Contacts of the helix formed by residues 554 - 563 (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 VAL 554 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B 1PE 4.5 26.5 - - - +
426B PHE* 6.3 0.2 - - + -
476B SER* 5.8 2.2 - - - +
479B LEU* 4.1 22.7 - - + -
486B GLN* 3.8 20.4 - - - +
548B ASN* 5.9 0.7 - - - +
551B THR* 3.1 34.3 - - + +
552B PRO 3.0 0.2 + - - -
553B GLY* 1.3 82.4 - - - +
555B LEU* 1.3 65.4 + - - +
556B ASN* 3.3 3.4 - - - -
557B TYR* 3.0 10.4 + - + +
558B VAL* 3.0 32.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 555 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B ASP* 4.7 7.2 - - - +
364B TYR* 3.2 50.9 - - + +
365B ILE* 3.6 20.0 - - + +
424B LEU* 4.1 18.4 - - + +
551B THR 4.1 1.5 + - - -
552B PRO* 3.2 17.5 + - + +
553B GLY 3.7 0.6 - - - -
554B VAL* 1.3 78.0 - - - +
556B ASN* 1.3 58.0 + - - +
558B VAL* 3.1 9.6 + - + +
559B THR* 2.9 51.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 556 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B LYS* 3.1 24.8 + - - -
361B ASP* 4.8 3.6 - - - -
479B LEU 5.7 1.6 - - - +
480B GLY* 4.0 26.3 + - - -
554B VAL* 3.3 0.8 - - - -
555B LEU* 1.3 77.5 - - - +
557B TYR* 1.3 57.7 + - - +
559B THR* 3.1 6.0 + - - -
560B THR* 2.8 36.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 557 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B 1PE 4.5 9.9 - - - -
454B LYS* 4.7 3.3 - - - +
455B HIS* 2.6 43.5 + + - -
479B LEU* 3.8 44.9 + - + +
554B VAL* 3.0 14.0 + - + +
556B ASN* 1.3 78.1 - - - +
558B VAL* 1.3 63.6 + - + +
560B THR* 3.5 5.6 + - - -
561B ASN* 2.8 32.8 + - - -
568B GLU* 2.9 45.5 + - + +
569B PHE* 3.8 22.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 558 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B 1PE 5.8 0.4 - - - +
424B LEU* 3.8 24.9 - - + +
426B PHE* 3.8 35.0 - - + -
548B ASN* 5.9 0.9 - - - +
551B THR* 5.7 0.7 - - - +
554B VAL* 3.0 31.5 + - + +
555B LEU* 3.5 11.7 - - + +
557B TYR* 1.3 75.1 - - + +
559B THR* 1.3 55.3 + - - +
561B ASN* 3.1 3.3 + - - +
562B VAL* 2.7 49.8 + - + +
569B PHE* 3.9 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 559 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B LYS* 3.5 13.7 + - - -
360B LEU* 4.0 19.0 - - + +
361B ASP* 2.7 30.2 + - - +
424B LEU* 3.6 25.1 - - + -
555B LEU* 2.9 27.6 + - + +
556B ASN 3.1 10.2 + - - -
558B VAL* 1.3 72.2 - - - +
560B THR* 1.3 68.2 + - - +
562B VAL* 4.1 5.8 - - - +
563B ALA* 2.9 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 560 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B LYS* 3.2 22.4 - - - +
556B ASN* 2.8 23.4 + - - -
557B TYR* 3.7 8.9 - - - -
558B VAL 3.3 0.2 - - - -
559B THR* 1.3 81.6 + - - +
561B ASN* 1.3 59.2 + - - +
563B ALA* 3.6 0.6 + - - -
564B GLY 3.3 1.6 + - - -
565B LEU* 3.0 51.9 + - + +
566B SER* 3.4 21.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 561 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B SER* 5.6 0.2 + - - -
415B LEU* 4.1 9.9 - - + +
557B TYR* 2.8 28.6 + - - +
558B VAL 3.1 7.6 + - - +
560B THR* 1.3 79.4 - - - +
562B VAL* 1.3 65.3 + - - +
564B GLY* 3.1 14.7 + - - -
566B SER* 3.6 24.7 + - - +
567B SER* 3.7 2.6 - - - -
568B GLU* 3.1 20.4 + - - -
569B PHE* 2.9 61.9 + - + +
570B TYR* 5.8 1.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 562 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B LYS* 2.7 37.4 + - - +
360B LEU* 3.8 18.2 - - + -
407B SER* 4.2 7.6 - - - +
408B SER* 5.6 1.6 + - - -
415B LEU* 4.1 15.5 - - + +
417B THR* 3.6 35.2 - - + +
424B LEU* 4.9 6.5 - - + -
426B PHE* 4.6 7.6 - - + -
558B VAL* 2.7 40.3 + - + +
559B THR* 4.1 5.8 - - - +
561B ASN* 1.3 72.9 - - - +
563B ALA* 1.3 55.6 + - - +
564B GLY 3.6 0.2 + - - -
569B PHE* 4.9 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 563 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B SER* 3.1 43.5 + - - +
356B LYS* 4.0 18.1 + - + +
357B LYS* 3.7 16.4 - - + +
360B LEU* 5.0 1.1 - - + -
559B THR 2.9 18.5 + - - +
562B VAL* 1.3 77.6 - - - +
564B GLY* 1.3 58.0 + - - +
565B LEU* 3.5 11.9 - - + -
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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