Contacts of the helix formed by residues 383 - 396 (chain F) in PDB entry 4E2I
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 ASP 383 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376F PHE* 4.0 2.0 - - - -
381F SER 3.9 2.4 + - - +
382F ALA* 1.3 71.5 - - - +
384F ILE* 1.3 66.7 + - - +
385F GLU* 2.9 43.7 + - - +
386F GLU* 3.2 33.6 + - - +
387F TRP* 3.1 19.1 - - - +
566F LYS* 4.6 4.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 384 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376F PHE* 3.4 41.2 - - + -
382F ALA 3.7 2.0 + - - -
383F ASP* 1.3 74.3 + - - +
385F GLU* 1.3 65.4 + - + +
387F TRP* 3.4 0.8 + - - -
388F MET* 3.0 40.6 + - + +
577F LEU* 4.3 21.1 - - + -
599F TRP* 5.0 4.0 - - + -
602F ARG* 4.6 15.3 - - + +
603F LEU* 4.9 11.0 - - + -
606F GLU* 4.6 20.0 - - + +
607F PHE* 4.1 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 385 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383F ASP* 2.9 20.5 + - - +
384F ILE* 1.3 82.4 - - + +
386F GLU* 1.3 61.5 + - - +
388F MET* 3.4 3.6 + - - +
389F ALA* 3.1 21.0 + - - +
607F PHE* 3.4 31.7 - - + -
611F VAL* 5.9 1.0 - - - +
615F MET* 4.4 0.5 - - - +
626F LEU* 3.5 36.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 386 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383F ASP* 3.2 26.1 + - + +
385F GLU* 1.3 75.1 - - + +
387F TRP* 1.3 61.3 + - + +
389F ALA* 3.0 6.4 + - - +
390F GLY 3.0 22.7 + - - -
562F PHE* 3.1 39.6 - - + +
563F LEU* 3.6 7.6 - - - +
566F LYS* 2.7 40.6 + - - +
568F ILE* 3.8 15.6 - - + +
626F LEU* 4.1 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 387 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375F MET* 3.5 25.0 - - + +
376F PHE* 3.8 16.8 - + + -
382F ALA* 4.1 10.4 - - + +
383F ASP 3.1 26.0 - - - +
384F ILE 3.4 4.9 + - - +
385F GLU 3.4 0.4 - - - -
386F GLU* 1.3 81.1 + - + +
388F MET* 1.3 59.6 + - - +
390F GLY* 3.4 2.1 + - - -
391F VAL* 3.1 27.1 + - - +
566F LYS* 4.3 14.0 - - + +
567F ARG 3.9 9.6 - - - -
568F ILE* 3.7 38.4 - - + +
571F SER* 3.2 33.7 - - - -
573F ILE* 3.6 22.9 - - + -
574F ALA* 3.9 15.5 - - - +
577F LEU* 3.6 18.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 388 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384F ILE* 3.0 36.3 + - + +
385F GLU* 3.6 6.7 - - - +
387F TRP* 1.3 76.7 - - - +
389F ALA* 1.3 63.3 + - - +
391F VAL* 3.4 23.1 + - + +
392F ALA* 3.5 4.2 + - - +
577F LEU* 3.5 49.6 - - + +
581F TRP* 3.5 35.4 - - + -
603F LEU* 3.7 14.6 - - + -
607F PHE* 4.2 15.5 - - + -
612F TYR* 4.0 6.4 - - + -
615F MET* 3.8 23.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 389 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385F GLU 3.1 13.2 + - - +
386F GLU* 3.0 14.1 + - - +
388F MET* 1.3 77.0 - - - +
390F GLY* 1.3 62.1 + - - +
392F ALA* 3.0 15.8 + - - +
393F TRP* 3.1 12.3 + - - +
562F PHE* 4.2 2.5 - - + -
563F LEU* 4.4 1.6 - - - -
615F MET* 3.7 9.6 - - - -
625F VAL* 3.4 33.5 - - + +
626F LEU* 3.6 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 390 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386F GLU 3.0 10.1 + - - -
387F TRP 3.4 4.9 + - - -
388F MET 3.3 0.4 - - - -
389F ALA* 1.3 73.1 - - - +
391F VAL* 1.3 58.3 + - - +
392F ALA 3.0 2.2 - - - -
393F TRP* 3.2 5.9 + - - +
394F LEU* 2.8 42.2 + - - +
563F LEU* 3.6 20.1 - - - +
568F ILE* 4.2 8.3 - - - -
569F ILE* 4.8 4.5 - - - -
574F ALA* 5.6 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 391 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387F TRP 3.1 18.1 + - - +
388F MET* 3.4 27.8 - - + +
389F ALA 3.2 0.6 - - - -
390F GLY* 1.3 75.7 - - - +
392F ALA* 1.3 56.5 + - - +
394F LEU* 4.0 8.9 - - - +
395F HIS* 3.2 26.2 + - - +
574F ALA* 3.8 21.0 - - - +
577F LEU* 3.9 5.6 - - + +
578F MET* 3.5 33.9 - - + +
581F TRP* 5.2 2.5 - - + -
582F TYR* 4.5 2.0 - - + -
612F TYR* 3.3 22.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 392 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388F MET 3.5 5.4 + - - +
389F ALA 3.0 13.4 + - - +
390F GLY 3.0 0.4 - - - -
391F VAL* 1.3 78.0 - - - +
393F TRP* 1.3 64.6 + - - +
395F HIS* 3.2 3.3 + - - +
396F CYS* 3.1 29.8 + - - -
612F TYR* 4.4 6.9 + - + -
615F MET* 4.1 12.8 - - + -
616F LYS* 3.5 39.4 - - + +
619F VAL* 4.6 2.9 - - + -
625F VAL* 4.9 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 393 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389F ALA 3.1 8.8 + - - +
390F GLY* 3.2 5.8 + - - +
392F ALA* 1.3 79.9 - - - +
394F LEU* 1.3 74.2 + - + +
396F CYS* 3.0 16.5 + - - +
397F LEU* 3.3 26.4 + - + +
430F SER 5.3 1.1 - - - -
431F GLY* 5.2 3.1 - - - -
434F THR* 3.9 18.4 - - + -
553F LEU* 3.2 55.0 + - + +
556F CYS* 3.4 25.8 - - - -
557F LEU* 3.7 26.5 - - + +
563F LEU* 4.4 11.2 - - + -
569F ILE* 3.5 44.9 - - + -
619F VAL* 4.4 5.8 - - + +
625F VAL* 4.7 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 394 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390F GLY 2.8 22.6 + - - +
391F VAL* 4.1 6.7 - - - +
393F TRP* 1.3 94.9 - - + +
395F HIS* 1.3 61.1 + - - +
397F LEU* 3.2 27.7 - - + +
401F MET* 3.2 21.7 - - + +
434F THR* 4.8 2.7 - - + +
435F LEU* 5.5 6.5 - - + -
438F ALA* 5.9 0.9 - - + -
569F ILE* 3.1 31.6 - - - +
571F SER 5.3 0.2 - - - +
574F ALA* 3.9 29.8 - - + -
575F LEU* 4.0 24.2 - - + -
578F MET* 4.4 9.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 395 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136 GLN 4.5 10.5 - - - -
146 ILE* 3.3 18.2 + - - +
391F VAL 3.2 19.2 + - - +
392F ALA 3.2 6.2 + - - +
394F LEU* 1.3 75.1 - - - +
396F CYS* 1.3 58.3 + - - +
397F LEU 3.2 3.4 - - - -
398F LEU 3.4 14.7 - - - +
400F LYS* 4.6 13.1 - - - -
401F MET* 3.8 7.5 + - + -
402F ASP* 2.9 38.1 + - + -
578F MET* 4.5 4.4 - - - -
582F TYR* 3.3 30.7 - + - +
616F LYS* 2.9 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 396 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146 ILE* 3.1 17.3 - - + -
156 PHE* 3.5 28.7 - - - -
392F ALA 3.1 21.0 + - - +
393F TRP 3.0 9.2 + - - +
395F HIS* 1.3 76.1 - - - +
397F LEU* 1.3 59.3 + - - +
398F LEU 3.6 0.4 - - - -
550F LYS* 3.6 1.7 + - - -
552F TYR* 2.7 28.0 + - + -
553F LEU* 3.4 8.4 - - + +
616F LYS* 4.1 16.8 - - - -
619F VAL* 3.6 29.8 - - + -
----------------------------------------------------------
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