Contacts of the helix formed by residues 567 - 583 (chain B) in PDB entry 3FO5
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 SER 567 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410B ILE* 4.9 8.7 - - - -
561B ASN* 3.9 1.8 - - - -
566B SER* 1.3 75.6 + - - +
568B GLU* 1.3 65.9 + - - +
569B PHE 3.1 2.9 - - - -
570B TYR* 3.1 25.5 + - - +
571B THR* 3.0 27.4 + - - -
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Residues in contact with GLU 568 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454B LYS* 3.9 23.1 + - - +
455B HIS* 4.6 2.7 - - + +
557B TYR* 2.9 45.3 - - - +
561B ASN* 3.1 5.5 + - - +
566B SER* 2.9 25.2 + - - +
567B SER* 1.3 78.2 - - - +
569B PHE* 1.3 58.3 + - - +
571B THR* 3.7 8.0 - - - -
572B THR* 2.9 33.1 + - - -
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Residues in contact with PHE 569 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B 1PE 3.9 22.8 - - - +
415B LEU* 4.0 15.9 - - + -
426B PHE* 3.3 53.4 - + - -
428B MET* 3.6 16.8 - - + +
455B HIS* 5.0 1.3 - + - -
557B TYR* 3.8 21.8 - + - -
558B VAL* 3.9 21.3 - - + -
561B ASN* 2.9 45.6 + - + +
562B VAL* 4.9 2.0 - - + -
568B GLU* 1.3 75.0 - - - +
570B TYR* 1.3 71.5 + - + +
571B THR 3.3 0.2 + - - -
572B THR* 3.8 4.4 - - - +
573B PHE* 3.0 24.9 + - - +
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Residues in contact with TYR 570 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B SER* 2.6 49.2 + - - -
409B GLU 3.5 0.3 + - - -
410B ILE* 3.5 44.4 - - + -
413B VAL* 3.4 33.1 - - + +
414B ARG 4.5 0.2 - - - -
415B LEU* 3.4 21.5 + - + +
428B MET* 3.4 21.1 - - + -
561B ASN 5.8 1.6 - - - -
566B SER 5.6 0.2 - - - -
567B SER* 3.1 22.7 + - - +
569B PHE* 1.3 81.7 - - + +
571B THR* 1.3 58.2 + - - +
573B PHE* 3.2 2.3 + - - +
574B LYS* 2.9 29.5 + - - +
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Residues in contact with THR 571 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454B LYS* 5.2 13.5 - - - +
567B SER* 3.0 19.4 + - - -
568B GLU* 3.7 11.7 - - - -
570B TYR* 1.3 75.2 - - - +
572B THR* 1.3 58.0 + - - +
574B LYS* 3.1 10.7 + - + +
575B ALA* 3.0 27.1 + - + +
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Residues in contact with THR 572 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B 1PE 3.7 20.2 - - - -
452B TRP* 3.8 13.8 + - + +
453B ASP* 3.4 30.7 + - + +
454B LYS* 4.1 13.5 + - - +
455B HIS* 3.2 23.7 + - - -
568B GLU 2.9 14.7 + - - -
569B PHE 3.9 2.9 - - - -
571B THR* 1.3 78.0 - - - +
573B PHE* 1.3 57.0 + - - +
575B ALA* 3.2 7.8 + - - +
576B CYS* 2.8 26.5 + - - +
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Residues in contact with PHE 573 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B 1PE 3.6 15.5 - - - -
413B VAL* 3.8 20.0 - - + -
428B MET* 3.5 46.2 - - + -
430B MET* 3.5 56.2 - - + +
532B PHE* 5.0 2.5 - + - -
544B VAL* 3.5 23.3 - - + -
546B TYR* 3.7 26.5 - - + -
569B PHE 3.0 17.7 + - - +
570B TYR 3.2 3.8 + - - +
572B THR* 1.3 75.4 - - - +
574B LYS* 1.3 58.3 + - - +
576B CYS* 3.3 13.6 - - + +
577B GLU 3.1 20.4 + - - -
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Residues in contact with LYS 574 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B VAL* 6.3 1.1 - - - +
430B MET* 5.6 0.4 - - - -
570B TYR 2.9 13.2 + - - +
571B THR* 3.1 11.6 + - + +
573B PHE* 1.3 74.1 - - - +
575B ALA* 1.3 60.7 + - - +
577B GLU* 3.2 14.4 + - - +
578B GLN* 3.1 26.2 + - - +
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Residues in contact with ALA 575 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452B TRP* 3.4 28.7 - - + +
571B THR* 3.0 14.0 + - + +
572B THR* 3.2 6.3 + - - +
574B LYS* 1.3 72.9 - - - +
576B CYS* 1.3 65.6 + - - +
578B GLN* 3.8 6.8 - - - +
579B PHE* 3.0 25.3 + - - +
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Residues in contact with CYS 576 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430B MET* 4.1 13.9 - - + -
443B LEU* 3.9 23.6 - - - -
452B TRP* 3.5 43.0 - - + -
532B PHE* 4.6 7.0 - - - -
544B VAL* 5.0 0.9 - - - -
572B THR 2.8 9.8 + - - +
573B PHE* 3.3 19.1 - - + +
574B LYS 3.2 0.2 - - - -
575B ALA* 1.3 76.1 - - - +
577B GLU* 1.3 63.2 + - - +
579B PHE* 3.2 4.9 + - - +
580B LEU* 3.0 31.3 + - - +
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Residues in contact with GLU 577 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B VAL* 6.1 0.7 - - - +
430B MET* 3.8 21.0 - - + +
431B VAL 4.3 12.9 - - - +
432B VAL* 4.1 19.3 - - + +
433B HIS* 5.1 3.1 + - - -
573B PHE 3.1 10.1 + - - +
574B LYS* 3.2 13.9 + - - +
576B CYS* 1.3 78.6 - - - +
578B GLN* 1.3 58.1 + - - +
580B LEU* 3.3 4.8 + - - +
581B LEU* 2.9 48.8 + - + +
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Residues in contact with GLN 578 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574B LYS 3.1 15.6 + - - +
575B ALA* 3.8 9.0 - - - +
576B CYS 3.2 0.2 - - - -
577B GLU* 1.3 76.1 - - - +
579B PHE* 1.3 57.1 + - - +
581B LEU* 3.4 13.9 + - - +
582B ASP* 2.6 76.1 + - - +
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Residues in contact with PHE 579 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442B LEU* 3.8 35.4 - - + -
443B LEU* 4.7 3.1 - - + -
448B GLN* 3.9 38.8 - - + -
451B GLU* 4.2 20.0 - - + -
452B TRP* 3.4 41.7 - + + -
575B ALA 3.0 17.5 + - - +
576B CYS 3.4 6.5 - - - +
578B GLN* 1.3 76.1 - - - +
580B LEU* 1.3 70.2 + - + +
582B ASP* 4.5 3.6 - - - -
583B ASN* 2.7 50.4 + - - +
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Residues in contact with LEU 580 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430B MET* 4.8 0.2 - - + -
432B VAL* 4.3 16.2 - - + -
434B VAL* 3.7 20.5 - - + +
439B ALA* 3.9 14.8 - - + -
442B LEU* 3.7 36.3 - - + +
443B LEU* 4.0 23.1 - - + -
544B VAL* 4.1 25.4 - - + -
576B CYS* 3.0 27.3 + - - +
577B GLU* 3.6 6.7 - - - +
578B GLN 3.3 0.2 - - - -
579B PHE* 1.3 76.6 - - + +
581B LEU* 1.3 58.5 + - - +
583B ASN 3.3 2.6 + - - -
584B ARG* 2.8 29.1 + - - -
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Residues in contact with LEU 581 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432B VAL* 4.3 4.9 - - + -
433B HIS* 3.5 35.0 - - + +
434B VAL* 3.9 7.0 - - + -
577B GLU* 2.9 45.5 + - + +
578B GLN* 3.8 15.9 - - - +
580B LEU* 1.3 73.2 - - - +
582B ASP* 1.3 69.0 + - - +
584B ARG* 3.0 49.2 + - - +
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Residues in contact with ASP 582 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578B GLN* 2.6 59.9 + - - +
579B PHE* 3.9 6.3 + - - +
581B LEU* 1.3 73.2 - - - +
583B ASN* 1.3 67.7 + - - +
584B ARG* 3.4 1.5 + - - +
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Residues in contact with ASN 583 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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438B GLN* 3.2 17.7 + - - -
442B LEU* 3.7 25.0 - - + +
448B GLN* 5.6 3.2 + - - -
579B PHE* 2.7 50.7 + - - +
580B LEU 3.4 3.4 - - - -
582B ASP* 1.3 86.8 - - - +
584B ARG* 1.3 63.7 + - - +
585B ASN 3.0 5.0 + - - -
586B ASP* 3.2 22.6 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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