Contacts of the helix formed by residues 356 - 373 (chain D) in PDB entry 3RIK
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 356 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D TYR* 4.4 2.2 - - - +
353D ARG* 3.3 25.0 + - - -
354D LEU 3.6 0.4 - - - -
355D GLY* 1.3 74.9 - - - +
357D TRP* 1.3 60.9 + - - +
358D ASP* 3.9 0.2 - - - +
359D ARG* 3.0 36.5 + - - +
360D GLY 3.6 7.6 + - - -
414D GLN* 4.2 0.8 + - - -
415D PRO* 3.3 17.9 - - - +
416D MET* 4.9 2.4 + - - +
502D SO4 2.8 31.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 357 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D SER* 3.2 14.3 + - - +
13D SER* 3.9 10.8 - - - -
42D SER* 3.6 29.6 - - - -
43D THR 3.4 11.7 - - - -
44D ARG* 3.4 44.6 - - + +
48D ARG* 3.5 25.1 - - - -
355D GLY 3.0 5.7 + - - -
356D SER* 1.3 70.3 - - - +
358D ASP* 1.3 65.6 + - - +
360D GLY* 3.2 3.6 + - - -
361D MET* 3.1 50.7 + - + +
415D PRO* 3.9 15.0 - - + -
418D TYR* 6.0 0.4 - - + -
419D HIS* 3.2 33.2 - + - -
461D LEU* 6.0 0.2 - - - +
487D TYR* 3.7 22.1 + + + +
488D SER* 4.1 6.1 - - - -
502D SO4 3.2 3.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 358 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242C SER* 5.2 6.4 + - - -
346D LYS* 5.6 2.4 + - - -
349D GLU* 6.0 0.9 - - - +
356D SER* 3.9 1.3 - - - +
357D TRP* 1.3 79.5 - - - +
359D ARG* 1.3 58.4 + - + +
361D MET* 3.0 39.2 + - + +
362D GLN* 2.7 42.3 + - - +
502D SO4 2.8 27.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 359 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315D ASP* 5.3 3.3 + - - +
343D VAL* 3.7 24.2 - - + +
344D GLY* 3.8 15.9 - - - +
345D SER 5.0 0.4 - - - +
349D GLU* 3.6 25.9 + - - +
350D GLN 2.7 21.2 + - - -
351D SER 2.9 27.1 + - - -
353D ARG* 3.5 28.1 - - - +
356D SER* 3.0 27.6 + - - +
358D ASP* 1.3 71.9 - - + +
360D GLY* 1.3 65.3 + - - +
362D GLN* 3.3 19.0 + - - +
363D TYR* 3.2 27.5 + - - -
399D ASP* 2.9 25.2 + - - +
416D MET* 3.8 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 360 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356D SER 3.6 6.1 + - - -
357D TRP 3.2 7.5 + - - -
359D ARG* 1.3 76.8 - - - +
361D MET* 1.3 63.0 + - - +
363D TYR* 3.0 11.4 + - - +
364D SER 3.0 10.9 + - - -
415D PRO* 4.2 0.9 - - - -
416D MET* 3.9 19.3 - - - +
419D HIS* 3.1 34.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 361 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357D TRP* 3.3 36.1 - - + +
358D ASP* 3.0 34.6 + - + +
360D GLY* 1.3 77.2 - - - +
362D GLN* 1.3 59.1 + - + +
364D SER* 3.4 7.3 + - - -
365D HIS* 2.8 34.8 + - - +
419D HIS* 4.0 7.6 - - + -
461D LEU* 4.1 4.0 - - + +
462D ASN 4.5 3.4 - - - +
463D ARG* 3.6 39.3 - - + +
487D TYR* 4.0 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 362 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314D LEU* 3.0 45.1 - - + +
315D ASP* 3.7 11.8 + - - +
343D VAL* 3.4 12.0 - - + +
346D LYS* 4.8 11.5 - - - +
358D ASP* 2.7 43.1 + - - +
359D ARG* 3.6 19.1 - - - +
360D GLY 3.2 0.2 - - - -
361D MET* 1.3 78.6 - - + +
363D TYR* 1.3 61.7 - - - +
365D HIS* 4.0 4.8 + - - +
366D SER* 3.0 26.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 363 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314D LEU* 3.3 28.3 - - + -
341D ALA 3.8 8.2 + - - -
342D CYS* 4.0 7.3 - - - +
343D VAL* 3.9 12.3 + - + +
359D ARG 3.2 16.0 + - - +
360D GLY* 3.0 10.3 + - - +
362D GLN* 1.3 75.7 - - - +
364D SER* 1.3 59.2 + - - +
366D SER* 3.1 4.6 + - - -
367D ILE* 2.8 33.3 + - + +
378D TRP* 3.7 20.3 - + + -
380D ASP* 2.7 39.4 + - - -
399D ASP 4.7 4.9 + - - -
401D PRO* 4.4 6.1 - - + +
416D MET* 3.5 31.8 - - + +
419D HIS* 4.5 9.2 - - + -
420D LEU* 3.5 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 364 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360D GLY 3.0 6.3 + - - -
361D MET* 3.4 4.7 + - - -
363D TYR* 1.3 76.1 - - - +
365D HIS* 1.3 64.0 + - - +
367D ILE* 3.1 1.8 + - - +
368D ILE* 2.9 28.2 + - - +
419D HIS* 2.7 29.6 + - - +
423D PHE* 3.7 17.0 - - - -
461D LEU* 3.7 12.9 - - - +
489D ILE* 3.5 27.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 365 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317D LEU* 4.2 25.9 - - + +
361D MET 2.8 20.8 + - - +
362D GLN* 4.0 5.3 + - - +
364D SER* 1.3 77.2 + - - +
366D SER* 1.3 57.6 + - - +
368D ILE* 3.3 3.7 + - + +
369D THR* 2.8 50.5 + - + -
445D ASP* 3.4 31.8 + - + -
461D LEU* 3.5 12.1 - - + +
463D ARG* 3.8 28.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 366 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312D TRP* 4.8 8.9 - - - +
314D LEU* 3.6 21.8 - - - +
362D GLN 3.0 20.6 + - - -
363D TYR 3.5 3.1 - - - -
365D HIS* 1.3 79.1 + - - +
367D ILE* 1.3 63.9 + - - +
369D THR* 3.1 6.1 + - - -
370D ASN* 2.8 40.0 + - - +
378D TRP* 3.4 18.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 367 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81D PHE* 4.0 17.9 - - + -
363D TYR 2.8 27.2 + - - +
364D SER 3.8 3.4 - - - +
366D SER* 1.3 70.7 - - - +
368D ILE* 1.3 56.6 + - - +
370D ASN* 3.4 2.6 + - - +
371D LEU* 2.9 34.2 + - + +
378D TRP* 3.4 36.1 - - + +
420D LEU* 3.8 34.3 - - + -
423D PHE* 3.6 48.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 368 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364D SER 2.9 20.6 + - - +
365D HIS* 3.8 4.0 - - + +
367D ILE* 1.3 73.9 - - - +
369D THR* 1.3 68.7 + - - +
371D LEU* 3.0 7.8 + - - +
372D LEU* 2.9 41.6 + - + +
423D PHE* 3.5 26.7 - - + -
445D ASP* 3.8 32.1 - - + +
446D ALA 4.1 18.6 - - - +
447D VAL* 4.1 8.5 - - + -
459D VAL* 4.5 10.1 - - + +
461D LEU* 3.9 20.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 369 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285D ARG* 5.4 4.7 - - - +
320D ALA* 4.2 24.0 - - + -
324D LEU* 5.2 0.6 - - + +
365D HIS* 2.8 45.0 + - + -
366D SER* 3.8 6.5 - - - -
368D ILE* 1.3 75.7 - - - +
370D ASN* 1.3 64.3 + - - +
372D LEU* 3.2 15.2 + - - -
373D TYR* 3.3 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 370 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285D ARG* 5.3 10.2 - - - +
310D VAL* 4.3 6.4 - - - +
312D TRP* 6.1 1.8 - - - +
324D LEU* 4.0 14.3 - - - +
338D ALA* 4.0 9.5 - - - +
366D SER* 2.8 44.5 + - - +
367D ILE 3.7 3.8 - - - +
369D THR* 1.3 72.9 - - - +
371D LEU* 1.3 67.3 + - + +
373D TYR 3.1 6.9 + - - -
375D VAL* 3.1 59.3 + - + +
378D TRP* 3.8 17.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 371 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D GLN* 3.0 26.7 + - - +
78D VAL* 4.5 18.2 - - + -
81D PHE* 4.8 10.8 - - + -
367D ILE* 2.9 38.0 + - + +
368D ILE 3.0 4.0 + - - +
370D ASN* 1.3 78.6 - - + +
372D LEU* 1.3 61.3 + - - +
373D TYR 3.3 0.3 + - - -
374D HIS 3.5 1.0 + - - -
375D VAL* 3.7 17.5 - - + +
376D VAL 5.5 2.7 - - - -
377D GLY* 5.7 0.7 - - - +
423D PHE* 4.2 9.6 - - + -
427D ILE* 4.5 11.0 - - + -
433D ARG* 3.1 13.5 - - + -
447D VAL* 3.9 34.8 - - + -
449D LEU* 4.6 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 372 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368D ILE* 2.9 37.4 + - + +
369D THR* 3.8 7.9 - - - +
370D ASN 3.2 0.4 - - - -
371D LEU* 1.3 78.3 - - - +
373D TYR* 1.3 73.1 + - + +
374D HIS* 3.4 5.0 + - - -
433D ARG* 3.2 38.2 + - - +
436D LEU* 6.5 1.1 - - + -
446D ALA 3.9 14.6 - - - +
447D VAL* 3.9 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 373 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320D ALA* 4.1 13.0 - - + -
321D LYS* 3.7 41.3 + - + +
324D LEU* 3.9 30.2 - - + +
325D GLY* 4.0 20.9 - - - -
336D LEU* 4.0 2.8 - - - +
369D THR* 3.3 36.8 + - + +
370D ASN 3.1 2.9 + - - +
371D LEU 3.1 0.4 - - - -
372D LEU* 1.3 92.1 - - + +
374D HIS* 1.3 76.5 + + + +
375D VAL* 3.3 8.6 + - - +
----------------------------------------------------------
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