Contacts of the helix formed by residues 400 - 415 (chain B) 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 LYS 400 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132 GLN* 5.3 11.7 - - + +
395B HIS* 4.6 11.2 - - - -
398B LEU 3.2 1.4 + - - -
399B PRO* 1.3 76.0 - - + +
401B MET* 1.3 65.3 + - - +
402B ASP* 3.4 7.6 - - - -
403B SER* 3.1 30.6 + - - +
404B VAL* 3.0 23.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 401 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B LEU* 3.2 34.5 - - + +
395B HIS* 3.9 12.9 + - - -
397B LEU* 3.5 32.1 - - + -
398B LEU* 3.1 40.2 + - + +
399B PRO 4.3 0.9 - - - -
400B LYS* 1.3 74.9 - - - +
402B ASP* 1.3 64.2 + - - +
404B VAL* 3.0 21.8 + - - +
405B VAL* 3.0 20.6 + - - +
435B LEU* 3.8 28.5 - - + -
578B MET* 3.5 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 402 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B HIS* 2.9 24.6 + - + -
400B LYS* 3.9 5.0 - - - -
401B MET* 1.3 76.1 - - - +
403B SER* 1.3 70.7 + - - +
405B VAL* 3.3 12.7 + - - +
406B TYR* 3.3 9.9 + - - +
578B MET* 3.7 35.6 - - + +
579B LEU* 4.5 4.8 - - + +
582B TYR* 3.2 40.2 - - + +
583B ARG* 3.7 21.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 403 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400B LYS* 3.1 44.4 + - - +
402B ASP* 1.3 84.9 + - - +
404B VAL* 1.3 58.1 + - - +
406B TYR* 3.4 5.9 + - - +
407B ASP* 2.7 33.1 + - - +
583B ARG* 2.8 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 404 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398B LEU* 5.7 6.1 - - + -
399B PRO 3.9 11.2 - - - +
400B LYS* 3.0 17.0 + - + +
401B MET* 3.0 14.6 + - - +
403B SER* 1.3 74.0 - - - +
405B VAL* 1.3 62.0 + - + +
407B ASP* 3.1 11.0 + - - +
408B PHE* 2.9 27.6 + - + +
422B TRP* 3.5 29.6 - - + -
435B LEU* 6.4 1.3 - - + -
543B LYS* 5.1 9.9 - - - -
545B ILE* 4.2 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 405 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401B MET* 3.0 24.4 + - + +
402B ASP 3.4 7.0 - - - +
403B SER 3.3 0.2 - - - -
404B VAL* 1.3 76.9 - - + +
406B TYR* 1.3 57.5 + - - +
408B PHE* 3.3 6.5 + - + +
409B LEU* 2.9 36.6 + - + +
435B LEU* 5.5 0.4 - - + -
439B LEU* 4.5 14.1 - - + -
442B LEU* 3.7 26.2 - - + -
575B LEU* 4.7 6.3 - - + -
578B MET* 3.5 24.7 - - + -
579B LEU* 3.5 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 406 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B ASP 3.3 3.9 + - - +
403B SER 3.7 7.9 - - - +
404B VAL 3.3 0.6 - - - -
405B VAL* 1.3 78.4 - - - +
407B ASP* 1.3 70.9 + - - +
409B LEU* 3.5 17.8 + - + +
410B LYS* 3.2 63.0 + - + +
579B LEU* 4.6 2.2 - - + +
583B ARG* 3.9 33.4 - - + +
587B GLU* 3.1 58.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 407 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403B SER* 2.7 23.9 - - - +
404B VAL* 3.1 10.1 + - - +
406B TYR* 1.3 82.9 - - - +
408B PHE* 1.3 59.7 + - - +
410B LYS* 4.0 4.1 - - - +
411B CYS* 2.8 31.0 + - - +
422B TRP* 4.2 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 408 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B VAL* 2.9 16.5 + - + +
405B VAL* 3.7 7.4 - - - +
407B ASP* 1.3 73.9 - - - +
409B LEU* 1.3 69.5 + - + +
411B CYS* 3.0 3.1 + - - +
412B MET* 2.9 63.8 + - + +
422B TRP* 3.9 40.3 - + + -
424B PHE* 6.1 0.2 - + - -
439B LEU* 4.4 26.2 - - + -
443B CYS* 3.9 14.8 - - - -
469B LEU* 3.7 22.4 - - + -
524B GLY 4.3 1.3 - - - -
525B ILE* 3.5 39.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 409 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B LEU* 4.2 10.5 - - + +
365B PHE* 3.9 28.0 - - + -
405B VAL* 2.9 27.1 + - + +
406B TYR* 3.6 21.5 - - + +
407B ASP 3.3 0.2 - - - -
408B PHE* 1.3 78.6 - - + +
410B LYS* 1.3 61.6 + - + +
412B MET* 3.0 22.1 + - - +
413B VAL* 3.0 17.8 + - - +
442B LEU* 4.3 7.6 - - + -
443B CYS* 3.5 28.3 - - - -
579B LEU* 3.9 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 410 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B GLU* 3.4 30.7 + - - +
406B TYR* 3.2 57.6 + - + +
407B ASP* 4.0 3.6 - - - +
409B LEU* 1.3 78.1 - - + +
411B CYS* 1.3 58.0 + - - +
413B VAL* 2.9 12.4 + - + +
414B TYR* 2.7 62.5 + - + +
587B GLU 4.0 11.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 411 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407B ASP 2.8 21.1 + - - +
408B PHE 3.2 6.3 - - - +
410B LYS* 1.3 76.0 - - - +
412B MET* 1.3 64.0 + - + +
414B TYR* 4.3 5.0 - - - +
415B ASN* 3.4 17.0 + - - -
416B ILE* 4.7 5.0 + - - +
419B LYS 4.2 15.3 - - - +
420B ARG* 3.9 16.0 - - - +
422B TRP* 3.2 32.3 - - + +
542B VAL* 4.4 10.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 412 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B ARG* 2.8 33.1 + - - +
408B PHE* 2.9 57.3 + - + +
409B LEU* 3.2 9.6 - - - +
411B CYS* 1.3 83.6 - - - +
413B VAL* 1.3 56.9 + - - +
415B ASN* 3.7 5.4 + - - +
420B ARG 3.2 27.1 - - - +
443B CYS* 5.2 0.2 - - - -
468B PHE* 3.7 25.4 - - + -
469B LEU* 4.0 12.1 - - + -
523B PRO* 3.6 32.5 - - + +
524B GLY 4.0 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 413 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B ARG* 3.7 23.3 - - + +
358B GLU* 3.5 43.3 - - + +
361B LEU* 3.5 25.8 - - + -
409B LEU* 3.1 15.7 - - + +
410B LYS* 2.9 21.3 + - + +
412B MET* 1.3 76.9 - - - +
414B TYR* 1.3 72.0 + - + +
415B ASN* 3.2 0.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 414 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B LYS* 2.7 57.1 + - + +
411B CYS* 4.3 4.7 - - - +
413B VAL* 1.3 79.6 - - + +
415B ASN* 1.3 71.2 + - - +
416B ILE* 4.0 24.2 - - + -
561C GLU* 5.5 5.2 - - + -
565C GLU* 3.6 60.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 415 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B ARG* 3.6 36.6 + - - +
411B CYS 3.4 10.3 + - - -
412B MET 4.0 4.3 - - - -
413B VAL 3.1 2.2 - - - +
414B TYR* 1.3 84.6 - - - +
416B ILE* 1.3 57.6 + - - +
417B PRO* 3.6 8.1 - - - +
420B ARG* 3.0 34.8 + - - +
520B ILE* 5.4 1.9 - - - +
523B PRO* 5.1 2.4 - - - +
564C LEU 4.0 3.5 - - - +
565C GLU 4.8 0.5 - - - +
567C ARG* 2.8 34.4 + - - +
----------------------------------------------------------
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