Contacts of the helix formed by residues 309 - 327 (chain B) in PDB entry 5FS9
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 309 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B GLY* 3.5 3.0 - - - -
308B GLY* 1.3 77.2 - - - +
310B PHE* 1.3 66.4 + - - -
311B LEU 3.4 2.2 - - - -
312B GLY 4.0 2.1 - - - +
313B SER* 2.9 26.7 + - - -
340B MET* 3.8 11.4 - - - -
343B ILE* 6.6 0.2 - - - -
397B ALA 5.2 2.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 310 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B GLY* 1.3 72.2 - - - -
311B LEU* 1.3 59.1 + - - +
313B SER* 3.2 2.0 + - - -
314B GLU* 2.8 37.4 + - - +
340B MET* 3.5 42.2 - - + -
343B ILE* 4.0 34.1 - - + -
344B LEU* 4.6 9.6 - - + -
482B PHE* 3.6 38.1 - + + -
484B SER* 3.3 27.4 - - - +
486B LEU* 6.0 0.4 - - + -
492B TYR* 4.0 23.1 - + + -
577B VAL* 6.2 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 311 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B SER* 3.6 30.1 - - - +
284B PHE* 3.9 23.1 - - + +
309B GLY 3.4 0.6 - - - -
310B PHE* 1.3 78.1 - - - +
312B GLY* 1.3 64.4 + - - +
314B GLU* 3.2 6.6 + - - +
315B LEU* 2.9 39.2 + - + +
397B ALA* 4.2 19.3 - - + +
1000B FAD 3.7 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 312 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B ILE* 3.7 12.1 - - - +
307B GLY 3.7 18.2 - - - -
309B GLY 3.4 5.5 + - - +
310B PHE 3.3 0.4 - - - -
311B LEU* 1.3 80.0 - - - +
313B SER* 1.3 56.8 + - - +
315B LEU* 3.5 2.0 + - - +
316B ALA* 3.0 28.2 + - - +
332B GLN* 3.5 7.7 + - - -
397B ALA* 3.8 19.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 313 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B GLY 3.3 3.3 + - - -
309B GLY 2.9 18.2 + - - -
310B PHE 3.8 1.8 - - - -
312B GLY* 1.3 73.4 - - - +
314B GLU* 1.3 64.8 + - - +
316B ALA* 3.3 5.2 + - - +
317B CYS* 3.1 28.2 + - - -
332B GLN* 3.3 7.0 + - - +
339B ASN* 3.0 26.0 + - - -
340B MET* 3.3 21.1 - - - -
352B THR* 5.3 0.2 - - - -
356B VAL* 4.5 6.7 - - - +
486B LEU* 3.8 12.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 314 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B SER* 2.7 43.1 + - - +
177B LYS* 2.8 23.4 + - + -
181B PHE* 5.9 0.3 - - - -
310B PHE* 2.8 23.6 + - - +
311B LEU* 3.5 8.4 - - - +
313B SER* 1.3 77.5 - - - +
315B LEU* 1.3 58.2 + - - +
317B CYS* 3.3 4.0 + - - +
318B ALA* 2.9 29.1 + - - +
482B PHE* 5.4 0.2 - - - -
484B SER* 2.5 38.4 + - - +
485B ASP 3.5 17.7 + - - +
486B LEU* 3.8 8.3 - - + +
1000B FAD 4.0 6.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 315 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B SER* 3.8 24.9 - - - +
180B TRP* 4.3 10.1 - - + +
284B PHE* 3.9 44.4 - - + -
293B LEU* 4.7 7.0 - - + -
305B ILE* 3.7 11.4 - - + -
311B LEU* 2.9 32.8 + - + +
312B GLY* 3.8 4.3 - - - +
314B GLU* 1.3 76.1 - - - +
316B ALA* 1.3 57.5 + - - +
318B ALA* 3.6 2.4 - - - +
319B LEU* 2.8 39.5 + - + +
395B VAL* 4.0 20.0 - - + -
397B ALA* 4.8 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 316 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B ILE* 3.2 20.1 - - + +
312B GLY 3.0 17.6 + - - +
313B SER 3.6 5.4 - - - +
314B GLU 3.2 0.2 - - - -
315B LEU* 1.3 76.4 - - - +
317B CYS* 1.3 52.4 + - - +
320B GLY 2.8 28.1 + - - -
330B VAL* 4.1 2.7 - - - +
332B GLN* 3.7 21.3 - - + +
356B VAL* 4.0 11.7 - - + -
361B VAL* 3.3 22.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 317 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B PHE* 4.7 8.5 - - + -
313B SER 3.1 18.0 + - - +
314B GLU* 3.8 6.7 - - - +
316B ALA* 1.3 75.0 - - - +
318B ALA* 1.3 59.2 + - - +
320B GLY* 3.8 0.2 - - - -
321B ARG* 3.0 29.1 + - - +
355B LYS* 4.6 2.5 - - - -
356B VAL* 3.9 24.5 - - - -
359B GLU* 3.9 35.4 - - + +
486B LEU* 4.0 32.8 - - + -
487B GLY 5.1 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 318 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B SER 4.0 7.0 - - - +
180B TRP* 3.5 44.0 - - + +
181B PHE* 4.3 13.4 - - + -
314B GLU 2.9 17.8 + - - +
315B LEU* 3.2 6.5 + - - +
317B CYS* 1.3 75.7 - - - +
319B LEU* 1.3 62.9 + - + +
321B ARG* 3.4 6.1 + - - +
322B LYS* 3.2 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 319 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B TRP* 3.7 35.0 - - + -
293B LEU* 4.3 19.1 - - + -
297B SER* 4.2 19.5 + - - +
303B ILE* 4.0 31.6 - - + -
305B ILE* 4.0 17.9 - - + -
315B LEU* 2.8 25.4 + - + +
316B ALA 4.1 1.3 - - - +
318B ALA* 1.3 70.3 - - + +
320B GLY* 1.3 56.0 + - - +
322B LYS* 3.3 5.0 + - - +
323B ALA* 2.8 36.2 + - - +
330B VAL* 3.6 16.2 - - + +
395B VAL* 4.8 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 320 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B ALA 2.8 19.5 + - - -
317B CYS* 3.8 1.6 - - - -
319B LEU* 1.3 77.4 - - - +
321B ARG* 1.3 61.3 + - - +
323B ALA* 3.3 3.5 + - - +
324B ARG* 3.1 22.2 + - - +
330B VAL* 3.8 11.4 - - - +
359B GLU 3.7 23.4 - - - +
360B GLY 4.4 3.4 - - - +
361B VAL* 4.3 5.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 321 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B TRP 3.3 23.6 + - - -
181B PHE* 3.5 57.4 + - + +
182B SER 3.9 2.4 + - - -
183B ASP* 3.0 30.6 + - - -
317B CYS 3.0 14.6 + - - +
318B ALA* 3.5 7.4 - - - +
320B GLY* 1.3 76.6 - - - +
322B LYS* 1.3 71.3 + - - +
324B ARG* 3.3 21.4 + - - +
325B ALA* 3.9 4.2 + - - +
359B GLU* 4.4 10.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 322 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B LEU 4.9 1.8 + - - -
180B TRP* 3.1 56.1 + - + +
182B SER 3.4 17.8 + - - -
183B ASP* 5.2 1.0 + - - +
294B GLU* 4.9 15.3 + - - +
297B SER* 3.7 20.6 - - - +
298B ARG* 6.5 0.7 - - + -
318B ALA 3.2 13.7 + - - +
319B LEU* 3.3 6.9 + - - +
321B ARG* 1.3 84.0 - - - +
323B ALA* 1.3 63.7 + - - +
325B ALA* 3.2 16.8 + - - +
326B LEU* 3.5 19.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 323 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B SER* 5.2 1.3 + - - -
319B LEU 2.8 21.3 + - - +
320B GLY* 3.6 6.1 - - - +
321B ARG 3.3 0.2 - - - -
322B LYS* 1.3 74.7 - - - +
324B ARG* 1.3 53.9 + - - +
326B LEU* 3.2 0.6 + - - +
327B GLY* 2.6 33.4 + - - -
328B THR* 3.1 44.0 + - - +
330B VAL* 3.9 17.0 - - + -
360B GLY 5.4 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 324 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B GLY 3.1 12.0 + - - +
321B ARG* 3.3 15.8 - - - +
322B LYS 3.2 0.2 - - - -
323B ALA* 1.3 78.6 - - - +
325B ALA* 1.3 61.3 + - - +
327B GLY* 3.7 7.8 + - - +
358B ARG 2.8 29.1 + - - -
359B GLU* 3.4 20.5 + - - +
360B GLY* 3.7 16.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 325 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B ARG 3.9 3.5 + - - +
322B LYS* 3.2 12.6 + - - +
324B ARG* 1.3 80.8 - - - +
326B LEU* 1.3 70.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 326 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B SER* 3.5 28.7 - - - +
298B ARG* 4.1 20.6 - - + +
301B LYS* 5.1 5.2 + - - -
322B LYS* 3.5 16.6 + - + +
323B ALA* 3.2 2.2 + - - +
325B ALA* 1.3 86.1 - - + +
327B GLY* 1.3 62.1 + - - +
328B THR* 3.4 23.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 327 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B ALA 2.6 15.1 + - - -
324B ARG* 3.7 5.7 + - - -
325B ALA 3.5 2.0 + - - -
326B LEU* 1.3 75.1 - - - +
328B THR* 1.3 60.7 + - - +
----------------------------------------------------------
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