Contacts of the helix formed by residues 268 - 273 (chain B) in PDB entry 5FHH
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 LEU 268 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B THR* 3.5 27.8 - - - +
254B ALA 4.6 1.6 - - - +
255B SER* 4.6 9.2 - - - -
267B THR* 1.3 79.3 - - - +
269B HIS* 1.3 71.3 + - + +
270B ALA 3.1 0.9 - - - +
271B PHE* 2.9 17.5 + - + +
272B ALA* 2.7 36.0 + - + +
305B ILE* 4.6 15.9 - - + -
311B VAL* 3.8 29.6 - - + -
315B LEU* 4.8 2.7 - - + -
319B LEU* 4.1 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 269 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B SER* 4.3 18.3 + - - -
267B THR* 3.4 14.9 + - + -
268B LEU* 1.3 89.0 - - + +
270B ALA* 1.3 60.1 + - - +
272B ALA* 4.3 4.4 - - - +
273B GLY* 3.4 15.8 + - - -
274B ILE 4.0 7.4 + - - -
275B GLY* 4.5 28.4 + - - +
276B SER* 5.7 0.4 - - - -
310B MET 5.5 4.9 - - - -
311B VAL* 5.6 0.7 - - + -
315B LEU* 3.2 37.6 - - + +
319B LEU* 6.4 1.1 - - + -
534B THR* 5.3 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 270 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B THR* 5.3 4.0 - - - -
267B THR* 3.5 17.1 - - + +
268B LEU 3.1 0.8 - - - -
269B HIS* 1.3 77.9 - - - +
271B PHE* 1.3 65.7 + - - +
273B GLY* 3.5 10.1 + - - -
293B VAL* 5.3 1.4 - - - +
465B ALA* 6.3 1.1 - - + -
531B VAL* 3.5 26.9 - - + -
532B GLN* 3.2 46.6 - - + +
534B THR 5.8 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 271 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B VAL* 3.9 27.6 - - + -
253B THR* 4.1 26.2 - - + -
266B THR* 4.7 7.2 - - - -
268B LEU* 2.9 22.5 + - + +
270B ALA* 1.3 81.8 - - - +
272B ALA* 1.3 69.5 + - + +
273B GLY 3.2 0.7 + - - -
293B VAL* 3.7 14.0 - - - +
296B GLY* 3.6 35.6 - - - -
297B TRP* 3.8 34.2 + + - -
300B CYS* 4.2 12.3 - - - -
303B LEU* 6.0 3.8 - - + -
319B LEU* 6.4 0.2 - - + -
333B PHE* 6.0 2.7 - + - -
336B ILE* 5.3 2.5 - - + -
532B GLN* 5.1 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 272 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B LEU* 2.7 20.9 + - + +
269B HIS* 4.3 5.8 - - - +
271B PHE* 1.3 79.0 - - + +
273B GLY* 1.3 59.9 + - - +
274B ILE* 3.6 21.5 + - + +
288B ALA* 4.2 1.7 - - - +
293B VAL* 3.4 2.8 - - - +
297B TRP* 2.5 39.7 + - + +
319B LEU* 4.1 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 273 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B HIS 3.4 8.0 + - - -
270B ALA 3.5 6.7 + - - -
271B PHE 3.2 3.2 - - - -
272B ALA* 1.3 79.1 - - - +
274B ILE* 1.3 57.1 + - - +
287B LEU* 3.7 23.0 - - - +
293B VAL* 3.8 21.8 - - - -
534B THR* 2.4 28.9 + - - -
535B GLY 3.9 1.2 + - - -
----------------------------------------------------------
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