Contacts of the strand formed by residues 446 - 457 (chain A) in PDB entry 40ER
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 TYR 446 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A ARG* 4.1 31.0 - - - +
438A ARG 3.6 14.8 - - - +
439A LYS* 4.7 4.5 - - + -
440A ASN 4.5 0.9 - - - +
444A SER 4.7 4.9 - - - +
445A THR* 1.3 83.3 - - - +
447A SER* 1.3 60.1 + - - +
448A LYS* 3.9 31.5 - - + +
470A ASP* 4.7 11.1 + - - -
533A HIS* 5.9 0.2 - - - -
536A GLU* 5.5 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 447 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A ARG* 3.5 1.2 - - - +
438A ARG* 3.1 35.6 + - - +
440A ASN* 5.3 3.5 + - - +
446A TYR* 1.3 72.6 - - - +
448A LYS* 1.3 64.6 + - - +
468A ILE* 5.1 0.4 - - - -
533A HIS* 4.5 17.9 - - - -
536A GLU* 3.5 33.7 + - - +
537A PHE* 5.4 1.1 - - - -
540A MET* 3.1 29.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 448 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A LYS* 4.9 1.2 - - - +
435A ARG* 4.9 15.9 - - - +
436A VAL 3.3 14.8 - - - +
437A ARG* 3.6 18.0 - - + +
446A TYR* 3.9 30.4 - - + +
447A SER* 1.3 81.2 - - - +
449A MET* 1.3 70.1 + - - +
467A SER* 5.4 0.2 - - - -
468A ILE* 3.1 43.1 + - + +
469A ASP 5.9 2.5 - - - -
533A HIS* 5.1 1.6 - - - -
537A PHE* 4.6 6.8 - - - +
540A MET* 4.5 2.5 - - - +
182B SER* 5.1 9.8 - - - +
192B GLU* 3.6 21.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 449 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A ARG* 3.8 2.1 - - - +
436A VAL* 2.9 46.5 + - + +
448A LYS* 1.3 78.7 - - - +
450A SER* 1.3 73.4 + - - +
451A LEU* 3.5 27.4 - - + -
465A PHE* 3.6 31.9 - - + -
466A ARG 3.2 16.4 - - - +
468A ILE* 3.8 6.9 - - - +
537A PHE* 3.9 9.0 - - + -
540A MET* 3.7 27.4 - - - +
541A CYS* 3.9 21.8 - - - -
544A LEU* 5.2 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 450 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A TYR* 3.9 7.1 + - - -
434A LEU 3.4 11.2 - - - -
435A ARG* 3.6 19.2 - - - -
449A MET* 1.3 81.7 + - - +
451A LEU* 1.3 64.7 + - - +
452A GLN 4.0 0.8 + - - -
464A ASP 3.5 4.0 - - - +
465A PHE* 3.8 1.9 - - - -
466A ARG* 3.0 62.0 + - - +
468A ILE* 4.2 12.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 451 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A MET* 4.8 1.5 - - + +
415A VAL* 4.6 8.7 - - + -
419A ILE* 5.0 4.3 - - + -
432A TYR 3.4 6.4 - - - +
433A TYR* 5.1 0.9 - - - -
434A LEU* 2.9 47.0 + - + +
436A VAL* 3.5 35.2 - - + -
449A MET* 3.5 25.8 - - + -
450A SER* 1.3 72.8 - - - +
452A GLN* 1.3 60.7 + - - +
453A LEU 4.0 0.2 - - - -
463A LEU* 3.6 32.2 - - + +
464A ASP 3.3 5.6 - - - +
465A PHE* 4.3 4.0 - - + -
544A LEU* 3.7 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 452 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A LEU* 5.5 3.0 - - - +
432A TYR* 3.2 18.4 - - - +
433A TYR* 3.5 39.2 - - + +
450A SER 4.0 1.4 + - - -
451A LEU* 1.3 73.8 - - - +
453A LEU* 1.3 68.9 + - - +
454A TYR* 3.3 40.3 + - + +
463A LEU* 4.3 1.1 - - - -
464A ASP* 3.0 33.7 + - - +
466A ARG* 4.5 10.3 - - - +
206B PRO* 4.2 17.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 453 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A PRO* 4.0 2.5 - - + +
411A ILE* 3.5 36.1 - - + -
412A MET* 3.7 24.2 - - + -
432A TYR* 3.1 40.8 + - + +
451A LEU 4.0 0.8 + - - -
452A GLN* 1.3 78.7 + - - +
454A TYR* 1.3 63.1 - - - +
461A TYR* 3.9 8.7 - - + -
462A LEU 3.4 24.2 - - - +
463A LEU* 4.1 11.6 - - + +
205B PRO* 4.1 16.8 - - + +
206B PRO* 3.7 21.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 454 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A PHE* 4.2 16.8 - - - -
191A LEU* 3.6 19.8 - - + +
452A GLN* 3.3 41.5 + - + +
453A LEU* 1.3 75.7 - - - +
455A GLN* 1.3 62.0 + - - +
456A VAL 4.1 0.2 - - - -
461A TYR* 3.5 12.9 - - - +
462A LEU* 2.7 34.1 + - + +
464A ASP* 3.5 26.2 + - + -
466A ARG* 4.6 2.8 + - - -
205B PRO* 4.8 1.6 - - - -
206B PRO* 3.3 13.5 - - + +
207B ILE 3.9 6.1 - - - -
208B LEU* 3.6 34.3 - - + -
209B PRO* 3.6 28.9 - - + -
212B LEU* 4.5 4.0 - - + -
240B HIS* 4.4 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 455 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A TYR* 1.3 75.2 - - - +
456A VAL* 1.3 61.1 + - - +
457A ASP* 3.1 27.0 + - - +
458A SER* 3.7 16.0 - - - +
460A THR 4.1 0.2 - - - -
461A TYR* 3.4 37.6 + - + -
204B SER* 5.0 4.0 - - - -
205B PRO* 3.9 20.0 - - + +
206B PRO 2.9 15.3 + - - +
207B ILE* 3.3 20.5 - - + +
208B LEU 3.2 16.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 456 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A ARG* 4.4 22.4 - - - +
454A TYR 4.1 0.4 + - - -
455A GLN* 1.3 72.5 - - - +
457A ASP* 1.3 80.3 + - - +
460A THR* 3.3 27.3 + - + +
461A TYR* 4.4 0.9 - - - +
462A LEU* 3.7 24.0 - - + -
207B ILE* 5.1 4.8 - - - +
208B LEU* 3.6 34.5 - - + -
213B LEU* 6.1 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 457 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455A GLN* 3.1 18.9 - - - +
456A VAL* 1.3 81.6 - - - +
458A SER* 1.3 62.3 + - - +
459A ARG* 3.4 34.8 + - - +
460A THR* 2.8 48.7 + - - +
461A TYR* 5.1 0.3 - - - -
207B ILE* 6.2 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