Contacts of the helix formed by residues 348 - 363 (chain B) in PDB entry 5ULM
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 HIS 348 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B ALA* 3.4 33.4 - - + +
343B PHE* 4.0 21.2 - + + -
344B ASP* 2.7 30.2 + - + -
345B LEU 2.9 11.3 + - - +
346B ALA 3.3 0.2 - - - -
347B SER* 1.3 92.1 + - - +
349B HIS* 1.3 65.0 + - - +
350B HIS 3.3 2.9 - - - -
351B VAL* 3.2 20.3 + - + +
352B LYS* 3.1 23.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 349 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B ALA 3.4 24.7 + - - -
347B SER* 3.5 12.4 + - - -
348B HIS* 1.3 71.4 - - - +
350B HIS* 1.3 65.6 + - + +
352B LYS* 3.3 5.4 + - + +
353B PHE* 2.8 27.7 + - - +
378B MET* 3.8 35.1 - - + +
382B GLU* 5.4 13.3 - - + +
389B MET* 4.3 7.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 350 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B ILE* 4.0 14.6 - - + -
348B HIS 3.3 0.6 - - - -
349B HIS* 1.3 80.8 - - + +
351B VAL* 1.3 63.5 + - - +
353B PHE* 3.3 5.9 + - + +
354B HIS* 2.9 36.8 + - + +
389B MET* 4.1 18.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 351 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B ALA* 4.9 4.7 - - + -
314B VAL* 4.1 27.1 - - + -
315B ILE* 3.7 26.7 - - + -
318B LEU* 4.2 11.1 - - + +
334B VAL* 4.2 10.8 - - + -
337B LEU* 4.8 3.6 - - + -
343B PHE* 4.8 5.8 - - + -
345B LEU* 3.6 21.1 - - + -
348B HIS* 3.2 27.2 + - + +
350B HIS* 1.3 76.2 - - - +
352B LYS* 1.3 57.7 + - - +
354B HIS* 3.3 3.1 + - - +
355B TYR* 3.0 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 352 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B LEU* 3.4 41.7 - - + +
346B ALA* 3.9 26.5 + - - +
348B HIS 3.1 14.8 + - - +
349B HIS* 3.6 7.1 - - - +
351B VAL* 1.3 71.3 - - - +
353B PHE* 1.3 65.7 + - - +
355B TYR* 3.3 9.5 + - + +
356B ALA* 3.0 25.3 + - - +
374B ILE* 3.9 33.8 + - + +
378B MET* 4.1 28.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 353 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B ARG* 5.1 5.2 - - - -
349B HIS 2.8 14.2 + - - +
350B HIS* 3.4 12.1 - + + +
352B LYS* 1.3 77.0 - - - +
354B HIS* 1.3 78.5 + + - +
356B ALA 3.3 0.2 + - - -
357B PHE* 3.0 45.9 + + + +
375B MET* 4.2 10.3 - - + -
378B MET* 4.2 1.0 - - - +
388B ASP* 3.5 39.7 - - + -
389B MET* 4.0 29.4 - - + -
392B LEU* 3.6 28.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 354 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B ILE* 4.0 19.5 - - + +
318B LEU* 3.8 32.3 - - + +
319B LEU* 3.7 31.5 - - + +
322B ARG* 4.0 23.9 + - - +
330B ILE* 4.0 6.7 - - + +
350B HIS* 2.9 35.8 + - + +
351B VAL 3.9 0.4 - - - +
353B PHE* 1.3 91.1 - + - +
355B TYR* 1.3 56.8 + - - +
357B PHE* 3.6 7.5 - - - +
358B ALA* 3.0 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 355 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B LEU* 5.0 0.4 - - - +
330B ILE* 4.6 1.1 - - - +
331B VAL* 4.1 25.8 - - + -
334B VAL* 3.5 37.9 - - + -
335B GLU* 3.6 22.1 + - + +
338B GLU* 6.1 2.1 - - + +
345B LEU* 4.4 14.8 - - + -
351B VAL 3.0 14.3 + - - +
352B LYS* 3.4 12.6 - - + +
354B HIS* 1.3 76.2 - - - +
356B ALA* 1.3 52.3 + - - +
358B ALA* 3.2 5.4 + - - +
359B LEU* 2.8 62.7 + - + +
370B LYS* 4.2 16.8 - - - +
374B ILE* 3.5 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 356 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B LYS 3.0 15.5 + - - +
353B PHE 3.7 3.4 - - - +
355B TYR* 1.3 73.7 - - - +
357B PHE* 1.3 60.1 + - - +
359B LEU* 3.3 7.9 + - - +
360B ASN* 2.8 31.9 + - - +
371B ALA* 3.6 22.8 - - + +
374B ILE* 4.4 5.4 - - + -
375B MET* 3.5 33.4 - - + -
392B LEU* 4.0 3.8 - - + -
396B ILE* 5.1 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 357 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B ARG* 4.0 19.7 - - - -
327B TYR* 3.8 32.1 - + - -
330B ILE* 6.3 0.4 - - + -
353B PHE* 3.0 32.9 + + + +
354B HIS* 3.6 11.9 - - - +
356B ALA* 1.3 77.0 - - - +
358B ALA* 1.3 57.8 + - - +
360B ASN* 3.3 4.5 + - - +
361B ARG* 3.1 33.5 + - + +
392B LEU* 3.8 29.5 - - + +
395B ARG* 3.3 30.1 - - - -
509B TRP* 3.7 31.9 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 358 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B TYR* 3.7 31.0 - - + +
330B ILE* 3.6 30.1 - - + -
331B VAL* 3.9 5.8 - - + -
354B HIS 3.0 17.9 + - - +
355B TYR 3.6 4.3 - - - +
357B PHE* 1.3 75.5 - - - +
359B LEU* 1.3 59.2 + - - +
361B ARG 3.3 0.5 + - - -
362B ARG* 2.8 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 359 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B VAL* 3.8 29.6 - - + +
335B GLU* 5.5 0.7 - - - +
355B TYR* 2.8 37.4 + - + +
356B ALA* 3.6 4.7 - - - +
358B ALA* 1.3 71.2 - - - +
360B ASN* 1.3 57.9 + - - +
362B ARG* 4.3 1.8 - - - +
363B ASN* 2.9 28.2 + - - -
367B ASP* 3.3 45.0 - - + +
370B LYS* 3.6 19.1 - - + -
371B ALA* 3.9 10.1 - - + +
374B ILE* 3.6 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 360 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B ALA 2.8 16.7 + - - +
357B PHE* 3.5 6.9 + - - +
358B ALA 3.3 0.2 - - - -
359B LEU* 1.3 76.8 - - - +
361B ARG* 1.3 68.5 + - - +
363B ASN* 3.6 2.1 - - - +
368B ARG* 2.8 69.7 + - + +
371B ALA* 4.4 1.8 - - + +
392B LEU* 5.2 3.2 - - + +
395B ARG* 4.2 9.5 + - - +
396B ILE* 3.6 37.0 - - + +
399B ASP* 2.8 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 361 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B TYR* 3.5 46.0 - - + +
357B PHE* 3.1 26.5 + - + +
360B ASN* 1.3 80.7 - - - +
362B ARG* 1.3 64.9 + - - +
363B ASN* 4.0 3.3 - - - +
368B ARG* 3.6 15.1 + - - +
395B ARG* 3.6 26.2 - - - +
399B ASP* 2.7 33.3 + - - -
403B ASP* 5.0 3.2 + - - -
512B LYS* 3.1 38.6 - - - +
516B GLU* 3.1 14.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 362 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B TYR* 4.3 9.3 - - + +
328B ASP* 2.9 46.2 + - + +
331B VAL* 3.6 33.7 - - - +
332B LYS* 4.5 10.5 - - - +
335B GLU* 4.6 6.7 + - - -
358B ALA 2.8 21.9 + - - +
359B LEU* 3.8 2.8 - - - +
361B ARG* 1.3 72.5 - - - +
363B ASN* 1.3 71.1 + - - +
364B LEU* 3.2 34.9 + - + +
367B ASP* 2.8 37.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 363 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B LEU 2.9 15.9 + - - -
360B ASN 3.6 14.1 - - - +
361B ARG 4.0 2.9 - - - +
362B ARG* 1.3 79.2 - - - +
364B LEU* 1.3 67.5 + - - +
365B PRO* 4.0 0.7 - - - +
367B ASP* 3.8 5.8 - - - -
368B ARG* 3.3 45.9 + - - +
403B ASP* 4.1 7.9 + - - +
----------------------------------------------------------
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