Contacts of the strand formed by residues 433 - 439 (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 433 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A GLU* 4.7 7.7 + - - -
428A VAL* 3.8 1.7 - - - -
429A VAL* 3.0 40.3 + - + -
430A ASN* 2.8 38.1 + - + +
432A TYR* 1.3 73.0 - - - +
434A LEU* 1.3 66.2 + - - +
435A ARG* 3.7 29.4 + - + -
450A SER* 3.9 11.7 + - - -
451A LEU 3.5 3.1 - - - -
452A GLN* 3.5 35.7 - - + +
466A ARG* 3.2 31.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 434 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A MET* 3.4 36.6 - - + +
415A VAL* 6.1 3.8 - - + -
416A CYS* 5.0 11.4 - - + +
419A ILE* 4.4 11.7 - - + -
426A TRP* 3.7 22.7 - - + -
427A LYS 3.8 3.6 - - - +
428A VAL* 3.6 29.8 - - + -
431A PRO 4.7 6.1 - - - +
432A TYR 4.3 0.7 - - - -
433A TYR* 1.3 83.6 - - - +
435A ARG* 1.3 67.0 + - - +
436A VAL* 4.0 10.5 - - + -
450A SER* 3.4 6.2 - - - -
451A LEU* 2.9 41.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 435 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A TRP* 3.6 0.3 - - - -
427A LYS* 2.8 79.9 + - + +
429A VAL* 3.7 18.6 - - + +
433A TYR* 3.7 23.9 + - + -
434A LEU* 1.3 75.6 - - - +
436A VAL* 1.3 60.7 + - - +
448A LYS* 4.9 9.9 - - - +
449A MET 3.8 4.0 - - - +
450A SER* 3.6 19.0 + - - -
468A ILE* 5.9 3.4 - - - +
182B SER* 3.2 36.5 - - - +
184B SER* 3.7 24.2 + - - -
185B PRO* 5.6 0.8 - - - +
192B GLU* 6.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 436 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A ILE* 3.3 31.6 - - + -
424A TYR* 6.3 2.9 - - + -
425A GLU 3.4 12.3 - - - +
426A TRP* 3.8 5.8 - - + -
434A LEU* 4.0 9.0 - - + -
435A ARG* 1.3 79.1 - - - +
437A ARG* 1.3 68.1 + - - +
448A LYS* 3.3 3.3 - - - +
449A MET* 2.9 59.7 + - + +
451A LEU* 3.5 24.7 - - + -
540A MET* 5.0 3.6 - - + -
544A LEU* 6.3 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 437 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A TYR* 3.7 4.8 - - - +
425A GLU* 3.0 51.5 + - + +
436A VAL* 1.3 80.3 - - - +
438A ARG* 1.3 66.6 - - - +
446A TYR* 4.1 30.3 - - + +
447A SER 3.5 13.0 - - - +
448A LYS* 3.6 26.5 - - + +
540A MET* 4.7 2.5 - - - -
192B GLU* 3.1 37.8 + - - +
193B MET* 3.4 28.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 438 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A TYR* 2.7 69.4 + - + +
425A GLU* 5.5 1.6 - - - -
437A ARG* 1.3 76.8 - - - +
439A LYS* 1.3 80.2 + - - +
440A ASN* 4.0 3.7 + - - +
441A PRO* 3.4 31.7 - - - +
446A TYR* 3.6 6.4 - - - +
447A SER* 3.1 30.9 + - - +
536A GLU* 5.4 5.1 + - - +
539A GLU* 4.2 22.8 + - - +
540A MET* 3.5 25.8 - - + +
543A ASN* 4.7 7.7 - - - +
80G GLN* 4.6 7.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 439 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A ARG* 1.3 86.9 + - - +
440A ASN* 1.3 78.2 + - - +
441A PRO* 3.3 7.7 + - - +
443A THR 4.5 3.0 + - - +
444A SER* 4.6 20.7 + - - +
445A THR 4.1 8.7 - - - +
446A TYR* 4.7 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