Contacts of the helix formed by residues 358 - 375 (chain A) in PDB entry 5I4E
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 358 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A GLY 3.4 4.2 + - - -
357A PHE* 1.3 76.0 - - - +
359A HIS* 1.4 58.0 + - - +
360A GLU* 3.8 18.4 + - - +
361A GLU* 3.0 35.0 + - - +
362A ILE* 3.0 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 359 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A SER* 1.4 72.0 - - - +
360A GLU* 1.3 72.5 + - + +
362A ILE* 3.5 10.0 + - - +
363A ILE* 3.0 57.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 360 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A SER* 3.8 15.6 + - - +
359A HIS* 1.3 95.0 + - + +
361A GLU* 1.3 58.1 + - - +
363A ILE* 4.3 6.1 - - - +
364A SER* 2.7 36.1 + - - +
632A ARG* 4.4 7.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 361 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A GLY 3.9 0.9 - - - +
357A PHE* 3.2 13.1 - - + -
358A SER* 3.0 41.5 + - - +
360A GLU* 1.3 73.9 - - + +
362A ILE* 1.3 64.9 + - - +
364A SER* 3.2 4.5 + - - -
365A MET* 3.1 28.9 + - - +
454A TRP* 3.7 14.2 - - + -
458A ARG* 2.8 48.9 + - - -
461A ARG* 5.0 2.1 + - - -
632A ARG* 4.1 19.9 + - - +
633A LEU* 4.6 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 362 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A LEU* 3.7 30.3 - - + +
352A LEU* 3.8 35.9 - - + -
353A ARG* 4.0 22.7 - - + +
357A PHE* 3.6 31.6 - - + +
358A SER 3.0 12.2 + - - +
359A HIS* 4.1 7.6 - - - +
361A GLU* 1.3 73.9 - - - +
363A ILE* 1.3 63.0 + - + +
365A MET* 3.2 11.3 + - - +
366A LEU* 3.1 33.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 363 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A LEU* 3.6 30.3 - - + -
318A ASP* 6.5 0.4 - - + -
319A LEU* 4.1 8.6 - - + +
359A HIS* 3.0 50.6 + - + +
360A GLU* 4.3 5.2 - - - +
362A ILE* 1.3 75.6 - - + +
364A SER* 1.3 57.3 + - - +
366A LEU* 3.4 11.0 + - + +
367A ARG* 2.9 52.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 364 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A GLU* 2.7 23.8 + - - +
361A GLU* 3.2 7.4 + - - -
363A ILE* 1.3 77.4 - - - +
365A MET* 1.3 53.8 - - - +
367A ARG* 3.1 30.6 + - - +
368A MET* 3.2 24.8 + - - +
631A ASP* 4.6 3.6 + - - +
632A ARG* 4.3 8.2 + - - +
633A LEU* 3.4 35.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 365 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A PHE* 3.4 33.2 - - + -
352A LEU* 3.6 38.1 - - + -
357A PHE* 4.2 10.3 - - - -
361A GLU 3.1 19.3 + - - +
362A ILE* 3.4 14.4 - - - +
364A SER* 1.3 75.1 - - - +
366A LEU* 1.4 59.6 + - + +
368A MET* 3.3 5.0 + - - +
369A VAL* 3.1 29.4 + - - +
451A LEU* 3.6 15.7 - - + +
454A TRP* 3.6 29.8 - - + -
455A LEU* 4.4 9.2 - - + -
633A LEU* 3.9 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 366 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A PHE* 5.0 6.3 - - + -
303A ILE* 4.4 20.9 - - + -
307A LEU* 3.6 16.8 - - + +
315A LEU* 4.3 12.8 - - + -
319A LEU* 3.8 15.6 - - + +
345A PHE* 3.9 36.3 - - + -
349A LEU* 4.3 4.9 - - + -
352A LEU* 5.8 2.5 - - + -
362A ILE* 3.1 35.1 + - + +
363A ILE* 3.8 11.9 - - + +
365A MET* 1.4 74.3 - - + +
367A ARG* 1.3 60.4 + - - +
368A MET 3.3 0.7 - - - -
369A VAL* 3.4 7.3 + - + +
370A SER* 3.1 27.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 367 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A ASP 5.3 4.2 + - - -
319A LEU* 3.7 17.2 - - + +
360A GLU 5.1 0.2 + - - -
363A ILE* 2.9 41.3 + - - +
364A SER* 3.1 33.7 + - - +
366A LEU* 1.3 77.4 - - - +
368A MET* 1.4 57.1 + - - +
370A SER* 3.5 6.8 + - - -
371A ALA* 2.9 27.4 + - - +
402A ARG 5.3 2.0 - - - -
403A LEU* 3.7 40.9 + - + +
631A ASP* 3.8 27.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 368 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A SER 3.2 11.3 + - - +
365A MET 3.4 10.3 - - - +
366A LEU 3.3 0.2 - - - -
367A ARG* 1.4 73.9 - - - +
369A VAL* 1.3 58.1 + - - +
371A ALA* 3.2 4.7 + - - +
372A VAL* 2.9 34.2 + - + +
403A LEU 5.5 2.2 - - - +
404A LEU* 3.8 26.0 - - - -
447A THR* 3.9 14.6 - - + +
451A LEU* 3.9 23.8 - - + -
631A ASP* 4.8 2.9 - - - +
633A LEU* 3.6 21.1 - - + -
634A THR* 3.6 25.8 - - - +
637A ILE* 3.5 33.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 369 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A PHE* 3.8 26.0 - - + -
303A ILE* 4.3 13.9 - - + -
304A PHE* 3.6 41.2 - - + +
307A LEU* 3.8 19.3 - - + -
365A MET 3.1 20.6 + - - +
366A LEU* 3.6 10.5 - - - +
367A ARG 3.3 0.2 - - - -
368A MET* 1.3 73.9 - - - +
370A SER* 1.3 62.7 + - - +
372A VAL* 3.1 12.2 + - - +
373A LEU* 3.1 20.0 + - + +
448A TYR* 4.6 3.8 - - + -
451A LEU* 4.0 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 370 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A LEU* 4.6 0.2 - - - +
319A LEU* 2.9 27.7 + - - -
320A LEU 4.5 3.8 + - - -
321A LEU* 3.8 21.1 - - - +
327A TYR* 4.9 4.8 + - - -
366A LEU 3.1 15.6 + - - -
367A ARG* 3.6 8.5 - - - -
369A VAL* 1.3 76.2 - - - +
371A ALA* 1.4 56.2 + - - +
373A LEU* 3.5 13.3 + - - +
374A GLN* 2.9 30.1 + - - +
403A LEU* 3.8 8.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 371 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A ARG 2.9 14.6 + - - +
368A MET* 3.2 12.5 + - + +
370A SER* 1.4 73.2 - - - +
372A VAL* 1.4 64.6 + - - +
374A GLN 3.2 5.5 + - - -
375A PHE* 3.2 7.1 + - + -
400A LEU* 3.2 23.7 - - + +
403A LEU* 3.9 22.6 - - + +
404A LEU* 3.7 32.3 - - + -
447A THR* 5.5 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 372 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A ALA* 4.1 26.2 - - + +
304A PHE* 4.2 11.7 - - + -
329A PHE* 3.3 24.7 - - + -
368A MET* 2.9 21.5 + - + +
369A VAL 3.4 7.2 - - - +
371A ALA* 1.4 74.0 - - - +
373A LEU* 1.4 62.6 + - - +
375A PHE* 3.6 13.7 - - - +
444A ALA* 3.4 29.3 - - + +
447A THR* 4.1 11.2 - - + +
448A TYR* 3.8 30.3 - - + +
451A LEU* 5.7 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 373 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A ALA 5.3 2.2 - - - +
304A PHE* 3.5 36.8 - - + +
307A LEU* 6.1 0.9 - - + -
308A LEU* 4.0 29.2 - - + -
321A LEU* 5.7 1.8 - - + -
327A TYR* 3.7 32.7 - - + +
328A ARG 5.8 0.2 + - - -
329A PHE* 3.9 22.2 - - + +
330A LEU* 3.9 27.6 - - + -
369A VAL* 3.1 13.3 + - + +
370A SER* 3.6 13.9 - - - +
371A ALA 3.2 0.2 - - - -
372A VAL* 1.4 76.9 - - + +
374A GLN* 1.3 61.4 + - - +
376A GLY* 3.0 17.7 + - - -
377A ASN 4.0 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 374 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A LEU* 4.7 2.9 - - - +
322A GLU* 3.1 22.6 + - - +
327A TYR* 4.3 5.2 + - - -
370A SER* 2.9 21.5 + - - +
371A ALA 3.2 5.8 + - - +
373A LEU* 1.3 69.1 - - - +
375A PHE* 1.3 65.2 + - - +
377A ASN* 2.9 38.8 + - - +
378A ILE* 3.8 7.3 - - - +
396A ALA* 3.2 47.2 - - - +
399A LYS* 3.8 16.9 - - + +
400A LEU* 3.7 21.1 - - + +
403A LEU* 4.1 9.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 375 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A ARG* 5.1 0.5 + - - -
329A PHE* 4.0 2.9 - - + -
371A ALA 3.2 26.3 + - - -
372A VAL* 3.6 10.3 - - - +
374A GLN* 1.3 76.0 - - - +
376A GLY* 1.3 59.9 + - - +
377A ASN 3.5 0.5 + - - -
378A ILE* 3.7 22.2 + - - +
400A LEU* 3.5 23.7 - - + +
404A LEU* 3.5 29.6 - - + -
411A PHE* 4.4 13.0 - + - -
440A LEU* 3.8 37.8 - - + +
443A LEU* 3.8 26.0 - - + -
444A ALA* 3.6 32.3 - - + -
447A THR* 4.2 15.9 - - + -
622A VAL* 5.5 0.7 - - + -
626A LEU* 5.0 7.0 - - + -
----------------------------------------------------------
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