Contacts of the helix formed by residues 443 - 456 (chain O) in PDB entry 6RQT
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 ALA 443 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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400O LEU* 6.0 3.8 - - + -
424O LEU* 4.7 22.4 - - + -
439O ILE* 3.4 19.7 + - + +
440O ILE* 3.7 4.0 - - - -
441O PHE 3.4 0.2 - - - -
442O VAL* 1.3 76.6 - - - +
444O SER* 1.3 61.6 + - - +
445O TYR* 3.2 2.7 - - - +
446O LEU* 3.2 21.4 + - + +
447O THR* 3.4 13.7 + - - +
480O LEU* 6.3 3.6 - - + -
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Residues in contact with SER 444 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440O ILE* 2.3 29.6 + - - +
441O PHE* 3.0 21.2 + - - -
442O VAL 3.2 2.6 - - - -
443O ALA* 1.3 74.8 - - - +
445O TYR* 1.3 54.4 + - - +
447O THR* 2.6 14.8 + - - -
448O SER* 2.5 35.8 + - - -
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Residues in contact with TYR 445 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404O ILE* 6.2 0.9 - - + -
408O PHE* 3.8 44.1 - + - +
442O VAL 4.2 7.9 + - - +
443O ALA* 3.2 1.0 - - - -
444O SER* 1.3 78.6 - - - +
446O LEU* 1.3 51.7 + - - +
448O SER* 3.2 14.9 - - - -
449O TRP* 2.5 37.2 + + + +
452O ARG* 2.5 42.7 + - - -
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Residues in contact with LEU 446 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408O PHE* 4.8 10.5 - - + -
421O LEU* 4.6 10.3 - - + -
424O LEU* 4.3 23.6 - - + -
443O ALA* 3.2 18.1 + - + +
444O SER 3.2 0.6 - - - -
445O TYR* 1.3 78.8 - - - +
447O THR* 1.3 60.0 + - + +
449O TRP* 3.3 24.3 - - + +
450O LEU* 3.2 27.7 + - + +
472O HIS* 4.5 7.6 - - - +
476O ALA* 4.0 41.1 - - + +
479O ALA* 6.2 1.1 - - + -
480O LEU* 5.3 13.7 - - + +
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Residues in contact with THR 447 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440O ILE* 5.1 8.9 + - + +
443O ALA 3.4 9.8 + - - +
444O SER* 2.6 29.0 + - - -
446O LEU* 1.3 77.3 - - + +
448O SER* 1.3 59.4 + - - +
449O TRP 3.3 0.4 - - - -
450O LEU* 3.4 12.1 + - - +
451O ASN* 3.5 18.9 + - - -
480O LEU* 4.1 25.1 - - + -
500O CYS* 6.5 1.6 - - - -
505O PHE* 3.6 24.7 - - + -
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Residues in contact with SER 448 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444O SER 2.5 21.5 + - - -
445O TYR* 3.2 19.7 - - - -
447O THR* 1.3 69.7 + - - +
449O TRP* 1.3 59.7 + - - +
450O LEU 3.3 0.2 - - - -
451O ASN* 3.8 12.3 - - - +
452O ARG* 3.0 27.2 + - - +
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Residues in contact with TRP 449 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408O PHE* 5.8 1.3 - + + -
445O TYR* 2.5 23.9 + + + +
446O LEU* 3.3 28.0 - - + +
447O THR 3.3 0.2 - - - -
448O SER* 1.3 74.2 - - - +
450O LEU* 1.3 82.2 + - + +
452O ARG* 3.4 36.7 - - - +
453O TYR* 2.5 72.9 + + + +
457O ARG* 4.5 6.6 - - - +
470O PHE* 5.8 0.4 - + - -
472O HIS* 3.3 63.9 + + + -
473O PHE* 3.7 23.3 - + + -
476O ALA* 5.1 3.8 - - + -
477O PHE 5.2 2.7 - - - -
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Residues in contact with LEU 450 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446O LEU* 3.2 15.4 + - + +
447O THR* 3.4 10.3 + - - +
448O SER 3.3 0.2 - - - -
449O TRP* 1.3 101.6 - - + +
451O ASN* 1.3 61.2 + - - +
453O TYR* 4.0 5.8 - - + +
454O VAL* 3.6 19.4 + - - +
473O PHE* 5.0 8.1 - - + -
477O PHE* 3.8 39.3 - - + +
480O LEU* 4.4 15.0 - - + -
505O PHE* 3.6 33.7 - - + -
506O PHE* 5.1 0.2 - - + -
508O ARG* 4.7 2.3 + - - -
509O MET* 4.6 16.4 - - + +
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Residues in contact with ASN 451 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447O THR 3.5 16.8 + - - -
448O SER* 3.9 12.1 - - - +
449O TRP 3.2 0.4 - - - -
450O LEU* 1.3 77.4 - - - +
452O ARG* 1.3 63.6 + - - +
453O TYR 3.2 0.4 - - - -
454O VAL* 3.3 4.8 - - - +
455O ILE* 3.2 39.2 + - + +
505O PHE* 4.0 11.8 - - - -
508O ARG* 3.0 33.9 + - - +
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Residues in contact with ARG 452 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408O PHE* 6.1 2.2 - - - -
445O TYR* 2.5 41.3 + - - -
448O SER* 3.0 18.9 + - - +
449O TRP* 2.9 32.1 + - - +
451O ASN* 1.3 77.4 - - - +
453O TYR* 1.3 61.7 + - - +
455O ILE* 4.7 4.0 - - - +
456O GLU* 3.4 38.4 + - - +
457O ARG* 3.1 39.7 + - - +
472O HIS* 5.6 1.6 - - - -
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Residues in contact with TYR 453 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449O TRP* 2.5 54.8 + + + +
450O LEU* 4.4 8.1 - - + +
451O ASN 3.2 0.2 - - - -
452O ARG* 1.3 74.3 - - - +
454O VAL* 1.3 56.3 + - - +
457O ARG* 3.2 47.2 - - + +
458O GLU* 3.8 3.0 - - - +
470O PHE* 3.0 51.0 - + - +
473O PHE* 3.4 35.9 - + - +
509O MET* 4.4 8.5 - - + -
514O PHE* 3.1 36.1 - + - -
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Residues in contact with VAL 454 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450O LEU 3.6 11.9 + - - +
451O ASN 3.3 14.3 - - - +
453O TYR* 1.3 80.6 - - - +
455O ILE* 1.3 67.8 + - + +
457O ARG 4.6 0.7 - - - -
458O GLU* 3.4 39.8 - - - +
508O ARG* 3.5 37.2 - - + +
509O MET* 4.2 17.0 - - + -
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Residues in contact with ILE 455 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451O ASN* 3.2 27.2 + - + +
452O ARG* 4.5 2.7 - - - +
453O TYR 3.6 0.2 - - - -
454O VAL* 1.3 86.8 - - + +
456O GLU* 1.3 75.7 + - + +
457O ARG 3.5 0.4 + - - -
458O GLU* 4.6 3.1 + - - +
459O GLU* 5.9 1.9 - - - -
508O ARG* 5.8 1.3 - - - +
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Residues in contact with GLU 456 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452O ARG* 3.4 29.4 + - + +
455O ILE* 1.3 92.5 - - + +
457O ARG* 1.3 74.2 + - + +
458O GLU 3.7 2.2 + - - -
459O GLU* 3.9 21.3 - - - +
460O GLU* 5.0 3.6 - - - +
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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