Contacts of the strand formed by residues 720 - 727 (chain A) in PDB entry 3FBY
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 GLY 720 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A SER* 3.5 8.7 + - - -
576A ALA* 3.4 2.4 - - - -
577A PHE* 2.9 38.0 + - - +
602A GLY* 3.4 12.4 + - - -
603A TYR 3.2 13.7 - - - -
604A GLN* 4.5 1.8 - - - -
688A HIS* 5.7 0.2 - - - -
719A GLY* 1.3 74.8 - - - -
721A ARG* 1.3 64.3 + - - -
722A LEU* 5.5 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 721 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535A GLN* 3.0 36.7 + - - +
572A VAL* 3.3 35.1 + - + +
573A GLY 2.9 23.5 + - - +
574A TYR* 3.9 20.2 + - - -
575A THR 3.3 20.9 - - - +
576A ALA* 3.7 16.8 - - + -
600A ILE* 4.0 0.3 - - - +
601A PHE* 3.6 2.4 - - - -
602A GLY 3.3 6.9 + - - -
603A TYR* 2.8 61.8 + - + +
604A GLN 4.9 4.3 + - - -
720A GLY* 1.3 73.7 - - - -
722A LEU* 1.3 63.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 722 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531A PHE* 3.5 16.5 - - + -
572A VAL* 3.4 4.0 - - - +
573A GLY* 2.9 25.8 + - - -
575A THR 4.0 5.3 + - - -
577A PHE* 3.7 23.6 - - + -
580A VAL* 3.8 14.6 - - + -
582A PHE* 3.7 33.7 - - + -
600A ILE* 3.5 1.3 - - - +
601A PHE* 3.3 32.1 - - + -
602A GLY 4.8 1.1 - - - +
686A LEU* 4.3 2.0 - - + -
720A GLY 5.8 0.2 - - - +
721A ARG* 1.3 76.6 - - - +
723A GLY* 1.3 57.7 + - - +
739A TYR* 3.4 36.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 723 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531A PHE* 4.2 9.8 - - - -
571A ALA 3.2 13.2 - - - -
572A VAL* 4.0 2.9 - - - -
582A PHE* 3.9 5.8 - - - -
599A PHE* 3.4 8.5 - - - +
600A ILE* 2.8 38.2 + - - +
722A LEU* 1.3 76.4 - - - +
724A VAL* 1.3 66.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 724 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531A PHE* 6.3 0.4 - - + -
551A TRP* 3.4 29.3 - - + -
560A ILE* 4.0 27.4 - - + -
569A GLY 4.0 0.2 - - - +
570A LEU* 3.3 7.8 - - - +
571A ALA* 2.9 37.3 + - + +
582A PHE* 5.1 4.3 - - + -
598A GLY 3.6 4.9 - - - +
599A PHE* 4.0 5.2 - - + +
600A ILE* 4.3 3.5 - - - +
684A TRP* 4.7 4.0 - - + -
723A GLY* 1.3 79.6 - - - +
725A PHE* 1.3 60.8 + - - +
734A TRP* 3.4 43.1 - - + +
737A LEU* 5.4 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 725 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539A LEU* 4.6 2.5 - - + -
551A TRP* 4.6 0.7 - - - -
568A PRO* 4.6 6.3 - - + -
569A GLY 3.6 5.2 - - - -
570A LEU* 3.4 26.2 - - + -
596A TYR* 4.4 8.1 - - + -
598A GLY 2.9 46.8 + - - +
600A ILE* 4.1 8.5 - - + -
609A PHE* 5.7 0.9 - + - -
611A VAL* 4.0 17.9 - - + -
613A MET* 4.0 33.7 - - + -
654A LEU* 4.2 24.7 - - + -
724A VAL* 1.3 75.0 - - - +
726A CYS* 1.3 74.7 + - - +
727A PHE* 3.6 35.2 - + + -
734A TRP* 3.3 7.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 726 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549A PRO* 4.0 11.4 - - - -
551A TRP* 3.9 9.4 - - - -
562A GLN* 3.6 38.8 - - - -
566A SER* 4.1 6.3 - - - -
567A ASP 4.0 0.2 - - - +
568A PRO* 3.4 2.1 - - - +
569A GLY 3.1 32.2 + - - -
596A TYR 3.8 5.4 - - - +
725A PHE* 1.3 82.8 - - - +
727A PHE* 1.3 63.5 + - - +
728A SER 5.4 0.7 - - - -
729A GLN 4.9 1.1 - - - +
732A ILE* 3.4 26.9 - - + -
734A TRP* 4.2 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 727 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566A SER 4.4 1.1 - - - -
567A ASP* 4.3 1.8 - - - -
568A PRO* 3.5 42.8 - - + -
595A ASP* 3.5 0.9 - - - +
596A TYR* 3.1 44.7 + + + +
621A TYR* 4.0 18.6 - + - -
622A TRP* 5.9 0.2 - + - -
651A ARG* 3.9 22.4 - - + -
654A LEU* 4.9 4.0 - - + -
655A TRP* 3.4 48.6 - + + -
725A PHE* 3.6 22.7 - + + -
726A CYS* 1.3 79.0 - - - +
728A SER* 1.3 77.8 + - - +
729A GLN 3.4 0.9 - - - -
----------------------------------------------------------
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