Contacts of the helix formed by residues 393 - 410 (chain B) in PDB entry 3V9G
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 393 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B THR* 4.1 21.6 - - + +
391B VAL* 3.4 1.5 + - - +
392B ILE* 1.3 88.3 - - - +
394B ALA* 1.3 60.2 + - - +
395B LYS* 4.1 11.1 - - - +
396B SER* 3.0 26.5 + - - -
397B PHE* 2.9 26.9 + - - +
427B TYR* 3.7 16.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 394 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B ASP* 1.3 73.2 - - - +
395B LYS* 1.3 61.5 + - - +
397B PHE* 3.2 3.3 + - + +
398B ALA* 2.8 31.8 + - - +
427B TYR* 3.6 33.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 395 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B ASP* 3.4 11.0 + - - +
394B ALA* 1.3 77.1 - - - +
396B SER* 1.3 61.6 + - - +
398B ALA* 3.5 5.6 + - - +
399B ARG* 3.2 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 396 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B PHE* 5.8 0.4 - - - -
346B GLN* 3.9 13.2 + - - -
391B VAL* 4.1 3.5 - - - +
392B ILE* 4.0 12.5 - - - +
393B ASP* 3.0 23.6 + - - -
395B LYS* 1.3 73.8 - - - +
397B PHE* 1.3 64.6 + - - +
399B ARG* 2.8 37.2 + - - +
400B ILE* 3.0 31.0 + - - +
449B PHE* 4.1 4.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 397 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B VAL* 3.9 6.6 - - + +
393B ASP 2.9 13.4 + - - +
394B ALA* 3.5 8.5 - - - +
396B SER* 1.3 76.5 - - - +
398B ALA* 1.3 64.6 + - + +
400B ILE* 3.4 5.6 + - - +
401B LYS* 3.0 23.5 + - + +
421B CYS* 3.6 32.8 - - + -
422B ASP 3.8 0.9 - - - -
423B ASP* 3.4 42.2 - - + -
427B TYR* 3.7 41.3 - + + -
428B PHE 3.3 24.5 - - - -
429B VAL* 3.9 7.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 398 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B ALA 2.8 19.2 + - - +
395B LYS* 3.8 7.0 - - - +
397B PHE* 1.3 75.4 - - + +
399B ARG* 1.3 66.2 + - - +
401B LYS* 3.0 7.6 + - - +
402B LYS* 2.9 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 399 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B LYS 3.2 10.3 + - - +
396B SER* 2.8 55.1 + - - +
398B ALA* 1.3 77.9 - - - +
400B ILE* 1.3 64.0 + - - +
402B LYS* 3.3 8.8 + - - +
403B TRP* 3.2 38.3 + - + +
447B GLU 5.2 3.6 + - - -
448B ILE* 3.0 27.5 + - - +
449B PHE* 3.4 19.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 400 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B VAL* 3.6 28.0 - - + -
396B SER* 3.0 22.8 + - - +
397B PHE* 3.8 4.3 - - - +
398B ALA 3.2 0.2 - - - -
399B ARG* 1.3 76.1 - - - +
401B LYS* 1.3 59.2 + - - +
403B TRP* 3.0 10.2 + - - +
404B LEU* 2.9 28.9 + - + +
429B VAL* 4.1 27.6 - - + -
448B ILE* 4.2 20.6 - - + +
449B PHE 3.9 5.8 - - - +
450B GLY* 3.5 22.9 - - - -
451B PRO* 4.3 0.9 - - + -
452B VAL* 4.2 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 401 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B PHE* 3.0 16.8 + - + +
398B ALA* 3.0 11.4 + - - +
400B ILE* 1.3 75.4 - - - +
402B LYS* 1.3 57.6 + - - +
404B LEU* 3.1 14.2 + - - +
405B GLU* 2.8 31.2 + - - +
408B ARG* 4.8 0.5 + - - -
421B CYS* 4.0 20.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 402 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398B ALA 2.9 12.4 + - - +
399B ARG* 3.6 11.7 - - - +
400B ILE 3.2 0.2 - - - -
401B LYS* 1.3 75.0 - - - +
403B TRP* 1.3 58.3 + - + +
405B GLU* 3.6 7.3 + - - +
406B HIS* 3.0 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 403 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399B ARG* 3.2 35.5 + - + +
400B ILE* 3.0 10.4 + - + +
402B LYS* 1.3 74.8 - - + +
404B LEU* 1.3 61.0 + - + +
406B HIS* 3.1 28.6 + + + +
407B ALA* 2.8 28.4 + - - +
442B PRO* 3.6 27.8 - - + -
443B ILE* 3.6 42.5 - - + +
446B GLU* 3.7 22.2 - - + -
447B GLU 4.9 3.0 + - - -
448B ILE* 4.0 42.8 - - + +
452B VAL* 5.6 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 404 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400B ILE* 2.9 19.6 + - + +
401B LYS* 3.1 8.5 + - - +
403B TRP* 1.3 76.3 - - - +
405B GLU* 1.3 62.0 + - - +
407B ALA* 3.0 17.7 + - + +
408B ARG* 3.3 32.3 + - - +
415B ILE* 4.3 3.1 - - + +
419B GLY* 3.8 23.8 - - - +
421B CYS* 4.3 20.2 - - + -
429B VAL* 4.2 22.7 - - + -
430B GLU 5.7 0.2 - - - +
432B CYS* 3.7 35.9 - - + -
452B VAL* 4.5 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 405 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401B LYS 2.8 18.5 + - - +
402B LYS* 3.9 7.2 - - - +
404B LEU* 1.3 72.0 - - - +
406B HIS* 1.3 53.3 + - - +
408B ARG* 3.1 22.1 + - - +
409B SER* 2.5 38.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 406 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B LYS 3.0 16.4 + - - +
403B TRP* 3.1 36.6 + + + +
405B GLU* 1.3 76.2 - - - +
407B ALA* 1.3 55.9 + - - +
409B SER* 4.1 7.2 - - - -
410B SER* 2.9 32.2 + - - -
413B LEU* 3.6 14.9 - - + +
441B GLU* 3.2 33.7 + - - -
442B PRO* 4.6 12.7 - - + +
443B ILE* 4.7 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 407 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403B TRP 2.8 15.0 + - - +
404B LEU* 3.0 12.7 + - + +
406B HIS* 1.3 71.4 - - - +
408B ARG* 1.3 63.6 + - - +
410B SER 3.9 0.2 - - - +
413B LEU* 3.2 39.4 - - + +
414B THR* 4.2 4.2 + - - -
415B ILE* 3.9 21.5 - - + +
434B VAL* 4.1 23.8 - - + -
443B ILE* 4.7 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 408 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401B LYS 4.8 0.4 + - - -
404B LEU* 3.3 17.4 + - - +
405B GLU* 3.1 40.5 + - - +
407B ALA* 1.3 75.5 - - - +
409B SER* 1.3 68.5 + - - +
410B SER 3.3 8.5 + - - +
413B LEU 4.4 1.0 - - - +
415B ILE* 3.8 17.2 - - + +
419B GLY* 2.9 31.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 409 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B GLU* 2.5 26.7 + - - +
406B HIS* 4.0 7.0 - - - -
408B ARG* 1.3 79.5 - - - +
410B SER* 1.3 61.7 + - - +
411B PRO* 3.4 7.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 410 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B HIS* 2.9 26.9 + - - -
407B ALA 3.9 0.3 - - - +
408B ARG 3.3 5.4 - - - +
409B SER* 1.3 77.2 - - - +
411B PRO* 1.3 68.6 - - - +
412B SER* 3.7 8.1 + - - -
413B LEU* 2.8 41.8 - - - +
441B GLU* 2.8 28.9 + - - -
----------------------------------------------------------
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