Contacts of the strand formed by residues 472 - 478 (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 472 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A ALA* 3.4 0.5 - - - -
432A GLY 3.4 18.8 + - - +
433A PHE* 4.8 8.9 - - + -
435A GLU* 2.9 59.9 - - + +
436A PRO* 3.4 17.8 - - - +
462A LEU* 6.3 2.2 - - + -
463A ASN 5.8 2.7 - - - +
471A LYS* 1.3 72.6 - - - +
473A VAL* 1.3 85.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 473 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A LEU* 3.8 18.4 - - + -
429A VAL* 5.0 3.8 - - + -
430A ALA 3.3 5.8 - - - +
431A ALA* 3.7 22.0 - - + -
435A GLU* 4.5 0.2 - - - +
462A LEU* 4.7 1.4 - - - -
463A ASN* 3.0 54.7 + - + +
464A SER 5.0 3.1 - - - +
468A PRO* 3.8 22.9 - - + -
471A LYS 3.8 1.1 + - - +
472A LEU* 1.3 88.6 - - - +
474A VAL* 1.3 60.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 474 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A CYS 4.2 0.6 - - - +
429A VAL* 3.3 10.4 - - - +
430A ALA 2.7 30.9 + - - +
435A GLU* 4.7 7.9 - - - +
436A PRO* 3.0 37.7 - - + +
438A ILE* 4.1 16.8 - - + -
461A THR 5.3 0.4 - - - -
462A LEU* 5.9 1.3 - - - +
463A ASN* 4.9 0.4 - - - -
472A LEU 4.1 1.2 + - - -
473A VAL* 1.3 73.1 - - - +
475A GLN* 1.3 61.4 + - - +
476A SER 4.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 475 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A GLN* 5.4 6.7 - - - +
428A CYS 4.0 4.7 - - - -
429A VAL* 4.2 15.0 - - + -
460A GLN* 2.8 10.7 - - + +
461A THR 2.7 48.7 + - - +
462A LEU 4.7 1.3 - - - +
463A ASN* 4.6 11.9 - - + -
473A VAL 4.3 0.2 + - - -
474A VAL* 1.3 76.8 - - - +
476A SER* 1.3 58.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 476 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A GLN* 4.1 1.2 - - - +
428A CYS 3.3 27.2 + - - -
438A ILE* 2.9 47.2 - - - +
440A TRP* 3.2 16.2 + - - -
458A ASP* 5.2 9.4 - - - -
460A GLN* 3.9 6.3 - - - +
474A VAL 4.3 0.4 - - - -
475A GLN* 1.3 75.6 - - - +
477A SER* 1.3 67.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 477 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A MET* 5.4 5.4 - - - -
426A LEU 3.4 11.6 + - - -
427A GLN* 3.6 27.5 + - - +
440A TRP* 4.4 5.9 + - - -
457A VAL 3.9 2.1 - - - +
458A ASP* 3.3 11.6 - - - -
459A VAL* 3.1 42.6 + - - +
460A GLN* 4.0 8.0 - - - +
476A SER* 1.3 78.9 + - - +
478A ILE* 1.3 64.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 478 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A MET* 3.2 13.6 - - - +
426A LEU* 3.1 36.2 + - + +
440A TRP* 4.4 25.1 - - + -
456A PRO* 4.5 18.4 - - + -
457A VAL 5.0 2.9 - - - +
458A ASP 5.5 0.2 - - - -
459A VAL* 5.2 3.1 - - - -
477A SER* 1.3 75.4 - - - +
479A ASP* 1.3 62.0 + - - +
480A SER* 4.7 3.6 - - - +
----------------------------------------------------------
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