Contacts of the helix formed by residues 347 - 362 (chain B) in PDB entry 3E4E
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 MET 347 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B GLU* 3.1 27.1 - - - +
329B ILE* 3.7 44.0 - - + +
332B VAL* 4.0 12.3 - - + -
333B ILE* 3.6 27.8 - - + -
343B ASP* 3.0 23.8 - - - +
344B ARG* 2.8 12.8 + - - +
346B GLU* 1.3 81.4 - - - +
348B PRO* 1.4 60.4 - - - +
349B TYR 3.3 2.7 - - - -
350B MET* 3.3 10.1 + - + -
351B ASP* 2.9 27.2 + - - +
448B PHE* 4.1 13.5 - - + -
452B CYS* 4.2 7.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 348 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B GLU* 3.3 9.4 - - - +
331B ARG* 6.0 1.3 - - - +
344B ARG 4.2 1.3 - - - +
345B GLN 5.0 2.7 - - - +
346B GLU 3.0 14.6 - - - +
347B MET* 1.4 85.1 - - - +
349B TYR* 1.3 65.3 + - + +
351B ASP* 3.7 7.0 - - + +
352B ALA* 2.9 25.8 + - - +
415B LEU* 3.6 3.5 - - + +
419B GLY 3.5 26.2 - - - +
420B LYS* 4.2 2.5 - - - -
421B PHE* 3.9 22.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 349 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B ILE* 3.3 42.9 - - + +
324B LYS* 3.4 58.1 + - + +
325B LEU* 3.4 22.2 - - + -
328B GLU* 2.9 22.2 + - + +
348B PRO* 1.3 78.6 - - + +
350B MET* 1.3 57.7 + - - +
352B ALA* 3.6 2.4 - - - +
353B VAL* 3.0 30.7 + - + +
411B PRO* 3.7 24.3 - - + +
412B GLU* 5.1 3.7 + - - -
415B LEU* 4.0 24.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 350 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B LEU* 3.5 24.8 - - + +
328B GLU* 3.5 15.0 + - - +
329B ILE* 5.1 4.9 - - + -
347B MET* 3.3 12.7 + - + +
349B TYR* 1.3 77.2 - - - +
351B ASP* 1.3 58.3 + - - +
352B ALA 3.2 0.2 - - - -
353B VAL* 3.7 14.4 - - + -
354B VAL* 2.8 42.3 + - + +
448B PHE* 3.6 27.8 - - + -
451B LEU* 3.6 38.6 - - + -
452B CYS* 4.0 23.8 - - - -
455B LEU* 4.8 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 351 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B ARG* 3.4 42.5 + - + +
345B GLN* 5.8 0.3 - - - -
347B MET 2.9 18.7 + - - +
348B PRO* 3.3 8.3 + - + +
350B MET* 1.3 77.6 - - - +
352B ALA* 1.3 59.6 + - - +
354B VAL* 3.5 6.0 + - - +
355B HIS* 2.7 53.3 + - - -
421B PHE* 3.8 28.4 - - + +
448B PHE* 5.1 2.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 352 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B PRO 2.9 17.5 + - - +
349B TYR 3.6 4.7 - - - +
351B ASP* 1.3 75.0 - - - +
353B VAL* 1.3 66.0 + - - +
355B HIS* 3.2 3.1 + - - +
356B GLU* 2.8 26.8 + - - +
411B PRO* 3.6 26.2 - - + +
414B PHE* 3.9 19.0 - - + +
415B LEU* 3.7 17.7 - - + -
421B PHE* 3.9 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 353 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B LEU* 4.4 8.5 - - + -
321B ILE* 3.9 16.4 - - + -
325B LEU* 3.9 17.9 - - + -
349B TYR* 3.0 21.0 + - + +
350B MET* 3.2 22.4 + - + +
352B ALA* 1.3 78.7 - - - +
354B VAL* 1.3 66.7 + - - +
356B GLU* 3.1 7.1 + - - +
357B ILE* 3.0 41.8 + - + +
409B PHE* 4.9 3.6 - - + -
411B PRO* 3.7 25.8 - - + -
451B LEU* 4.5 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 354 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B ARG* 5.9 1.6 - - - +
350B MET* 2.8 44.6 + - + +
351B ASP* 3.9 6.5 - - - +
353B VAL* 1.3 79.0 - - - +
355B HIS* 1.3 64.6 + - + +
357B ILE* 3.6 11.4 + - - +
358B GLN* 3.2 33.8 + - - +
444B ARG* 5.1 2.7 - - + +
447B LEU* 4.0 20.0 - - + +
448B PHE* 4.3 24.7 - - + +
451B LEU* 4.0 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 355 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B ARG* 5.3 4.7 - - - -
351B ASP* 2.7 38.9 + - - +
352B ALA 3.2 4.5 + - - +
354B VAL* 1.3 80.5 - - + +
356B GLU* 1.3 60.2 + - - +
358B GLN* 3.1 5.9 + - - +
359B ARG* 2.9 28.2 + - - +
414B PHE* 3.7 27.1 - + + -
421B PHE* 3.4 26.3 - + - -
423B TYR* 6.2 1.5 - + - -
427B PHE* 3.5 42.1 - + + -
444B ARG* 3.0 26.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 356 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B ALA 2.8 20.0 + - - +
353B VAL 3.8 3.1 - - - +
355B HIS* 1.3 73.1 - - - +
357B ILE* 1.3 58.6 + - - +
359B ARG* 3.1 32.2 + - - -
360B PHE* 2.8 34.1 + - - +
408B LYS 3.6 0.9 - - - +
409B PHE* 3.5 22.3 - - + -
410B LYS 2.8 32.3 + - - +
411B PRO* 4.4 4.5 - - + -
413B HIS* 2.4 33.8 + - - +
414B PHE* 3.3 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 357 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B THR* 3.8 35.2 - - + +
311B GLY* 3.7 30.7 - - - +
314B ILE* 4.4 9.0 - - + -
315B LEU* 5.1 3.8 - - + -
353B VAL* 3.0 28.5 + - + +
354B VAL* 3.8 6.5 - - - +
355B HIS 3.2 0.4 - - - -
356B GLU* 1.3 76.6 - - - +
358B GLN* 1.3 60.6 + - - +
361B ILE* 3.1 35.5 + - + +
409B PHE* 3.8 22.2 - - + -
451B LEU* 4.0 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 358 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B THR* 4.3 8.7 - - + -
354B VAL* 3.2 31.8 + - - +
355B HIS* 3.1 7.1 + - - +
357B ILE* 1.3 76.8 - - + +
359B ARG* 1.3 60.8 + - - +
361B ILE* 3.9 9.9 - - - +
362B THR* 3.7 14.0 + - - -
363B LEU* 4.8 1.0 + - - +
397B LEU* 4.0 8.5 - - - +
427B PHE* 3.6 22.6 - - + -
429B PRO* 4.1 12.7 - - + +
430B PHE* 3.5 31.5 - - - -
444B ARG* 5.3 7.1 - - - +
447B LEU* 3.5 29.0 - - + +
500B HEM 4.9 4.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 359 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B HIS 2.9 16.1 + - - +
356B GLU* 3.1 32.2 + - - +
358B GLN* 1.3 77.1 - - - +
360B PHE* 1.3 97.8 + - - +
361B ILE 3.4 0.2 + - - -
362B THR* 3.5 10.0 - - - +
397B LEU* 3.0 46.3 + - + +
398B TYR* 3.5 16.0 - - - -
403B PHE* 3.9 21.4 - - + +
406B PRO* 2.4 49.0 + - - +
408B LYS 4.2 0.2 + - - -
413B HIS* 3.3 16.1 + - - -
414B PHE* 4.0 17.3 - - + -
427B PHE* 4.5 2.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 360 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B TYR* 5.3 2.5 - + - -
314B ILE* 3.9 20.6 - - + -
318B TYR* 5.8 0.7 - - - -
356B GLU 2.8 22.7 + - - +
357B ILE 4.1 2.2 - - - +
359B ARG* 1.3 93.1 - - - +
361B ILE* 1.3 65.1 + - + +
362B THR* 3.4 0.6 - - - +
398B TYR* 2.6 31.6 + - - -
407B GLU 3.0 28.0 - - - -
408B LYS 4.1 0.2 - - - -
409B PHE* 3.7 32.5 - + + -
471B LEU* 4.1 43.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 361 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B THR* 4.1 37.7 - - + +
310B TYR* 3.6 46.0 - - + -
314B ILE* 3.8 19.1 - - + -
357B ILE* 3.1 20.6 - - + +
358B GLN* 3.9 8.1 - - - +
359B ARG 3.3 0.2 - - - -
360B PHE* 1.3 85.0 - - + +
362B THR* 1.3 77.1 + - - +
363B LEU* 3.2 18.9 + - + +
473B PRO* 5.9 0.5 - - - +
480B CYS* 3.4 16.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 362 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B GLN 3.7 4.2 + - - -
359B ARG 3.5 7.2 - - - +
360B PHE 4.8 0.3 + - - -
361B ILE* 1.3 80.6 + - - +
363B LEU* 1.3 65.6 + - - +
364B VAL 3.3 4.0 + - - -
365B PRO* 3.3 12.8 - - - +
394B ASP* 3.9 26.5 - - + +
397B LEU* 3.7 24.7 - - + -
398B TYR* 3.5 37.3 - - + -
480B CYS* 3.2 20.4 - - - -
----------------------------------------------------------
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