Contacts of the strand formed by residues 433 - 438 (chain A) in PDB entry 3I8E
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 THR 433 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A VAL* 3.8 15.9 - - + -
427A LEU 3.5 20.6 - - - +
429A PHE* 4.4 1.3 - - - -
432A GLN* 1.3 82.8 + - - +
434A ARG* 1.3 66.7 + - - +
435A VAL* 6.2 0.9 - - + -
451A PHE* 5.6 1.6 - - + -
452A VAL 3.6 15.5 + - - +
453A ASP* 2.9 33.2 + - - +
455A GLN 3.1 12.8 + - - -
457A THR* 2.7 32.1 + - - +
470A GLN* 3.7 9.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 434 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A VAL* 4.6 1.0 - - - +
427A LEU* 4.0 40.7 + - + +
429A PHE* 4.7 11.5 - - + +
432A GLN* 3.4 38.9 + - - +
433A THR* 1.3 84.4 + - - +
435A VAL* 1.3 71.9 + - - +
436A LEU* 3.8 4.0 + - + +
445A GLU* 3.5 31.6 + - + +
446A THR 4.3 13.8 + - - -
453A ASP* 4.0 12.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 435 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A THR* 4.8 4.0 - - + -
426A VAL* 4.8 14.6 - - + -
433A THR* 6.2 1.3 - - + -
434A ARG* 1.3 78.6 - - - +
436A LEU* 1.3 68.0 + - - +
437A MET* 4.0 32.3 - - + +
444A GLU 4.1 0.7 - - - -
445A GLU* 3.3 24.4 - - - +
446A THR* 3.4 28.5 - - - +
447A GLU 5.0 0.4 - - - -
448A LEU* 3.6 34.1 - - + +
451A PHE* 5.6 5.8 - - + -
453A ASP* 3.7 14.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 436 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A LEU* 4.6 13.7 - - + -
424A THR* 3.5 3.6 - - - +
425A LEU* 2.8 62.4 + - + +
427A LEU* 3.7 30.3 - - + -
434A ARG* 4.5 7.2 - - + +
435A VAL* 1.3 83.4 - - - +
437A MET* 1.3 59.4 + - - +
438A LEU* 4.9 6.6 - - + +
443A VAL* 3.9 25.8 - - + -
444A GLU 3.4 9.6 - - - +
445A GLU* 4.3 10.5 - - + -
699A LEU* 5.6 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 437 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A SER* 4.2 20.2 - - - +
423A ASP* 3.9 3.8 - - - +
424A THR* 3.6 33.0 - - + +
435A VAL* 4.0 12.8 - - + +
436A LEU* 1.3 75.2 - - - +
438A LEU* 1.3 67.9 + - - +
442A GLU 3.8 0.2 - - - +
444A GLU* 3.2 44.1 + - + +
446A THR* 5.2 8.7 - - - +
447A GLU 5.8 0.2 - - - +
448A LEU* 3.7 38.1 - - + -
484A LYS* 5.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 438 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A TYR 4.9 0.9 - - - +
423A ASP* 3.2 29.7 + - + +
424A THR* 5.1 3.6 - - - +
425A LEU* 5.9 3.4 - - + +
436A LEU* 4.9 7.9 - - + +
437A MET* 1.3 79.9 - - - +
439A ASN* 1.3 58.6 + - - +
440A GLY* 2.9 25.7 + - - +
442A GLU 3.3 23.6 - - - +
443A VAL* 4.4 12.3 - - + -
444A GLU* 6.0 0.2 - - - -
682A LEU* 5.4 5.4 - - + -
684A SER* 3.4 30.1 - - - +
685A ASP* 5.2 1.6 - - - +
687A TYR* 4.6 16.2 - - + -
----------------------------------------------------------
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