Contacts of the strand formed by residues 113 - 119 (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 LEU 113 (chain 3).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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873 VAL* 3.6 29.2 - - + +
893 ILE* 4.0 22.9 - - + -
993 ILE* 4.5 8.1 - - + -
1093 TRP* 4.1 22.9 - - + -
1113 GLY 4.8 0.4 - - - +
1123 SER* 1.3 75.2 - - - +
1143 ARG* 1.3 62.9 + - - +
1153 PHE* 3.7 27.1 - - + -
1653 LEU 3.9 0.3 - - - +
1663 VAL* 3.3 5.4 - - - +
1673 VAL* 2.7 40.6 + - + +
2133 VAL* 4.9 2.5 - - + -
2143 SER 3.8 4.3 - - - +
2153 GLY* 4.8 0.2 - - - -
2163 CYS* 4.0 1.8 - - - -
2193 PHE* 3.9 33.4 - - + -
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Residues in contact with ARG 114 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421 THR* 4.0 4.1 - - - +
431 ASN* 3.1 27.6 + - - -
441 LYS* 3.7 22.8 - - - +
451 ILE* 2.5 52.9 + - + -
461 GLN* 3.7 15.6 - - - +
483 GLN* 4.2 4.6 + - - +
503 ASP* 4.6 1.3 - - - +
1133 LEU* 1.3 72.6 - - - +
1153 PHE* 1.3 61.6 + - - +
1163 SER* 4.0 13.8 + - - +
1643 SER* 4.4 7.0 - - - -
1653 LEU 3.8 2.9 - - - +
1663 VAL* 4.6 2.5 - - + +
2123 PHE 4.4 0.2 - - - -
2133 VAL* 3.3 5.8 - - - -
2143 SER* 2.8 51.3 + - - +
2153 GLY 2.8 27.8 + - - -
2163 CYS* 4.0 12.6 - - - +
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Residues in contact with PHE 115 (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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533 ILE* 3.9 19.3 - - + -
853 ILE* 4.5 7.9 - - + -
873 VAL* 4.4 5.4 - - + -
943 LEU* 3.9 31.0 - - + -
1133 LEU* 3.7 24.2 - - + -
1143 ARG* 1.3 75.8 - - - +
1163 SER* 1.3 61.2 + - - +
1173 PHE* 3.7 23.0 - + + -
1643 SER* 3.2 2.1 - - - -
1653 LEU* 2.7 45.6 + - + +
1673 VAL* 3.5 22.4 - - + -
1893 ILE* 3.4 33.9 - - + -
2123 PHE 3.4 4.9 - - - -
2133 VAL* 3.7 21.1 - - + -
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Residues in contact with SER 116 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371 ALA* 6.2 0.2 - - - -
431 ASN* 5.0 2.9 - - - +
503 ASP* 4.0 12.7 + - - -
1143 ARG* 4.0 8.9 + - - +
1153 PHE* 1.3 72.8 - - - +
1173 PHE* 1.3 70.3 + - - +
1623 THR* 4.1 9.6 - - - +
1633 VAL 3.2 8.7 - - - -
1643 SER* 2.9 21.1 + - - -
2113 CYS* 3.4 1.7 - - - -
2123 PHE* 2.8 53.9 + - - +
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Residues in contact with PHE 117 (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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533 ILE* 5.8 0.4 - - + -
553 ILE* 5.6 0.2 - - + -
833 PHE* 3.6 25.8 - + - -
1153 PHE* 3.7 39.3 - + + -
1163 SER* 1.3 80.6 - - - +
1183 MET* 1.3 59.8 + - - +
1313 LEU* 3.6 38.6 - - + -
1553 TRP* 3.4 27.3 - + + -
1623 THR* 3.2 6.2 - - - -
1633 VAL* 2.9 33.7 + - + -
1653 LEU* 4.5 5.8 - - + -
1893 ILE* 5.2 5.6 - - + -
2093 MET* 4.4 11.0 - - + -
2103 LEU 3.2 5.6 - - - +
2113 CYS* 3.6 30.5 - - + -
2123 PHE* 4.6 0.7 - - - -
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Residues in contact with MET 118 (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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371 ALA* 4.0 14.1 - - - -
381 GLU* 3.7 31.6 - - - +
1212 THR* 4.1 12.1 - - + -
1892 PHE* 4.0 23.1 - - + -
1912 ASN* 3.9 2.9 - - - +
1173 PHE* 1.3 73.0 - - - +
1193 PHE* 1.3 69.9 + - - +
1203 CYS* 3.7 5.5 + - - -
1553 TRP* 4.1 2.5 - - - -
1613 SER* 3.6 16.4 - - - +
1623 THR* 3.7 7.0 - - - +
2093 MET* 3.3 4.7 - - - -
2103 LEU* 2.9 64.2 + - + +
2123 PHE* 3.9 16.9 - - + -
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Residues in contact with PHE 119 (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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1912 ASN* 2.9 20.6 + - - -
1932 ARG* 3.5 30.1 - - - +
723 LEU* 3.7 31.0 - - + -
1183 MET* 1.3 73.3 - - - +
1203 CYS* 1.3 61.7 - - - +
1213 GLY* 3.3 31.0 - - - -
1253 THR* 3.6 34.3 - - + -
1273 LEU* 3.9 18.8 - - + -
1553 TRP* 3.8 22.5 - + + -
1573 VAL* 3.6 23.1 - - + -
1613 SER* 3.2 11.5 + - - +
1973 PHE* 4.4 4.3 - + - -
2073 ALA* 3.8 13.7 - - + -
2083 GLU 4.2 2.9 - - - -
2093 MET* 4.6 1.3 - - + +
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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