Contacts of the strand formed by residues 452 - 456 (chain U) in PDB entry 6QX2
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 GLN 452 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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421U CYS* 3.5 5.7 - - - +
430U GLU* 3.0 30.9 + - + +
432U PHE* 3.6 23.3 - - + -
447U ARG* 2.8 52.0 + - + +
448U ASP* 2.8 40.9 + - - +
449U SER* 4.1 0.2 - - - -
451U THR* 1.3 84.4 - - - +
453U ALA* 1.3 53.4 + - - +
592U TRP* 3.4 9.4 - - - -
596U MET* 2.8 31.5 + - + +
598U PRO* 4.7 3.6 - - - +
601U ARG* 3.5 2.2 - - - +
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Residues in contact with ALA 453 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418U LEU* 4.2 2.7 - - + -
419U ALA 3.3 12.1 - - - +
420U ASP* 3.8 11.0 - - - +
421U CYS* 3.9 3.7 - - - +
430U GLU 2.8 8.4 + - - +
431U ILE* 3.5 8.2 - - + -
432U PHE* 2.9 26.2 + - - -
447U ARG* 3.9 0.7 - - - +
452U GLN* 1.3 72.7 - - - +
454U ILE* 1.3 67.3 + - - +
500U TYR* 3.5 38.4 - - + +
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Residues in contact with ILE 454 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418U LEU* 3.4 5.2 - - - +
419U ALA* 2.8 38.1 + - - +
431U ILE* 4.7 0.2 - - - -
432U PHE* 3.4 10.5 - - + +
434U VAL* 4.0 24.2 - - + -
440U GLY* 4.3 13.2 - - - +
443U THR* 3.4 31.9 - - + +
444U LYS* 3.5 37.9 - - + +
447U ARG* 3.5 25.8 - - + +
453U ALA* 1.3 78.7 - - - +
455U LEU* 1.3 62.0 + - - +
456U PRO* 3.7 10.3 - - + +
596U MET* 4.9 1.8 - - + -
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Residues in contact with LEU 455 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417U LYS* 4.3 0.4 - - + -
418U LEU* 4.2 22.0 - - + +
431U ILE* 4.1 11.5 - - + +
432U PHE 2.9 8.4 + - - -
433U LEU* 3.5 23.2 - - + +
434U VAL* 3.4 20.0 + - - -
454U ILE* 1.3 71.9 - - - +
456U PRO* 1.4 72.0 - - + +
457U LEU* 3.5 10.6 + - + +
480U GLN* 3.7 32.1 - - + +
481U MET* 3.7 44.9 - - + +
484U ALA* 4.2 9.6 - - + -
485U PHE* 5.6 0.2 - - + -
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Residues in contact with PRO 456 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417U LYS* 2.9 46.4 - - + +
434U VAL* 3.6 15.7 - - + +
436U GLY 3.7 21.8 - - - +
437U ASP* 3.9 19.2 - - - +
440U GLY* 4.2 11.7 - - - -
444U LYS* 5.6 4.9 - - + -
454U ILE* 3.7 8.1 - - + +
455U LEU* 1.4 86.4 - - - +
457U LEU* 1.3 63.2 + - - +
458U ARG* 5.1 2.3 - - - +
477U GLU* 5.0 2.6 - - - +
480U GLN* 4.9 0.9 - - - +
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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