8.1 - - - -
1433 SER* 3.4 32.5 - - - -
1443 ARG* 3.5 36.6 - - + -
1473 ALA* 3.4 18.5 - - + +
1903 THR* 2.8 35.9 + - - -
1913 CYS* 1.3 81.9 - - - +
1933 TYR* 1.3 60.7 + - - +
1943 GLN 3.4 0.2 + - - -
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Residues in contact with TYR 193 (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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713 THR 4.6 1.4 + - - -
723 LEU* 3.5 14.5 - - + +
733 SER 3.2 32.6 + - - -
753 GLN* 3.4 39.4 + - + -
793 ALA* 3.6 8.7 + - - +
803 GLU* 3.1 39.4 + - + +
813 GLU 5.0 1.6 - - - -
823 ILE* 3.4 28.3 - - + +
1273 LEU* 3.8 29.8 - - + -
1283 LYS 4.2 1.8 - - - -
1293 VAL* 4.5 1.6 - - - -
1443 ARG* 2.9 23.7 + - - -
1923 TRP* 1.3 72.2 - - - +
1943 GLN* 1.3 60.2 + - - +
1953 THR 3.9 11.0 - - - +
1963 ASN* 4.4 9.6 - - - -
1973 PHE* 4.3 5.4 - - + -
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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