Contacts of the helix formed by residues 328 - 343 (chain D) in PDB entry 5FLZ
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 328 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
666B ARG* 5.8 8.3 - - - +
289D HIS* 3.4 12.2 - - + +
327D GLU* 1.4 94.1 - - + +
329D ARG* 1.4 60.6 + - - +
330D GLN* 3.4 2.4 + - + +
331D ILE* 3.5 27.5 - - + +
332D SER 3.1 20.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 329 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658B GLU* 4.4 3.9 + - + -
659B GLU* 3.1 30.5 - - + +
662B LYS* 3.7 36.4 - - + +
666B ARG* 5.3 10.0 - - - +
249D TYR* 3.4 16.2 + - - -
325D ASN 5.7 0.4 + - - -
326D VAL* 3.6 37.1 - - + +
327D GLU 3.2 7.2 + - - +
328D PRO* 1.4 69.2 - - - +
330D GLN* 1.3 55.8 + - + +
332D SER* 3.0 5.8 + - - -
333D ARG* 2.9 32.4 + - - +
359D ARG* 3.3 56.9 + - - +
360D SER 5.1 0.8 - - - +
361D PRO* 4.9 13.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 330 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659B GLU* 4.2 20.9 - - + +
663B GLU* 5.4 9.2 + - - +
666B ARG* 5.6 4.2 + - - -
328D PRO* 3.4 1.6 - - + +
329D ARG* 1.3 73.1 - - + +
331D ILE* 1.3 59.8 + - + +
333D ARG* 3.3 10.8 + - - +
334D ALA* 3.0 25.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 331 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289D HIS* 3.5 26.7 - - + +
290D SER* 5.6 1.8 - - - +
328D PRO* 3.5 31.0 - - + +
330D GLN* 1.3 72.6 - - + +
332D SER* 1.4 65.7 + - - +
334D ALA* 3.3 7.3 + - + +
335D MET* 3.1 29.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 332 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289D HIS* 3.6 19.9 + - - -
323D ILE* 4.7 6.6 - - - +
327D GLU 5.0 1.3 - - - -
328D PRO 3.1 9.3 + - - -
329D ARG* 3.0 12.3 + - - -
331D ILE* 1.4 75.2 - - - +
333D ARG* 1.4 52.9 + - - +
335D MET* 3.3 18.6 - - - +
336D THR* 2.6 40.0 + - - -
359D ARG* 3.7 31.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 333 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
651B TYR* 3.7 18.6 - - - -
654B ASN* 3.5 30.5 - - - +
655B CYS* 3.5 37.9 - - + +
659B GLU* 3.4 28.3 - - + +
329D ARG 2.9 13.1 + - - +
330D GLN* 3.6 7.9 - - - +
331D ILE 3.3 0.2 - - - -
332D SER* 1.4 74.4 + - - +
334D ALA* 1.4 63.6 + - - +
336D THR* 3.6 31.5 + - - +
337D LYS* 3.1 39.7 + - - +
357D GLY 5.8 2.2 + - - -
359D ARG* 3.9 18.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 334 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330D GLN 3.0 14.6 + - - +
331D ILE* 3.3 10.5 + - + +
333D ARG* 1.4 76.6 - - - +
335D MET* 1.4 61.8 + - - +
337D LYS* 3.5 21.5 + - - +
338D LEU* 3.6 9.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 335 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289D HIS* 3.5 50.7 - - + +
290D SER* 4.6 3.6 - - - -
292D TYR* 4.6 9.0 - - + -
293D ASP* 3.6 45.5 - - + +
323D ILE* 5.7 4.3 - - + -
331D ILE* 3.1 21.2 + - + +
332D SER* 3.3 23.6 - - - +
334D ALA* 1.4 70.8 - - - +
336D THR* 1.4 61.2 + - - +
338D LEU* 3.1 9.8 + - + +
339D GLN* 2.9 32.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 336 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
651B TYR* 5.1 14.4 - - + +
293D ASP* 5.3 1.0 + - - -
332D SER* 2.6 27.8 + - - -
333D ARG* 3.3 32.0 + - - +
335D MET* 1.4 79.8 - - - +
337D LYS* 1.4 61.7 + - - +
339D GLN* 3.2 10.7 + - + +
340D GLN* 3.1 23.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 337 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
651B TYR* 6.5 0.7 - - + -
655B CYS* 5.5 9.6 - - - +
830B LEU* 3.6 28.1 + - + +
831B LYS* 3.1 33.0 + - + +
833B ASP* 3.6 16.4 + - - +
333D ARG* 3.1 30.6 + - - +
334D ALA* 3.7 12.6 - - - +
336D THR* 1.4 75.2 - - + +
338D LEU* 1.4 61.9 + - - +
340D GLN* 3.2 15.4 - - - +
341D ARG 3.2 18.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 338 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
831B LYS* 3.4 14.8 - - - +
334D ALA 3.6 6.5 + - - +
335D MET* 3.1 14.7 + - - +
337D LYS* 1.4 75.9 - - - +
339D GLN* 1.3 68.5 + - - +
341D ARG* 3.5 3.3 + - + -
342D ILE* 2.9 48.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 339 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293D ASP* 3.0 32.3 + - - +
297D ASP* 3.0 40.7 + - - +
335D MET* 2.9 22.2 + - - +
336D THR* 3.2 10.2 + - + +
338D LEU* 1.3 91.0 - - - +
340D GLN* 1.3 63.2 + - - +
342D ILE* 3.4 15.6 - - - +
343D LYS* 3.4 5.9 + - - -
344D PHE* 3.4 18.7 + - + -
345D PRO* 5.9 0.7 - - - +
355D ASN* 5.2 3.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 340 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647B LYS* 5.3 5.5 - - - +
651B TYR* 4.1 23.6 + - - +
827B ARG* 5.3 5.1 + - - +
830B LEU* 6.0 4.0 - - - +
831B LYS* 4.4 4.3 - - - +
336D THR* 3.1 17.7 + - + +
337D LYS* 3.2 20.5 - - - +
339D GLN* 1.3 75.3 - - - +
341D ARG* 1.4 110.5 + - - +
343D LYS* 3.4 10.4 + - - +
353D HIS* 2.9 47.3 + - + +
355D ASN* 4.3 19.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 341 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
827B ARG* 3.1 53.8 + - - +
828B ALA* 4.2 2.6 - - - +
831B LYS* 3.9 37.3 - - + +
337D LYS 3.2 11.0 + - - +
338D LEU* 3.9 5.4 - - + +
340D GLN* 1.4 115.9 + - - +
342D ILE* 1.3 61.7 + - - +
343D LYS* 3.4 12.6 + - - +
353D HIS* 3.7 17.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 342 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338D LEU* 2.9 36.0 + - + +
339D GLN* 3.4 17.0 - - - +
341D ARG* 1.3 72.4 - - - +
343D LYS* 1.4 66.3 + - - +
344D PHE* 3.3 49.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 343 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
827B ARG* 5.9 0.4 - - - +
339D GLN 3.4 6.1 + - - -
340D GLN 3.4 18.8 + - - +
341D ARG* 3.3 11.6 - - - +
342D ILE* 1.4 77.8 - - - +
344D PHE* 1.4 64.2 + - - +
345D PRO* 3.3 12.2 - - - +
347D TRP* 3.7 24.2 - - + +
352D MET* 3.7 26.9 - - - +
353D HIS* 3.5 29.6 - - + -
355D ASN* 6.1 0.7 - - - -
----------------------------------------------------------
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