Contacts of the helix formed by residues 428 - 438 (chain B) in PDB entry 2E3P
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 428 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B VAL* 1.3 76.0 - - - +
429B GLY* 1.3 60.5 + - - +
430B HIS* 3.4 3.9 + - - -
431B GLU* 3.0 20.4 + - - +
432B VAL* 2.9 30.5 + - - +
531B THR* 4.1 11.9 - - + -
547B ILE* 4.1 11.4 - - + -
549B CYS* 4.1 3.4 - - - -
596B ILE* 3.5 31.9 - - + -
597B LEU 2.6 23.5 + - - +
598B PHE* 3.8 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 429 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428B THR* 1.3 73.2 - - - +
430B HIS* 1.3 62.1 + - - +
432B VAL* 3.9 0.2 - - - -
433B CYS* 2.9 30.8 + - - +
500B TRP* 4.1 6.5 - - - -
529B CYS* 3.6 27.5 - - - +
531B THR* 2.9 22.4 + - - -
549B CYS* 3.7 8.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 430 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428B THR* 3.2 8.8 + - - +
429B GLY* 1.3 75.2 - - - +
431B GLU* 1.3 58.8 + - - +
433B CYS* 3.9 0.9 - - - +
434B ASN* 2.9 52.9 + - - -
500B TRP* 3.4 58.3 - + - +
531B THR* 4.5 0.8 + - - -
597B LEU* 3.6 22.9 - - + +
598B PHE 2.6 33.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 431 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B VAL* 3.5 3.6 - - - +
428B THR* 3.0 36.3 + - - +
430B HIS* 1.3 76.7 - - - +
432B VAL* 1.3 62.8 + - - +
434B ASN* 3.2 6.7 + - - +
435B TYR* 3.0 35.2 + - + -
544B ARG* 2.8 45.4 + - - -
587B VAL* 4.4 4.3 - - + -
591B THR* 3.9 19.9 - - + +
595B PRO 3.9 1.4 - - - +
597B LEU* 3.0 36.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 432 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B VAL* 5.5 0.9 - - + -
427B VAL* 3.6 27.4 - - + -
428B THR 2.9 23.0 + - - +
429B GLY 3.9 0.2 - - - +
431B GLU* 1.3 70.9 - - - +
433B CYS* 1.3 58.4 + - - +
435B TYR* 3.3 0.7 + - - -
436B PHE* 3.0 24.6 + - - +
527B MET* 3.8 7.0 - - - -
529B CYS* 3.6 26.2 - - - -
549B CYS* 3.7 10.3 - - - -
551B ILE* 3.8 13.7 - - + -
583B PHE* 3.5 29.5 - - + -
584B THR* 5.7 1.1 - - + -
587B VAL* 4.3 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 433 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429B GLY 2.9 12.8 + - - +
430B HIS 4.1 1.8 - - - +
432B VAL* 1.3 77.2 - - - +
434B ASN* 1.3 57.1 + - - +
436B PHE* 3.2 2.8 + - - -
437B TRP* 2.9 33.6 + - - +
486B ILE* 3.7 12.3 - - + -
500B TRP* 3.6 38.6 - - + -
501B ILE 3.9 2.0 - - - -
502B VAL* 3.5 18.7 - - + +
527B MET* 3.9 14.1 - - - -
529B CYS* 3.7 22.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 434 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430B HIS* 2.9 34.1 + - - +
431B GLU* 3.2 6.0 + - - +
433B CYS* 1.3 75.3 - - - +
435B TYR* 1.3 64.5 + - + +
437B TRP* 4.1 4.3 - - - +
438B ASN* 2.8 37.4 + - + +
486B ILE* 3.3 19.3 - - - +
500B TRP* 5.0 0.3 - - - -
597B LEU* 3.4 31.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 435 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431B GLU* 3.0 34.3 + - + +
432B VAL 3.9 0.4 - - - +
434B ASN* 1.3 81.8 - - + +
436B PHE* 1.3 62.1 + - - +
438B ASN* 3.9 3.5 + - - +
441B VAL* 3.5 28.7 - - + +
445B TRP* 3.4 17.7 + - - -
583B PHE* 3.8 4.0 - - + -
586B TYR* 3.7 27.4 - + + -
587B VAL* 3.8 28.3 - - + -
590B LYS* 3.6 41.7 + - + +
591B THR* 3.9 20.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 436 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B VAL 3.0 17.6 + - - +
433B CYS* 3.2 5.1 + - - +
435B TYR* 1.3 77.8 - - - +
437B TRP* 1.3 57.6 + - - +
442B ARG* 3.0 20.3 + - - -
445B TRP* 3.6 34.8 - + - -
502B VAL* 3.6 35.7 - - + -
504B ASN* 3.9 18.9 + - - -
525B VAL* 4.5 3.8 - - + -
527B MET* 3.6 37.9 - - + -
553B TYR* 4.1 10.5 - + - -
579B PHE* 3.8 18.6 - + - -
583B PHE* 3.6 13.6 - + + -
700B 16C 3.5 22.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 437 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433B CYS 2.9 15.8 + - - +
434B ASN* 4.1 4.3 - - - +
436B PHE* 1.3 79.8 - - - +
438B ASN* 1.3 76.3 + - + +
439B VAL* 3.1 9.6 + - - +
442B ARG* 3.3 10.9 + - - +
460B ASP 3.3 21.8 - - - -
461B ASN* 3.5 23.4 + - - -
462B ALA 3.8 2.9 - - - -
463B ILE* 4.2 26.0 - - + +
484B SER* 3.0 50.2 + - - -
485B VAL 4.0 1.8 - - - -
486B ILE* 3.6 32.8 - - + -
502B VAL* 3.9 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 438 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434B ASN* 2.8 24.0 + - + +
435B TYR* 3.9 3.2 + - - +
436B PHE 3.6 0.8 - - - -
437B TRP* 1.3 83.8 - - + +
439B VAL* 1.3 66.2 + - - +
440B ASP* 3.0 30.9 + - - +
441B VAL* 3.3 43.6 + - + +
442B ARG* 3.6 7.1 + - - +
----------------------------------------------------------
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