Contacts of the strand formed by residues 426 - 433 (chain A) in PDB entry 2EC8
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 LEU 426 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A ASP 3.9 3.4 - - - -
420A ARG* 4.6 14.4 - - + -
422A VAL* 5.9 2.2 - - + -
424A GLY* 3.8 16.6 - - - +
425A MET* 1.3 74.6 - - - +
427A GLN* 1.3 60.1 + - - +
440A TRP* 4.2 15.8 - - + -
477A SER* 3.4 6.7 - - - -
478A ILE* 3.1 35.5 + - + +
480A SER* 4.3 16.6 - - - +
504A PHE* 3.9 43.1 - - + -
505A ASN 6.1 1.3 - - - +
506A PHE* 5.9 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 427 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A ASP* 2.9 49.3 + - + +
420A ARG* 5.5 0.4 - - - -
421A LEU* 5.5 4.8 - - + +
425A MET 4.1 1.8 + - - +
426A LEU* 1.3 73.9 - - - +
428A CYS* 1.3 70.6 + - - +
429A VAL* 4.2 18.8 - - + +
440A TRP* 4.3 0.9 - - - -
475A GLN* 5.4 7.4 - - + +
476A SER 3.9 4.5 - - - +
477A SER* 3.6 21.8 + - - +
504A PHE* 3.0 28.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 428 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A ILE* 3.7 14.8 - - + -
417A THR 3.9 4.7 - - - -
418A TYR* 4.7 2.5 - - - -
427A GLN* 1.3 82.0 - - - +
429A VAL* 1.3 67.3 + - - +
438A ILE* 4.8 8.0 - - + +
440A TRP* 3.6 15.3 - - + -
474A VAL 4.2 0.5 - - - +
475A GLN* 4.0 0.5 - - - -
476A SER* 3.3 24.9 + - - +
491A CYS* 2.0 50.5 - - - -
502A ALA* 4.3 9.9 - - - -
504A PHE* 4.4 5.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 429 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A ILE* 3.3 6.8 - - - +
416A LEU* 2.7 47.1 + - + -
417A THR* 2.9 36.1 + - + +
419A ASP* 4.8 0.2 - - - +
427A GLN* 4.2 20.4 - - + +
428A CYS* 1.3 79.8 - - - +
430A ALA* 1.3 59.8 - - - +
463A ASN* 5.9 1.8 - - + -
473A VAL* 5.0 6.5 - - + -
474A VAL 3.3 15.3 - - - +
475A GLN* 4.2 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 430 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A PRO* 4.8 0.9 - - + -
414A GLU 3.3 17.3 - - - +
415A ILE* 3.9 12.3 - - + +
416A LEU* 3.9 4.3 - - - +
428A CYS 4.4 0.2 - - - -
429A VAL* 1.3 75.0 - - - +
431A ALA* 1.3 60.5 + - - +
436A PRO* 3.9 6.4 - - + +
438A ILE* 4.3 10.6 - - + +
473A VAL* 3.3 5.0 - - - +
474A VAL 2.7 37.9 + - - +
493A ALA* 4.1 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 431 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A PRO* 3.1 3.3 - - - +
414A GLU* 2.7 39.2 + - + +
416A LEU* 4.0 16.6 - - + -
430A ALA* 1.3 77.9 - - - +
432A GLY* 1.3 56.9 + - - +
436A PRO* 4.0 3.4 - - - -
468A PRO* 4.7 2.9 - - + -
471A LYS* 4.5 20.0 + - + +
472A LEU 3.4 8.1 - - - +
473A VAL* 3.7 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 432 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A THR* 4.3 4.3 - - - -
413A PRO* 4.0 13.0 - - - -
431A ALA* 1.3 77.8 - - - +
433A PHE* 1.3 67.1 + - - +
434A PRO 3.6 8.3 - - - +
436A PRO* 3.9 4.2 - - - +
471A LYS* 3.9 19.0 - - - +
472A LEU 3.4 25.6 + - - +
495A ASN* 4.6 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 433 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A PHE* 3.2 44.2 - + - -
408A TYR* 3.6 21.8 - + + -
409A VAL 3.3 24.5 - - - +
410A ASN* 3.4 20.2 - - - -
411A THR* 3.2 29.9 + - + +
432A GLY* 1.3 77.2 - - - -
434A PRO* 1.4 88.1 + - + +
435A GLU 4.4 2.9 - - - -
470A GLY 4.3 15.3 - - - +
471A LYS* 5.3 0.2 - - + -
472A LEU* 4.8 11.0 - - + -
495A ASN* 3.3 6.3 + - - +
497A VAL* 3.4 8.3 - - - +
----------------------------------------------------------
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