Contacts of the strand formed by residues 69 - 72 (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 THR 69 (chain 3).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2262 VAL 3.5 24.0 - - - +
2272 CYS* 4.1 9.9 - - - -
563 ASN* 3.0 31.3 + - - +
653 VAL 4.5 5.4 - - - +
663 SER* 3.2 18.2 + - - -
673 MET 3.4 0.2 - - - -
683 TYR* 1.3 85.4 - - + +
703 VAL* 1.3 64.3 + - - +
713 THR* 5.1 0.3 + - - -
2083 GLU* 3.3 23.6 + - + -
2093 MET 3.5 5.4 - - - -
2103 LEU* 3.6 18.2 - - + -
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Residues in contact with VAL 70 (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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2821 LEU* 4.2 23.8 - - + -
553 ILE* 3.4 30.5 - - + -
563 ASN* 4.8 1.8 - - - +
693 THR* 1.3 74.2 - - - +
713 THR* 1.3 70.0 + - - +
723 LEU* 4.4 1.5 - - + +
823 ILE* 3.7 29.2 - - + -
833 PHE* 4.5 7.9 - - + -
2073 ALA 3.7 0.2 - - - +
2083 GLU* 3.4 5.1 - - - -
2093 MET* 3.0 55.5 + - + +
2113 CYS* 4.3 6.1 - - - -
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Residues in contact with THR 71 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2821 LEU* 5.2 4.6 - - - +
563 ASN* 5.3 1.2 - - - +
693 THR* 4.3 0.9 + - - -
703 VAL* 1.3 79.0 - - - +
723 LEU* 1.3 79.5 + - - +
733 SER* 5.4 1.6 - - - -
823 ILE* 5.0 2.1 - - - +
1933 TYR* 4.6 1.7 + - - -
2063 THR* 3.9 20.0 - - + -
2073 ALA 3.4 7.6 - - - +
2083 GLU* 3.0 22.9 + - - +
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Residues in contact with LEU 72 (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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703 VAL* 4.4 6.1 - - + +
713 THR* 1.3 77.5 - - - +
733 SER* 1.3 65.1 + - - +
823 ILE* 3.7 42.8 - - + -
1193 PHE* 3.7 28.5 - - + -
1273 LEU* 3.9 12.6 - - + -
1293 VAL* 5.2 1.1 - - + -
1933 TYR* 3.5 13.5 - - + +
1973 PHE* 3.6 15.5 - - + -
2063 THR* 3.2 5.2 - - - -
2073 ALA 2.8 33.3 + - - +
2093 MET* 3.9 31.6 - - + -
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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