Contacts of the helix formed by residues 355 - 366 (chain B) in PDB entry 1KKQ
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 355 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B PHE* 5.6 0.9 - - + -
321B LEU* 4.4 10.1 - - + -
325B MET* 4.7 7.0 - - - -
330B MET* 4.9 2.0 - - - +
344B LEU* 4.1 25.6 - - + -
351B PHE 4.9 0.8 + - - -
352B CYS 5.5 0.4 - - - -
354B ILE* 1.3 78.8 - - + +
356B GLU* 1.3 63.4 + - - +
357B PRO 3.4 0.4 - - - -
358B LYS* 3.4 26.2 + - + +
359B PHE* 3.2 28.7 + - + -
440B HIS* 6.0 0.9 - - + -
776B 471 3.1 98.6 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
341B ARG* 2.9 55.9 + - - +
344B LEU* 5.9 1.3 - - - +
345B LYS* 4.2 31.4 + - + +
352B CYS 4.2 17.4 + - - +
353B ASP* 5.1 0.9 - - - -
354B ILE 3.3 1.2 - - - +
355B MET* 1.3 77.7 - - - +
357B PRO* 1.3 64.2 - - + +
359B PHE* 3.0 6.4 + - - +
360B ASP* 2.8 30.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 357 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B ASP* 3.1 20.0 - - - +
354B ILE 2.9 16.2 - - - +
356B GLU* 1.3 93.9 - - + +
358B LYS* 1.3 59.9 + - - +
360B ASP* 3.2 10.3 - - + +
361B PHE* 3.0 24.9 + - - +
436B LEU* 4.0 21.8 - - + +
439B GLU* 5.7 2.7 - - - +
443B LEU* 4.5 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 358 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B PHE* 3.8 32.8 - - + -
321B LEU* 5.0 2.5 - - + -
325B MET* 4.3 11.8 - - + +
354B ILE* 3.1 29.3 + - + +
355B MET* 3.6 24.0 - - - +
356B GLU 3.1 0.6 - - - -
357B PRO* 1.3 82.3 - - - +
359B PHE* 1.3 54.4 + - - +
361B PHE* 3.0 8.4 + - + +
362B ALA* 2.6 38.3 + - - +
436B LEU* 3.1 36.3 - - + +
440B HIS* 3.0 44.4 + - + +
443B LEU* 5.0 3.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 359 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B MET* 4.0 22.9 - - + -
326B ASN 3.7 12.6 - - - -
329B GLY* 3.3 50.5 - - - -
330B MET* 3.7 13.5 - - + -
341B ARG* 3.6 48.0 + - + +
344B LEU* 4.2 21.3 - - + -
355B MET* 3.2 24.3 + - + -
356B GLU* 3.0 12.7 + - - +
358B LYS* 1.3 74.0 - - - +
360B ASP* 1.3 69.3 + - - +
362B ALA* 3.7 4.1 - - - +
363B MET* 3.1 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 360 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B ARG* 4.3 8.5 + - - +
356B GLU* 2.8 15.4 + - - +
357B PRO* 3.2 15.3 - - + +
359B PHE* 1.3 79.2 - - - +
361B PHE* 1.3 64.7 + - - +
363B MET* 3.6 8.7 + - - +
364B LYS* 3.4 38.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 361 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B PHE* 4.1 12.6 - - + -
319B ALA* 4.5 2.0 - - - -
322B SER* 3.8 15.3 - - - -
357B PRO 3.0 15.7 + - - +
358B LYS* 3.0 10.7 + - + +
360B ASP* 1.3 75.7 - - - +
362B ALA* 1.3 66.5 + - - +
364B LYS* 3.0 12.6 + - + +
365B PHE* 2.9 55.0 + + + +
429B LYS* 4.3 27.6 - - + -
432B ASP* 4.7 15.5 - - + -
433B LEU* 3.8 31.6 - - + -
436B LEU* 4.3 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 362 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B SER* 3.5 31.2 - - - +
325B MET* 3.5 25.6 - - + -
358B LYS 2.6 20.1 + - - +
359B PHE* 3.3 4.7 + - - +
361B PHE* 1.3 74.2 - - - +
363B MET* 1.3 59.9 + - - +
365B PHE* 4.4 0.4 - - - -
366B ASN* 2.8 41.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 363 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B ARG* 5.5 1.6 - - - +
325B MET 4.7 0.4 - - - +
326B ASN* 3.5 44.2 - - - +
327B LYS* 3.5 15.7 - - + +
341B ARG* 4.6 11.7 - - - +
359B PHE* 3.1 23.7 + - - +
360B ASP* 3.9 5.2 - - - +
361B PHE 3.1 0.2 + - - -
362B ALA* 1.3 83.2 - - - +
364B LYS* 1.3 63.4 + - + +
366B ASN* 3.8 19.5 + - + +
367B ALA* 3.6 17.5 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
360B ASP* 3.4 31.6 + - - +
361B PHE* 3.0 10.7 + - + +
363B MET* 1.3 77.2 - - + +
365B PHE* 1.3 64.2 + - - +
367B ALA* 3.5 17.9 + - - +
368B LEU* 4.1 8.5 - - - +
429B LYS* 3.9 23.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 365 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B LYS* 5.9 2.2 - - - -
319B ALA* 3.8 16.8 - - + -
322B SER* 4.0 18.6 - - - -
323B SER* 6.0 0.7 - - - -
361B PHE* 2.9 43.4 + + + +
362B ALA* 3.8 4.3 - - - +
364B LYS* 1.3 78.5 - - - +
366B ASN* 1.3 64.6 + - - +
367B ALA 3.1 1.6 + - - -
368B LEU* 3.2 38.4 + - + +
369B GLU 4.3 0.5 + - - -
370B LEU* 3.7 26.7 + - + +
375B ILE* 4.3 13.0 - - + -
378B PHE* 3.9 24.7 - + - -
426B LEU* 3.6 22.9 - - + -
429B LYS* 3.9 17.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 366 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B LYS* 3.4 25.2 + - - +
226B ARG* 3.8 20.6 - - - +
322B SER* 2.5 41.3 + - - +
323B SER* 4.2 0.5 + - - -
325B MET 4.3 2.0 + - - -
362B ALA* 2.8 30.3 + - - +
363B MET* 4.2 16.2 - - + +
365B PHE* 1.3 75.0 - - - +
367B ALA* 1.3 57.3 + - - +
368B LEU 3.2 0.2 - - - -
369B GLU* 3.1 23.6 + - - +
----------------------------------------------------------
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