Contacts of the helix formed by residues 327 - 345 (chain D) in PDB entry 6PI7
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 GLY 327 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326D VAL* 1.4 78.5 - - - +
328D SER* 1.3 65.5 + - - -
329D ARG 3.2 2.7 - - - -
330D SER* 2.8 20.7 + - - -
331D LEU* 3.1 21.6 + - - +
58F TYR* 5.0 6.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 328 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327D GLY* 1.3 69.9 - - - -
329D ARG* 1.3 57.5 + - - +
331D LEU* 3.4 13.2 + - - +
332D GLN* 2.9 50.0 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
325D ILE* 3.5 23.3 - - + +
327D GLY 3.2 0.8 - - - -
328D SER* 1.3 78.5 + - - +
330D SER* 1.3 58.2 + - - +
332D GLN* 3.3 13.1 + - - +
333D LEU* 2.9 29.3 + - - +
412D LEU* 4.7 0.8 - - + +
415D GLN* 3.2 32.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 330 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311D TYR* 4.2 7.1 - - - -
324D GLN* 6.3 1.8 - - - -
325D ILE 3.2 4.2 + - - -
326D VAL* 3.1 13.0 - - - -
327D GLY 2.8 26.7 + - - -
329D ARG* 1.3 76.4 - - - +
331D LEU* 1.3 58.0 + - - +
333D LEU* 3.4 3.4 + - - +
334D ASP* 3.1 35.7 + - - +
415D GLN* 5.3 0.7 - - - -
58F TYR* 3.4 22.8 + - - -
104F TYR* 4.5 0.2 - - - -
105F ARG* 3.3 16.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 331 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327D GLY 3.1 20.2 + - - +
328D SER* 3.6 10.8 - - - +
330D SER* 1.3 72.2 - - - +
332D GLN* 1.3 65.5 + - - +
334D ASP* 3.5 11.5 + - + +
335D LYS* 3.2 22.7 + - - +
58F TYR* 3.4 42.6 - - + +
60F SER* 5.9 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 332 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328D SER* 2.9 37.1 + - - +
329D ARG* 3.5 8.7 - - - +
331D LEU* 1.3 77.7 - - + +
333D LEU* 1.4 55.7 + - - +
335D LYS* 3.5 8.5 + - - +
336D LEU* 3.1 25.8 + - - +
412D LEU* 3.1 29.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 333 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324D GLN* 3.6 28.9 - - + +
329D ARG 2.9 17.0 + - - +
330D SER* 3.7 6.3 - - - +
331D LEU 3.3 0.2 - - - -
332D GLN* 1.4 71.7 - - - +
334D ASP* 1.3 59.6 + - - +
336D LEU* 3.1 7.9 + - + +
337D VAL* 2.9 31.4 + - + +
390D ASP* 3.7 34.1 - - + +
391D PHE* 4.2 17.9 - - + -
412D LEU* 3.7 14.5 - - + +
415D GLN* 4.0 19.7 - - + +
105F ARG* 4.0 15.3 - - - +
107F TRP* 5.3 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 334 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330D SER 3.1 14.8 + - - +
331D LEU* 3.6 16.4 - - + +
333D LEU* 1.3 75.9 - - - +
335D LYS* 1.3 59.9 + - - +
337D VAL* 3.5 1.4 + - - +
338D ASN* 2.6 37.7 + - - +
58F TYR* 4.6 1.6 - - - -
104F TYR* 2.6 32.8 + - - -
105F ARG* 2.8 33.9 + - - -
107F TRP* 3.3 18.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 335 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331D LEU 3.2 10.5 + - - +
332D GLN* 3.5 11.7 - - - +
333D LEU 3.3 0.2 - - - -
334D ASP* 1.3 77.4 - - - +
336D LEU* 1.3 53.0 + - - +
338D ASN* 3.4 5.1 + - - +
339D GLU* 2.8 51.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 336 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332D GLN 3.1 14.3 + - - +
333D LEU* 3.1 17.0 + - + +
335D LYS* 1.3 72.6 - - - +
337D VAL* 1.3 59.9 + - - +
339D GLU* 3.4 12.6 + - - +
340D MET* 2.9 44.8 + - + +
372D ARG* 6.0 5.2 - - - +
390D ASP* 6.0 0.4 - - - +
409D PHE* 5.8 4.3 - - + +
412D LEU* 4.3 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 337 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333D LEU* 2.9 19.5 + - + +
334D ASP 3.9 4.3 - - - +
335D LYS 3.5 0.2 - - - -
336D LEU* 1.3 74.4 - - - +
338D ASN* 1.3 54.9 + - - +
340D MET* 4.7 1.3 - - - -
341D THR* 2.7 38.8 + - - +
369D SER* 5.5 2.0 - - - -
370D TRP 3.7 17.0 - - - +
371D TYR* 4.7 8.5 - - + -
391D PHE* 5.6 0.7 - - + -
107F TRP* 4.0 34.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 338 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334D ASP* 2.6 31.3 + - - +
335D LYS* 3.8 5.4 - - - +
337D VAL* 1.3 74.7 - - - +
339D GLU* 1.3 62.8 + - - +
341D THR* 3.4 7.5 + - - -
342D GLN* 3.0 24.3 + - - +
93E PHE* 5.1 10.7 - - - +
107F TRP* 3.5 35.8 - - - +
112F TYR* 5.0 3.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 339 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335D LYS* 2.8 36.8 + - + +
336D LEU* 3.4 10.2 + - - +
338D ASN* 1.3 68.5 - - - +
340D MET* 1.3 59.0 + - - +
342D GLN* 3.2 9.0 + - - +
343D HIS* 3.0 28.8 + - - +
406D ARG* 5.8 1.2 + - - -
409D PHE* 4.0 21.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 340 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336D LEU* 2.9 29.1 + - - +
337D VAL* 3.8 4.3 - - - +
339D GLU* 1.3 71.0 - - - +
341D THR* 1.3 57.4 + - - +
343D HIS 3.3 0.7 + - - -
344D TYR* 2.9 40.2 + - + +
361D ALA* 4.0 11.2 - - + -
370D TRP* 3.9 12.6 - - + +
371D TYR* 3.5 36.3 - - - +
372D ARG* 3.7 23.3 - - - +
405D LEU* 3.7 25.1 - - + -
409D PHE* 3.8 37.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 341 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337D VAL 2.7 22.8 + - - -
338D ASN* 3.6 9.1 - - - -
340D MET* 1.3 74.8 - - - +
342D GLN* 1.3 55.4 + - - +
345D GLU* 2.8 39.5 + - + +
368D GLY 4.1 8.7 - - - +
369D SER* 3.3 25.4 + - - +
370D TRP* 3.1 26.0 + - + +
31E SER* 4.3 23.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 342 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338D ASN 3.0 13.9 + - - +
339D GLU* 3.5 11.0 - - - +
341D THR* 1.3 76.5 - - - +
343D HIS* 1.3 61.4 + - - +
345D GLU* 4.1 9.3 - - - +
346D ASN 5.2 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 343 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339D GLU 3.0 16.2 + - - +
340D MET 3.7 2.7 - - - +
342D GLN* 1.3 79.1 - - - +
344D TYR* 1.3 111.3 + + - +
345D GLU 3.8 0.3 + - - -
346D ASN 4.6 1.4 + - - -
347D SER* 4.1 11.6 + - - -
406D ARG* 3.5 39.9 + - + +
409D PHE* 3.9 12.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 344 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340D MET* 2.9 32.0 + - + +
343D HIS* 1.3 105.6 - + - +
345D GLU* 1.3 66.5 - - - +
346D ASN 3.3 2.5 - - - -
347D SER* 2.9 27.8 + - - +
361D ALA* 3.5 22.0 - - + -
370D TRP* 3.4 40.9 - + + -
403D ARG* 3.7 20.9 - - + -
404D ALA 2.8 28.0 + - - -
405D LEU* 3.4 2.9 - - - -
406D ARG 2.9 19.9 + - - -
409D PHE* 3.6 20.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 345 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341D THR* 2.8 28.2 + - + +
342D GLN* 4.1 9.6 - - - +
343D HIS 3.5 0.2 - - - -
344D TYR* 1.3 76.0 - - - +
346D ASN* 1.3 70.9 + - + +
347D SER 3.9 1.6 + - - +
368D GLY 5.7 0.7 - - - +
370D TRP* 3.8 14.6 + - - +
29E SER* 5.8 6.7 - - - -
31E SER* 5.4 8.7 - - - -
----------------------------------------------------------
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