Contacts of the strand formed by residues 453 - 465 (chain A) in PDB entry 4BL8
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 PRO 453 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A THR* 3.3 23.5 + - - +
452A GLY* 1.3 83.8 - - - +
454A SER* 1.3 59.1 + - - +
455A GLY 3.4 19.0 + - - +
456A PHE 4.5 3.1 - - - +
457A GLY* 3.8 14.4 - - - -
532A PHE 3.9 1.6 - - - +
533A GLY* 4.0 0.9 - - - -
534A VAL* 3.9 8.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 454 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A SER* 3.1 15.9 - - - -
437A ASP* 3.0 32.0 + - - +
453A PRO* 1.3 67.4 - - - +
455A GLY* 1.3 64.6 + - - +
457A GLY* 2.9 12.1 + - - -
530A THR* 4.5 3.1 - - - +
532A PHE* 3.6 12.5 - - - +
533A GLY* 3.7 17.5 - - - -
534A VAL 3.1 20.7 + - - +
535A VAL* 3.6 15.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 455 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A LEU 4.0 0.2 - - - -
437A ASP* 3.8 11.8 - - - +
445A HIS* 3.5 32.5 - - - +
446A GLU 5.3 6.2 + - - -
448A THR* 5.3 0.6 + - - -
453A PRO* 3.4 18.6 + - - +
454A SER* 1.3 71.5 - - - +
456A PHE* 1.3 62.8 + - - -
457A GLY 3.1 1.0 + - - -
532A PHE 4.9 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 456 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A LEU* 3.0 36.3 + - + +
445A HIS* 3.6 15.5 - + - -
453A PRO* 4.5 3.9 - - - +
455A GLY* 1.3 71.5 - - - -
457A GLY* 1.3 59.5 + - - +
458A PHE* 3.4 25.8 - - + -
488A VAL* 3.5 27.4 - - + -
489A PHE* 3.7 46.9 - + - -
492A GLU* 4.2 24.9 - - + -
494A THR* 3.5 34.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 457 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A LEU 4.3 0.4 + - - -
453A PRO* 3.8 14.6 - - - -
454A SER 2.9 16.0 + - - -
455A GLY 3.0 0.6 - - - -
456A PHE* 1.3 78.6 - - - +
458A PHE* 1.3 60.9 + - - +
534A VAL 3.4 17.9 - - - +
535A VAL* 4.1 2.7 - - - -
536A THR* 3.0 25.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 458 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A LEU* 3.1 51.2 - - + +
436A SER* 3.5 7.6 + - - -
454A SER 4.5 0.8 + - - -
456A PHE* 3.6 28.3 - - + -
457A GLY* 1.3 82.1 - - - +
459A GLU* 1.3 73.4 - - - +
460A LEU* 3.9 14.6 - - + -
488A VAL* 4.3 20.0 - - + -
494A THR* 4.3 4.5 - - - -
495A PHE* 3.9 33.9 - + + -
535A VAL* 4.2 2.9 - - - -
536A THR* 3.1 23.3 - - - +
538A LEU* 4.0 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 459 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A ILE* 3.9 19.5 - - + +
432A SER* 2.8 42.4 + - - +
433A PHE* 3.7 1.7 - - - -
434A GLY 2.9 25.3 + - - -
435A LEU* 3.3 7.7 + - - +
436A SER* 2.8 33.6 + - - +
438A LEU* 4.1 0.5 - - - +
458A PHE* 1.3 78.6 - - - +
460A LEU* 1.3 64.1 + - - +
535A VAL* 4.0 6.5 - - + -
536A THR 3.1 5.3 + - - -
537A PHE* 3.5 21.2 - - + -
538A LEU 3.1 22.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 460 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A LEU* 5.1 0.9 - - + -
431A ILE* 3.6 0.2 - - - -
432A SER* 2.8 36.6 + - - +
435A LEU* 3.6 20.4 - - + +
458A PHE* 3.9 19.5 - - + -
459A GLU* 1.3 74.2 - - - +
461A THR* 1.3 65.7 + - - +
481A MET* 3.6 36.2 - - + +
484A LEU* 3.9 41.3 - - + -
485A ALA* 4.4 2.9 - - + +
488A VAL* 6.4 0.7 - - + -
495A PHE* 5.6 2.5 - - + -
519A LEU* 4.8 7.4 - - + -
538A LEU* 3.3 13.9 - - + +
540A ILE* 4.5 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 461 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A HIS* 3.7 4.0 - - - -
430A TYR 2.9 15.3 - - - +
431A ILE* 4.1 15.3 - - + -
459A GLU 4.2 0.7 - - - +
460A LEU* 1.3 80.4 - - - +
462A PHE* 1.3 62.3 + - - +
481A MET* 3.4 3.6 - - - -
522A ASP* 2.8 28.7 + - - +
525A MET* 4.5 1.6 - - + -
537A PHE* 4.1 24.9 - - + -
538A LEU 2.7 9.6 + - - +
539A GLN* 3.1 19.3 + - - +
540A ILE* 2.8 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 462 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A TRP 3.3 1.0 - - - +
429A HIS* 3.3 6.9 - - - -
430A TYR* 2.9 42.2 + + + -
461A THR* 1.3 76.1 - - - +
463A ARG* 1.3 66.0 + - - +
464A LEU* 4.0 15.9 - - + -
476A TRP* 3.9 29.4 - + - -
477A PRO* 3.8 21.5 - - + -
480A LEU* 4.8 6.3 - - + -
481A MET* 3.8 15.0 - - + -
507A LEU* 4.7 8.7 - - + -
539A GLN* 4.4 3.1 - - - -
540A ILE* 3.5 41.1 - - + -
542A GLY 4.5 2.5 - - - -
576A THR* 3.5 38.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 463 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A ASN* 3.4 15.8 - - - +
427A HIS* 3.1 37.6 + - + -
428A TRP 3.2 4.0 - - - -
429A HIS* 3.3 31.1 + - + -
462A PHE* 1.3 85.2 - - - +
464A LEU* 1.3 59.8 + - - +
522A ASP* 2.8 23.2 + - - -
523A PRO* 3.9 8.2 - - - +
524A GLN* 3.4 22.4 + - - +
539A GLN* 2.9 32.0 + - - +
540A ILE 4.6 3.2 + - - -
573A TRP* 3.7 22.0 - - - -
574A LEU 4.7 0.2 - - - +
575A ILE* 4.2 17.3 - - + -
576A THR* 2.9 33.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 464 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A HIS* 3.1 3.1 - - - +
428A TRP* 2.9 38.2 + - + +
430A TYR* 3.9 17.5 - - + +
462A PHE* 4.0 14.3 - - + -
463A ARG* 1.3 73.2 - - - +
465A LYS* 1.3 76.6 + - - +
470A GLU* 5.9 0.4 - - - +
474A PRO* 3.5 34.3 - - + -
476A TRP* 3.7 22.2 - - + +
477A PRO* 4.1 2.2 - - + -
576A THR 3.7 5.6 - - - +
578A MET* 3.4 34.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 465 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A PRO* 4.8 17.7 - - + -
426A GLU 4.6 4.5 - - - +
427A HIS* 4.1 3.1 - - - -
428A TRP* 4.6 0.2 - - - -
464A LEU* 1.3 82.5 - - - +
466A ARG* 1.3 74.8 + - - +
467A GLU* 3.3 20.8 + - - +
470A GLU* 4.6 1.4 - - - +
575A ILE* 3.7 14.5 - - + +
576A THR 3.0 19.2 + - - +
577A ASP* 3.3 43.2 + - + +
578A MET 5.2 0.4 - - - +
----------------------------------------------------------
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