Contacts of the helix formed by residues 400 - 412 (chain E) in PDB entry 3HYW
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 PRO 400 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388E TYR* 3.4 22.0 - - + +
391E TRP* 5.6 2.0 - - + -
392E LYS* 3.7 6.7 - - + -
397E ASN* 3.5 23.3 - - - +
398E ILE 3.4 8.5 - - - +
399E ALA* 1.4 90.0 - - - +
401E SER* 1.3 67.1 + - - +
402E PHE* 3.2 12.8 - - + -
403E GLU* 3.0 26.6 + - + +
404E GLU* 3.8 3.5 + - - +
391F TRP* 3.5 34.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 401 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397E ASN* 5.0 0.2 - - - +
399E ALA 3.5 3.8 + - - -
400E PRO* 1.3 71.3 - - - +
402E PHE* 1.3 65.7 + - - +
403E GLU 3.2 0.9 + - - -
404E GLU* 3.3 15.9 + - - +
405E LYS* 3.4 28.3 + - - +
391F TRP* 3.3 12.1 - - - +
394F ARG* 4.1 5.5 + - - -
432F SO4 2.7 34.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 402 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388E TYR* 3.2 33.2 - + - -
391E TRP* 5.8 0.7 - + - -
400E PRO* 3.1 24.8 + - + -
401E SER* 1.3 80.6 + - - +
403E GLU* 1.3 55.2 + - - +
405E LYS* 3.2 12.1 + - - +
406E VAL* 2.8 45.9 + - + +
500E DCQ 3.6 26.0 - - + -
387F LYS* 3.8 10.5 - - + +
388F TYR* 3.7 50.9 - + + +
391F TRP* 3.5 42.0 - + + -
402F PHE* 4.8 1.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 403 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318E GLU* 3.8 4.4 - - - +
388E TYR* 2.6 38.1 + - - +
392E LYS* 2.8 27.9 + - - -
398E ILE 3.8 2.4 - - - +
399E ALA* 5.3 2.0 - - - -
400E PRO* 3.0 19.9 + - + +
402E PHE* 1.3 85.0 - - + +
404E GLU* 1.3 60.5 + - - +
406E VAL* 3.3 4.7 + - - +
407E LEU* 2.9 38.7 + - + +
500E DCQ 3.7 43.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 404 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322E MET* 5.3 6.4 - - + +
400E PRO 3.8 3.4 + - - +
401E SER* 3.3 12.5 + - - +
403E GLU* 1.3 78.7 - - - +
405E LYS* 1.3 58.3 + - + +
407E LEU* 3.5 9.0 + - - +
408E GLU* 3.0 35.2 + - - +
413E VAL 4.4 2.8 - - - +
414E HIS* 5.2 5.9 + - - -
415E PRO* 3.8 38.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 405 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401E SER* 3.4 25.3 + - - +
402E PHE* 3.2 9.7 + - - +
404E GLU* 1.3 75.4 - - + +
406E VAL* 1.3 59.0 + - - +
408E GLU* 3.3 15.8 + - - +
409E ILE* 3.0 37.0 + - + +
387F LYS* 3.7 50.1 - - + +
394F ARG* 5.8 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 406 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402E PHE* 2.8 29.6 + - + +
403E GLU* 3.3 4.9 + - - +
405E LYS* 1.3 73.6 - - - +
407E LEU* 1.3 58.9 + - + +
409E ILE* 3.2 10.0 - - + +
410E PHE* 3.0 45.6 + - + +
500E DCQ 3.8 36.8 - - + -
600E LMT 4.0 16.4 - - + -
384F ALA* 3.8 30.7 - - + +
387F LYS* 5.2 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 407 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315E MET* 3.9 25.4 - - + -
319E GLN* 6.2 0.4 - - - +
346E ILE* 4.5 1.1 - - + -
403E GLU* 2.9 40.4 + - + +
404E GLU* 3.8 7.4 - - - +
406E VAL* 1.3 74.5 - - + +
408E GLU* 1.3 60.1 + - - +
410E PHE 4.7 0.2 - - - +
411E LEU* 2.8 45.0 + - + +
412E LYS 3.2 5.5 + - - -
413E VAL* 3.5 25.2 + - + +
415E PRO* 6.6 0.4 - - + -
500E DCQ 3.7 34.1 - - + -
600E LMT 5.1 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 408 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404E GLU* 3.0 22.9 + - + +
405E LYS* 3.4 17.7 - - - +
407E LEU* 1.3 76.9 - - - +
409E ILE* 1.3 64.0 + - + +
412E LYS* 2.9 30.1 + - - +
413E VAL 3.6 19.2 + - - +
414E HIS* 4.1 29.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 409 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405E LYS* 3.0 23.6 + - + +
406E VAL* 3.2 16.8 - - + +
408E GLU* 1.3 83.5 - - + +
410E PHE* 1.3 67.6 + - + +
412E LYS* 5.8 1.5 - - - +
380F TYR* 4.0 32.2 - - + +
383F THR* 4.3 17.7 - - + +
384F ALA* 3.7 38.1 - - + +
387F LYS* 5.1 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 410 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406E VAL* 3.0 32.2 + - + +
409E ILE* 1.3 84.0 - - + +
411E LEU* 1.3 69.3 + - + +
412E LYS* 3.8 2.0 - - - +
600E LMT 3.8 65.7 - - + +
377F TRP* 4.6 9.9 - - + -
380F TYR* 3.8 36.6 - + + -
381F PHE* 3.8 12.3 - + - -
384F ALA* 3.7 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 411 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346E ILE* 3.7 27.1 - - + -
357E PHE* 5.0 2.5 - - + -
359E PHE* 3.8 31.3 - - + -
361E ASP* 5.1 1.0 - - - +
369E ARG* 4.3 7.8 + - - -
371E ILE* 3.7 29.6 - - + -
407E LEU* 2.8 22.5 + - + +
410E PHE* 1.3 83.6 - - + +
412E LYS* 1.3 74.8 + - - +
413E VAL* 3.2 14.7 + - + -
600E LMT 3.6 44.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 412 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431C SO4 4.0 24.9 + - - +
361E ASP* 4.5 9.0 - - - +
369E ARG* 3.5 34.1 + - - +
407E LEU 3.2 0.2 + - - -
408E GLU* 2.9 22.9 + - - +
409E ILE 5.8 0.9 - - - +
410E PHE 5.5 1.6 - - - +
411E LEU* 1.3 79.7 - - - +
413E VAL* 1.3 61.0 + - - +
414E HIS* 3.8 12.6 + - - -
----------------------------------------------------------
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