Contacts of the strand formed by residues 512 - 522 (chain A) in PDB entry 4BGJ
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 TRP 512 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507A ARG* 4.3 5.2 - - - -
508A ASN 3.2 17.0 + - - -
509A LEU* 2.8 44.9 + - + +
510A ALA 3.2 4.6 - - - +
511A ALA* 1.3 80.8 - - - +
513A LYS* 1.3 60.7 + - - +
514A ILE* 5.1 0.9 - - + -
543A VAL* 3.9 17.7 - - + -
544A GLU 3.2 9.6 - - - +
545A ARG* 3.3 45.7 - - + +
547A ASP* 3.1 20.2 + - - -
558A TRP* 4.1 21.8 - + - -
615A LEU* 3.5 22.3 - - + +
616A GLN* 4.9 2.4 + - - -
627A ALA* 4.4 17.7 - - + -
630A LEU* 4.1 31.0 - - + -
631A SER* 4.4 5.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 513 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511A ALA 4.1 1.0 + - - -
512A TRP* 1.3 74.1 - - - +
514A ILE* 1.3 62.0 + - - +
542A ASP 4.1 0.3 - - - +
544A GLU* 2.8 47.2 + - + +
546A ASN* 4.6 9.3 - - - +
615A LEU* 5.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 514 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512A TRP* 4.1 2.6 + - + -
513A LYS* 1.3 81.1 - - - +
515A SER* 1.3 74.3 + - - +
516A ILE* 4.6 1.8 - - + -
541A ILE* 4.2 6.1 - - + -
542A ASP 3.2 13.7 - - - +
543A VAL* 4.1 22.9 - - + -
608A GLN* 4.0 7.9 - - + +
611A LEU* 3.8 35.4 - - + -
612A GLN* 2.9 39.6 + - + +
615A LEU* 3.8 27.2 - - + +
630A LEU* 4.5 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 515 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A ILE* 1.3 81.0 - - - +
516A ILE* 1.3 64.7 + - - +
517A PRO* 3.4 9.4 - - - +
541A ILE* 3.5 3.3 - - - +
542A ASP* 2.8 45.9 + - - +
608A GLN* 3.4 15.3 - - - -
612A GLN* 4.8 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 516 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A ILE* 4.6 4.9 - - + -
515A SER* 1.3 76.0 - - - +
517A PRO* 1.3 54.8 - - - +
518A TYR 4.0 6.1 - - - +
539A PHE* 4.0 22.0 - - + -
540A CYS 3.4 13.5 - - - +
541A ILE* 4.3 11.4 - - + -
567A PHE* 4.2 11.4 - - + -
604A ARG* 2.6 50.6 + - + +
607A PHE* 3.9 16.2 - - + +
608A GLN* 2.7 45.6 + - + +
611A LEU* 4.1 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 517 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515A SER* 3.4 17.0 - - - +
516A ILE* 1.3 84.2 - - - +
518A TYR* 1.3 85.7 + - + +
540A CYS* 3.2 15.9 - - - +
542A ASP* 3.5 27.4 - - - +
604A ARG* 4.1 14.4 + - - +
608A GLN* 5.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 518 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516A ILE* 3.3 5.9 - - - +
517A PRO* 1.3 99.9 - - + +
519A VAL* 1.3 76.3 + - - +
520A ASP* 3.7 20.3 + - + -
540A CYS* 3.2 54.9 + - + +
542A ASP* 5.5 1.1 + - - -
561A TYR* 4.3 6.2 + - - -
597A TYR* 6.0 0.9 - - - +
604A ARG* 4.0 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 519 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518A TYR* 1.3 84.1 - - - +
520A ASP* 1.3 69.6 + - - +
537A PRO* 4.6 2.9 - - + -
538A VAL 3.4 17.0 - - - +
539A PHE* 4.0 18.4 - - + -
597A TYR* 3.6 42.7 + - + -
600A LEU* 4.0 22.7 - - + +
601A LYS* 3.9 28.9 - - + +
604A ARG* 4.7 7.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 520 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518A TYR* 3.7 21.0 + - + -
519A VAL* 1.3 76.3 - - - +
521A PHE* 1.3 85.5 + - - +
537A PRO* 3.5 2.6 - - - +
538A VAL* 2.9 32.7 + - + +
540A CYS* 4.8 0.7 - - + -
561A TYR* 3.6 34.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 521 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520A ASP* 1.3 95.1 + - - +
522A PHE* 1.3 58.3 + - - +
534A GLU* 4.1 23.3 + - + -
535A ARG 4.0 24.5 - - - -
536A ILE 3.5 16.6 - - - -
537A PRO* 4.1 15.3 - - + -
538A VAL* 4.3 3.1 - - - -
561A TYR* 5.9 1.0 - - - -
597A TYR* 3.7 41.1 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 522 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521A PHE* 1.3 73.3 - - - +
523A GLU* 1.3 69.3 + - + +
534A GLU 4.2 2.2 - - - -
535A ARG 3.0 24.1 + - - -
536A ILE* 2.9 20.6 + - + +
538A VAL* 4.3 19.3 - - + +
561A TYR* 5.7 4.7 - - + -
----------------------------------------------------------
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