Contacts of the helix formed by residues 361 - 378 (chain B) in PDB entry 5KJH
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 ARG 361 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A GLN* 5.4 2.2 + - - +
242A ASN* 2.8 35.9 + - - +
243A ASN* 3.3 22.8 + - - +
261A HIS* 5.8 0.8 - - - +
360B PRO* 1.4 68.0 - - - +
362B SER* 1.4 58.6 + - - +
364B LYS* 3.0 10.8 + - - +
365B ILE* 2.9 55.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 362 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B PRO* 3.4 2.4 + - - -
361B ARG* 1.4 77.6 - - - +
363B GLN* 1.3 70.6 + - - +
365B ILE* 3.7 8.6 + - - +
366B ALA* 3.2 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 363 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B PRO* 3.1 30.8 + - + +
362B SER* 1.3 87.3 - - - +
364B LYS* 1.3 55.4 + - - +
366B ALA* 3.3 7.4 + - - +
367B LYS* 2.8 37.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 364 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A GLN* 3.4 36.2 + - - +
322B ASN* 3.9 23.6 + - - +
360B PRO 3.0 11.1 + - - +
361B ARG* 3.0 13.9 + - - +
363B GLN* 1.3 75.1 - - - +
365B ILE* 1.4 58.0 + - + +
367B LYS* 3.5 7.9 + - + +
368B ARG* 2.9 58.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 365 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A ASN* 3.8 35.0 + - + +
361B ARG* 2.9 59.6 + - + +
362B SER* 4.0 7.0 - - - +
364B LYS* 1.4 76.5 - - + +
366B ALA* 1.3 61.9 + - - +
368B ARG* 3.4 4.0 + - - +
369B ALA* 3.1 24.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 366 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362B SER 3.2 19.0 + - - +
363B GLN* 3.3 11.4 + - - +
365B ILE* 1.3 77.2 - - - +
367B LYS* 1.4 50.4 + - - +
369B ALA* 3.3 7.4 + - - +
370B GLN* 2.9 54.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 367 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B GLN 2.8 22.3 + - - +
364B LYS* 3.7 8.5 - - + +
366B ALA* 1.4 69.1 - - - +
368B ARG* 1.4 55.8 + - + +
370B GLN* 3.2 12.2 + - + +
371B ALA* 2.8 37.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 368 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A GLN* 4.9 4.8 + - - -
238A SER* 2.8 30.4 + - - -
239A GLU* 3.9 34.8 + - + +
241A HIS 3.1 16.8 + - - -
242A ASN* 3.1 26.6 + - - +
294A GLN* 3.0 37.6 + - - +
322B ASN 5.7 1.6 + - - -
364B LYS* 2.9 44.0 + - + +
365B ILE 3.8 4.0 - - - +
366B ALA 3.4 0.2 - - - -
367B LYS* 1.4 74.6 - - + +
369B ALA* 1.3 63.1 + - - +
371B ALA* 3.3 7.8 + - - +
372B GLU* 3.1 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 369 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B ILE* 3.1 19.6 + - + +
366B ALA* 3.5 7.0 - - - +
368B ARG* 1.3 77.4 - - - +
370B GLN* 1.3 59.5 + - + +
372B GLU* 3.5 8.3 + - - +
373B TYR* 3.2 22.3 + - - +
455B ARG* 4.5 21.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 370 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B ALA* 2.9 37.3 + - - +
367B LYS* 3.2 11.0 + - + +
369B ALA* 1.3 74.4 - - + +
371B ALA* 1.3 58.4 + - - +
373B TYR* 3.2 3.8 + - - +
374B ALA* 2.8 31.7 + - - +
455B ARG* 5.9 0.7 - - - -
456B ARG* 3.2 72.2 + - + +
457B VAL* 4.4 7.4 - - + +
461B ASP* 6.4 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 371 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A GLN* 4.7 2.8 + - - -
367B LYS* 2.8 23.1 + - + +
368B ARG* 3.6 9.0 - - - +
370B GLN* 1.3 71.8 - - - +
372B GLU* 1.3 62.2 + - + +
374B ALA* 3.4 7.5 + - - +
375B ALA* 3.1 22.5 + - - +
465B LEU* 5.2 7.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 372 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A GLU 4.2 4.2 - - - +
312A PHE* 3.8 29.5 - - + -
314A ARG* 2.7 56.7 + - - +
507A PRO* 5.8 0.5 - - - +
508A VAL* 5.1 3.6 - - - +
368B ARG* 3.1 21.0 + - - +
369B ALA* 3.8 9.9 - - - +
370B GLN 3.3 0.2 - - - -
371B ALA* 1.3 76.2 - - + +
373B TYR* 1.3 59.1 + - - +
375B ALA* 3.3 7.5 + - - +
376B THR* 3.0 31.3 + - - +
455B ARG* 5.8 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 373 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B VAL* 5.2 4.7 - - + +
369B ALA 3.2 15.0 + - - +
370B GLN* 3.2 6.7 + - - +
372B GLU* 1.3 78.2 - - - +
374B ALA* 1.3 55.8 + - - +
376B THR* 3.4 8.8 + - + -
377B LEU* 3.1 55.9 + - + +
448B PHE* 3.8 25.6 - + - -
455B ARG* 3.3 81.9 + - + +
456B ARG* 3.7 15.7 - - - +
457B VAL* 3.9 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 374 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A GLN* 4.1 2.2 - - - -
370B GLN 2.8 16.6 + - - +
371B ALA* 3.6 7.4 - - - +
373B TYR* 1.3 73.2 - - - +
375B ALA* 1.4 59.4 + - - +
377B LEU 3.4 0.3 + - - -
378B ALA* 3.0 32.7 + - - +
457B VAL* 3.8 20.1 - - + +
461B ASP* 4.7 4.3 - - + +
462B ILE* 4.0 19.0 - - + +
465B LEU* 4.2 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 375 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A GLN* 3.4 23.8 - - - +
310A ALA* 4.0 26.4 - - + +
371B ALA 3.1 12.7 + - - +
372B GLU* 3.3 10.3 + - - +
374B ALA* 1.4 73.1 - - - +
376B THR* 1.3 63.4 + - - +
378B ALA* 3.9 2.1 + - - +
379B PRO* 3.2 21.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 376 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A THR* 5.9 2.8 - - - +
507A PRO* 5.5 3.7 - - + +
213B VAL* 3.8 28.0 - - + -
217B HIS* 6.0 4.5 - - + +
372B GLU 3.0 14.9 + - - -
373B TYR* 3.5 17.1 - - + +
374B ALA 3.3 0.2 - - - -
375B ALA* 1.3 77.2 - - - +
377B LEU* 1.4 58.2 + - + +
379B PRO* 3.3 14.4 - - - +
380B TYR* 3.3 16.5 - - + -
455B ARG* 4.4 15.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 377 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B VAL* 3.8 31.2 - - + -
373B TYR* 3.1 38.4 + - + +
376B THR* 1.4 74.4 - - - +
378B ALA* 1.4 65.7 + - - +
379B PRO* 3.4 1.1 - - - -
380B TYR* 3.0 20.8 + - - +
381B LEU* 3.5 6.4 + - - +
384B TRP* 4.3 7.0 - - + -
444B TRP* 3.9 11.7 - - + -
448B PHE* 3.5 38.8 - - + -
457B VAL* 3.6 26.7 - - + -
462B ILE* 3.8 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 378 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A PRO* 3.6 25.2 - - + +
306A GLN* 4.4 17.3 - - + +
374B ALA 3.0 17.9 + - - +
375B ALA 4.1 3.1 - - - +
377B LEU* 1.4 74.0 - - - +
379B PRO* 1.4 66.4 - - + +
380B TYR 3.1 1.2 + - - -
381B LEU* 3.4 14.1 + - - +
382B GLU 4.7 1.4 + - - -
395B LYS* 4.8 3.3 + - - +
462B ILE* 4.1 25.2 - - + +
----------------------------------------------------------
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