Contacts of the helix formed by residues 395 - 403 (chain B) in PDB entry 5E9W
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 PHE 395 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B PHE* 4.4 4.0 - + + -
176B ASN* 3.9 14.1 - - - -
179B MET* 3.4 36.0 - - + +
285B PHE* 4.1 14.8 - + - -
317B THR* 3.6 17.5 - - + -
394B THR* 1.3 71.5 - - - +
396B LEU* 1.3 57.0 + - - +
398B PHE* 3.7 1.3 - - - +
399B TYR* 2.8 31.1 + - - +
461B TRP* 5.6 1.8 - - - -
464B THR* 3.1 51.1 - - + +
465B SER* 4.6 2.6 + - - -
467B TYR* 2.9 43.3 + + + +
468B LEU 3.6 8.1 - - - -
469B VAL* 3.4 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 396 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B THR* 3.1 8.4 + - - +
395B PHE* 1.3 75.6 - - - +
397B GLU* 1.3 67.2 + - + +
399B TYR* 3.1 6.3 + - + +
400B GLU* 2.8 36.7 + - + +
450B ARG 5.1 5.6 - - - +
451B LEU* 4.3 14.8 - - + -
452B PRO* 3.5 35.0 - - + -
461B TRP* 3.9 15.9 - - + -
465B SER* 3.8 29.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 397 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B LYS* 4.4 3.8 + - - +
393B LYS* 3.5 19.9 - - + +
394B THR* 3.0 45.1 + - - +
396B LEU* 1.3 75.4 - - + +
398B PHE* 1.3 64.2 + - - +
400B GLU* 3.2 9.4 + - - +
401B GLU* 3.0 23.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 398 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B TRP* 5.8 0.4 - + - -
179B MET* 3.4 47.6 - - + -
182B VAL* 4.3 5.6 - - + -
183B LEU* 4.0 25.6 - - + -
391B TYR* 3.4 23.3 - + - -
393B LYS* 4.0 22.8 - - + +
394B THR 2.9 16.4 + - - +
395B PHE 3.7 3.4 - - - +
397B GLU* 1.3 76.4 - - - +
399B TYR* 1.3 57.3 + - - +
401B GLU* 3.4 4.2 + - - +
402B LYS* 2.9 72.8 + - + +
469B VAL* 3.6 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 399 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B PHE* 3.5 37.0 - + + -
178B TRP* 3.8 14.5 - + - -
179B MET* 4.5 5.8 - - - -
395B PHE 2.8 19.5 + - - +
396B LEU* 3.4 7.0 - - + +
398B PHE* 1.3 77.3 - - - +
400B GLU* 1.3 83.0 + - - +
403B ILE* 3.1 61.9 + - + +
412B LEU* 4.4 0.4 - - + -
452B PRO* 4.5 8.5 - - + -
454B GLY* 4.2 6.8 - - - -
455B THR* 2.5 29.3 + - + -
461B TRP* 3.6 24.2 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 400 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B LEU* 2.8 26.6 + - + +
397B GLU* 3.2 10.7 + - - +
399B TYR* 1.3 90.0 - - + +
401B GLU* 1.3 60.4 + - - +
403B ILE* 4.0 9.4 - - - +
404B LYS* 3.4 25.2 - - - +
452B PRO* 4.2 22.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 401 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B GLU* 4.9 1.2 - - - +
391B TYR* 6.1 1.2 - - - -
393B LYS* 3.1 35.8 + - - +
397B GLU 3.0 15.8 + - - +
398B PHE* 3.9 3.4 - - - +
400B GLU* 1.3 76.6 - - - +
402B LYS* 1.3 94.3 + - + +
404B LYS* 3.1 31.1 + - + +
405B ASN* 4.3 0.7 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
178B TRP* 4.2 14.8 - - + -
182B VAL* 3.6 24.3 - - + +
186B GLU* 3.0 37.7 + - - +
398B PHE* 2.9 54.0 + - + +
401B GLU* 1.3 102.3 + - + +
403B ILE* 1.3 57.3 + - - +
404B LYS 3.2 0.4 - - - -
405B ASN* 3.2 12.3 + - - +
408B ASN* 3.0 31.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 403 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B TRP* 4.5 7.2 - - + -
399B TYR* 3.1 64.4 + - + +
400B GLU* 4.0 10.8 - - - +
401B GLU 3.3 0.4 - - - -
402B LYS* 1.3 75.0 - - - +
404B LYS* 1.3 58.4 + - + +
405B ASN 3.0 14.4 + - - +
408B ASN* 4.9 0.2 - - - -
409B LYS* 3.9 38.6 + - + +
412B LEU* 3.8 18.4 - - + -
413B LYS* 4.6 6.5 - - - +
455B THR* 4.4 1.6 - - - +
----------------------------------------------------------
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