Contacts of the helix formed by residues 307 - 320 (chain B) in PDB entry 2R9R
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 SER 307 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B LEU* 3.1 14.1 + - - -
304B SER 3.5 2.3 + - - +
305B ARG 3.6 1.2 - - - -
306B HIS* 1.3 79.9 - - - +
308B LYS* 1.3 62.5 + - - +
309B GLY* 4.0 0.2 - - - -
310B LEU* 3.0 33.5 + - - +
311B GLN* 3.1 27.9 + - - +
510B PGW 3.3 31.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 308 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B HIS 4.1 1.8 + - - -
307B SER* 1.3 71.6 - - - +
309B GLY* 1.3 55.6 - - - +
311B GLN* 3.0 29.0 + - - +
312B ILE* 2.8 45.2 + - + +
416B GLU* 4.2 12.6 - - + -
510B PGW 2.5 17.8 + - - +
512B PGW 3.7 48.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 309 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B SER* 4.0 1.3 - - - -
308B LYS* 1.3 73.8 - - - +
310B LEU* 1.3 54.9 + - - +
312B ILE* 3.0 14.9 + - - +
313B LEU* 2.7 30.9 + - - +
409B PHE* 4.9 5.1 - - - -
413B TYR* 6.0 2.2 - - - -
510B PGW 2.7 27.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 310 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B ILE 5.2 3.6 - - - +
301B PHE* 5.3 11.7 - - + -
303B LEU* 4.1 12.6 - - + -
304B SER* 3.6 36.1 - - - +
307B SER* 3.0 24.7 + - - +
309B GLY* 1.3 76.1 - - - +
311B GLN* 1.3 58.0 + - - +
313B LEU* 3.7 23.2 - - + +
314B GLY 3.0 21.0 + - - -
511B PGW 6.1 3.8 - - + -
512B PGW 3.5 26.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 311 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B MET* 4.1 4.5 - - + +
304B SER 3.0 25.2 + - - +
305B ARG 3.8 15.2 + - - -
306B HIS 4.7 0.4 - - - -
307B SER 3.1 20.7 + - - +
308B LYS* 3.0 34.8 + - + +
310B LEU* 1.3 76.4 - - - +
312B ILE* 1.3 59.4 + - + +
314B GLY* 3.1 2.3 + - - -
315B GLN* 2.9 34.6 + - + +
512B PGW 3.6 48.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 312 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B LYS* 2.8 31.8 + - + +
309B GLY* 3.4 13.7 - - - +
311B GLN* 1.3 74.1 - - + +
313B LEU* 1.3 56.6 + - - +
315B GLN* 3.2 13.8 + - - +
316B THR* 2.7 37.4 + - - -
409B PHE* 3.7 22.0 - - + -
412B PHE* 3.8 28.3 - - + +
413B TYR* 3.6 45.3 - - + +
416B GLU* 4.4 12.8 - - + -
510B PGW 6.0 0.2 - - - +
512B PGW 6.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 313 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B GLY 2.7 20.1 + - - +
310B LEU* 3.7 24.0 - - + +
312B ILE* 1.3 72.5 - - - +
314B GLY* 1.3 57.7 + - - +
316B THR* 3.2 11.8 + - + -
317B LEU* 2.9 50.7 + - + +
409B PHE* 4.3 15.7 - - + -
506B PGW 3.8 37.7 - - + -
511B PGW 4.4 13.7 - - + -
512B PGW 4.7 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 314 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B LEU 3.0 10.7 + - - -
311B GLN 3.1 4.6 + - - -
313B LEU* 1.3 73.6 - - - +
315B GLN* 1.3 65.0 + - - +
317B LEU* 3.2 5.3 + - - +
318B LYS* 3.0 23.7 + - - +
512B PGW 3.8 45.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 315 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B GLN* 2.9 20.0 + - - +
312B ILE* 3.2 20.1 + - - +
314B GLY* 1.3 75.6 - - - +
316B THR* 1.3 63.2 + - - +
318B LYS* 3.4 8.7 + - - +
319B ALA* 3.1 24.1 + - - +
412B PHE* 3.5 40.0 - - + +
415B ARG* 3.9 7.9 + - - +
512B PGW 3.8 67.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 316 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B ILE* 2.7 22.7 + - - +
313B LEU* 3.3 14.1 - - + -
315B GLN* 1.3 75.1 - - - +
317B LEU* 1.3 64.4 + - + +
319B ALA* 3.3 3.3 + - - +
320B SER* 2.7 36.9 + - - +
405B ILE* 3.8 17.5 - - + +
408B ASN* 4.1 1.1 + - + -
409B PHE* 3.3 52.8 - - + +
412B PHE* 4.0 12.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 317 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B LEU* 2.9 39.6 + - + +
314B GLY* 3.9 3.8 - - - +
316B THR* 1.3 77.8 - - + +
318B LYS* 1.3 66.7 + - - +
320B SER* 3.0 14.0 + - - +
321B MET* 3.3 19.4 + - - +
324B LEU* 4.0 23.5 - - + +
405B ILE* 5.2 7.0 - - + -
506B PGW 4.0 32.5 - - + -
511B PGW 6.1 0.4 - - + -
512B PGW 4.0 44.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 318 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B GLY 3.0 16.2 + - - +
315B GLN* 3.6 7.2 - - - +
316B THR 3.3 0.2 - - - -
317B LEU* 1.3 77.3 - - - +
319B ALA* 1.3 60.9 + - - +
321B MET* 3.5 21.2 - - + +
512B PGW 3.5 52.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 319 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B GLN 3.1 16.6 + - - +
316B THR 3.8 4.3 - - - +
317B LEU 3.2 0.2 - - - -
318B LYS* 1.3 76.5 - - - +
320B SER* 1.3 58.1 + - - +
321B MET 3.5 1.2 + - - -
322B ARG 5.2 0.2 + - - -
323B GLU* 3.5 9.2 - - - +
408B ASN* 3.7 13.0 + - - +
412B PHE* 3.9 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 320 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B THR 2.7 22.9 + - - -
317B LEU* 3.0 6.8 + - - -
319B ALA* 1.3 77.4 - - - +
321B MET* 1.3 53.6 + - - +
322B ARG 3.2 3.4 - - - -
323B GLU* 3.1 22.4 + - - -
324B LEU* 2.7 38.1 + - - +
405B ILE* 3.8 25.9 - - - +
408B ASN* 2.8 19.8 + - - +
----------------------------------------------------------
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