Contacts of the helix formed by residues 318 - 336 (chain M) in PDB entry 2DFS
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 318 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316M GLY 3.1 10.7 + - - -
317M ILE* 1.4 71.0 - - - +
319M ASP* 1.3 57.8 + - - +
320M SER* 2.8 23.8 + - - -
321M TYR* 2.7 44.6 + - - +
322M GLN 2.9 9.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 319 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309M ARG* 5.5 4.9 + - - -
313M THR* 4.2 13.2 + - - +
317M ILE 4.3 1.4 - - - +
318M SER* 1.3 72.1 - - - +
320M SER* 1.3 60.6 + - - +
322M GLN* 3.4 31.8 + - - +
323M MET* 3.2 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 320 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318M SER* 2.8 26.4 + - - -
319M ASP* 1.3 77.2 - - - +
321M TYR* 1.3 61.4 + - - -
323M MET* 3.9 6.0 + - - +
324M GLY* 3.4 14.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 321 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317M ILE* 3.8 18.8 - - + -
318M SER* 2.7 30.7 + - - +
320M SER* 1.3 77.7 + - - +
322M GLN* 1.4 62.6 + - - +
324M GLY* 3.0 12.1 + - - +
325M ILE* 3.0 17.2 + - - +
414M TRP* 3.3 34.9 - + + -
418M HIS* 5.6 5.9 - + - -
587M LYS* 2.7 29.9 + - + -
588M LEU* 4.0 25.5 - - + +
591M GLU* 2.6 26.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 322 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309M ARG* 3.4 36.0 + - - +
312M CYS* 3.4 22.6 - - + +
313M THR* 3.1 26.7 + - - +
317M ILE* 3.4 22.6 + - + +
318M SER 2.9 8.8 + - - +
319M ASP* 3.4 32.7 + - - +
321M TYR* 1.4 74.3 - - - +
323M MET* 1.4 61.3 + - + +
325M ILE* 3.1 21.6 + - - +
326M PHE* 3.1 32.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 323 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273M GLU* 3.5 40.8 - - + +
274M PHE* 4.2 19.1 - - + -
276M THR* 5.5 2.5 - - - +
277M LEU* 4.5 16.9 - - + +
309M ARG* 5.3 5.4 - - - -
319M ASP* 3.2 16.4 + - + +
320M SER* 4.0 6.5 - - - +
322M GLN* 1.4 74.3 - - + +
324M GLY* 1.4 57.0 + - - +
326M PHE* 3.6 8.2 + - + +
327M ARG* 3.0 33.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 324 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320M SER 3.4 9.3 + - - -
321M TYR* 3.0 12.1 + - - -
323M MET* 1.4 77.8 - - - +
325M ILE* 1.3 59.2 + - - +
327M ARG* 4.6 0.2 - - - -
328M ILE* 3.2 28.4 + - - +
586M PHE* 3.6 20.1 - - - -
588M LEU* 3.6 13.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 325 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206M ILE* 6.0 0.9 - - + -
261M ILE* 6.1 0.4 - - + -
312M CYS* 5.2 8.1 - - - -
317M ILE* 4.3 20.2 - - + -
321M TYR 3.0 14.4 + - - +
322M GLN* 3.1 9.6 + - - +
324M GLY* 1.3 72.7 - - - +
326M PHE* 1.3 73.1 + - + +
328M ILE* 3.2 5.4 + - - +
329M LEU* 3.1 34.9 + - + +
411M LEU* 3.9 17.0 - - + +
414M TRP* 4.2 20.0 - - + -
415M ILE* 4.0 38.4 - - + -
588M LEU* 4.3 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 326 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261M ILE* 4.4 12.6 - - + -
265M LEU* 3.9 6.7 - - + +
274M PHE* 3.6 24.5 - + + -
277M LEU* 3.5 19.0 - - + +
305M MET* 3.6 22.2 - - + -
308M THR* 5.4 3.4 - - + -
309M ARG* 3.8 33.2 - - + -
312M CYS* 5.4 6.3 - - - -
322M GLN* 3.1 43.4 + - + +
323M MET* 4.1 10.5 - - - +
325M ILE* 1.3 87.0 - - + +
327M ARG* 1.3 57.2 + - - +
329M LEU* 3.4 16.7 + - + +
330M ALA* 2.9 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 327 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276M THR* 2.9 38.2 + - - +
277M LEU* 4.3 13.1 - - + +
278M ARG* 4.5 3.2 - - - +
323M MET* 3.0 21.0 + - - +
324M GLY* 3.7 4.7 - - - +
325M ILE 3.3 0.2 - - - -
326M PHE* 1.3 73.6 - - - +
328M ILE* 1.4 63.5 + - - +
330M ALA* 3.5 6.3 + - - +
331M GLY* 3.1 18.0 + - - -
362M ASP* 3.9 7.1 + - - -
363M LEU* 2.9 63.2 + - - +
364M MET* 4.9 1.2 - - - +
585M LYS* 6.0 3.8 - - - +
586M PHE* 3.7 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 328 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324M GLY 3.2 3.5 + - - +
325M ILE 3.2 8.2 + - - +
327M ARG* 1.4 73.9 - - - +
329M LEU* 1.4 57.5 + - - +
331M GLY* 3.1 4.0 + - - -
332M ILE* 3.0 27.2 + - + +
364M MET* 4.5 14.0 - - + +
407M ILE* 3.5 31.6 - - + -
411M LEU* 3.8 17.5 - - + -
586M PHE* 3.3 24.5 - - + -
588M LEU* 3.9 28.5 - - + -
589M LEU* 4.2 13.7 - - + -
592M LEU* 3.8 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 329 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206M ILE* 5.7 3.4 - - + -
261M ILE* 3.6 35.0 - - + -
262M PHE* 3.8 16.7 - - + -
265M LEU* 4.1 14.1 - - + -
325M ILE* 3.1 29.8 + - + +
326M PHE* 3.6 12.6 - - + +
328M ILE* 1.4 74.7 - - - +
330M ALA* 1.4 54.2 + - - +
332M ILE* 3.3 10.2 + - + +
333M LEU* 3.0 30.9 + - - +
408M TYR* 3.7 32.5 - - + -
411M LEU* 4.0 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 330 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265M LEU* 4.0 7.9 - - + +
277M LEU* 3.7 32.3 - - + +
279M LEU* 4.6 4.0 - - + -
326M PHE 2.9 17.0 + - - +
327M ARG 3.6 2.9 - - - +
328M ILE 3.4 0.2 - - - -
329M LEU* 1.4 73.7 - - - +
331M GLY* 1.3 58.0 + - - +
333M LEU* 3.3 7.8 + - - +
334M HIS* 2.9 34.8 + - - -
363M LEU* 3.6 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 331 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327M ARG 3.1 9.7 + - - -
328M ILE 3.1 8.6 + - - -
330M ALA* 1.3 72.7 - - - +
332M ILE* 1.3 59.2 + - - +
334M HIS* 3.8 2.2 - - - -
335M LEU* 2.8 26.2 + - - +
360M PHE* 3.2 30.8 - - - -
363M LEU* 3.6 15.0 - - - +
364M MET* 5.0 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 332 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249M VAL* 4.5 5.4 - - + -
262M PHE* 4.5 14.1 - - + -
287M TYR* 3.2 42.5 - - + -
328M ILE* 3.0 18.6 + - + +
329M LEU* 3.5 16.4 - - + +
331M GLY* 1.3 73.2 - - - +
333M LEU* 1.3 62.8 + - - +
335M LEU* 3.5 7.5 + - - +
336M GLY 3.2 6.4 + - - -
364M MET* 5.9 0.9 - - + -
404M ALA* 4.0 16.8 - - + +
407M ILE* 3.9 36.1 - - + -
408M TYR* 4.1 30.1 - - + +
411M LEU* 5.1 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 333 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262M PHE* 3.6 33.4 - - + +
265M LEU* 4.3 10.5 - - + -
266M CYS* 4.3 15.7 - - - -
279M LEU* 3.7 25.4 - - + -
285M PHE* 3.4 39.9 - - + +
286M HIS 5.4 0.2 + - - -
287M TYR* 4.5 14.0 - - + -
288M THR* 3.8 22.0 - - + -
329M LEU 3.0 16.1 + - - +
330M ALA* 3.5 8.7 - - - +
331M GLY 3.3 0.2 - - - -
332M ILE* 1.3 74.5 - - - +
334M HIS* 1.3 60.0 + - - +
336M GLY* 3.4 13.3 + - - -
337M ASN 3.9 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 334 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277M LEU 3.6 13.2 + - - -
278M ARG 3.4 24.8 + - - -
279M LEU* 4.5 1.5 - - + -
284M TYR* 4.9 8.3 - + - -
285M PHE* 3.5 30.1 - + - -
330M ALA 2.9 30.4 + - - +
331M GLY* 4.0 3.6 - - - +
333M LEU* 1.3 70.5 - - + +
335M LEU* 1.4 64.7 + - - +
337M ASN* 3.1 12.1 + - - -
338M VAL* 3.7 2.6 + - - +
356M PRO* 3.6 39.9 + - - +
359M ILE* 3.5 41.8 - - + +
360M PHE* 4.3 10.3 - - + +
363M LEU* 4.8 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 335 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287M TYR* 4.3 1.1 - - - +
331M GLY 2.8 22.0 + - - +
332M ILE* 3.5 8.3 - - - +
333M LEU 3.4 0.2 - - - -
334M HIS* 1.4 70.5 - - - +
336M GLY* 1.3 60.8 + - - +
338M VAL* 3.2 32.5 + - + +
360M PHE* 3.8 41.6 - - + -
375M LEU* 4.8 17.0 - - + -
400M ARG* 3.6 37.7 - - + +
403M LEU* 4.2 17.5 - - + -
404M ALA* 4.3 17.3 - - + +
407M ILE* 4.7 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 336 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286M HIS* 3.1 28.3 - - - +
287M TYR* 3.3 34.7 - - - -
332M ILE 3.2 7.9 + - - -
333M LEU 3.4 4.9 + - - -
334M HIS 3.2 1.0 - - - -
335M LEU* 1.3 78.9 - - - +
337M ASN* 1.3 59.9 + - - +
338M VAL 3.4 0.4 - - - -
400M ARG* 3.2 9.7 + - - -
----------------------------------------------------------
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