Contacts of the helix formed by residues 361 - 371 (chain B) in PDB entry 5IXC
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 361 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B GLY* 4.0 3.8 - - - -
360B ILE* 1.3 84.4 - - - +
362B GLY* 1.3 62.2 + - - +
364B THR* 2.5 33.3 + - - +
365B TRP* 3.7 8.8 - - - -
463B LEU 4.6 1.8 + - - -
527B TRP 3.5 22.6 + - - -
528B SER* 3.5 5.4 - - - -
650B TYR 5.5 0.4 - - - -
901B 7FA 1.6 56.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 362 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B GLY* 4.2 1.4 - - - -
331B GLY* 3.4 31.4 - - - +
334B ALA* 4.2 4.3 - - - -
335B MET* 3.8 7.8 - - - +
360B ILE 3.2 0.8 + - - -
361B SER* 1.3 80.8 + - - +
363B SER* 1.3 60.8 + - - +
365B TRP* 3.1 34.0 + - - +
366B THR 3.8 2.4 + - - -
901B 7FA 3.5 4.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 363 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B ALA* 3.3 21.4 - - - +
328B THR 2.7 20.5 + - - -
334B ALA* 4.0 7.0 - - - +
338B LEU* 3.6 13.3 - - - +
359B GLY* 4.0 3.6 - - - -
360B ILE 3.0 22.9 + - - -
362B GLY* 1.3 75.2 - - - +
364B THR* 1.3 61.6 + - - +
365B TRP 3.1 0.4 + - - -
366B THR* 3.4 9.0 + - - -
367B MET* 3.1 23.9 + - - +
674B TYR* 3.6 11.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 364 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B GLY 3.8 24.2 - - - +
360B ILE* 3.9 0.7 - - - -
361B SER 2.5 33.3 + - - +
363B SER* 1.3 74.0 - - - +
365B TRP* 1.3 64.4 + - - +
366B THR 3.4 0.2 - - - -
367B MET* 3.5 9.3 - - - +
368B ALA* 2.7 37.5 + - - +
462B TYR* 3.8 21.1 - - + -
463B LEU 4.9 1.1 - - - +
524B GLU* 5.0 0.4 - - - -
527B TRP* 3.5 36.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 365 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B GLY* 3.6 37.5 - - - -
332B ALA* 3.7 4.0 - - - -
335B MET* 3.9 27.8 - - - -
339B TYR* 4.7 0.2 + - - -
361B SER 3.7 2.8 + - - -
362B GLY* 3.1 13.8 + - - +
364B THR* 1.3 86.6 - - - +
366B THR* 1.3 64.0 + - - +
368B ALA* 3.4 1.7 + - - +
369B HIS* 3.3 23.7 + - - +
428B TRP* 4.6 0.9 - + - -
432B LEU* 3.7 26.8 - - + +
436B LEU* 4.1 20.3 - - + +
524B GLU* 4.0 20.6 - - + +
528B SER* 2.9 37.1 + - - -
771B MET* 3.8 33.2 - - + -
901B 7FA 4.0 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 366 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B MET* 2.7 37.9 + - - +
338B LEU* 3.7 25.2 - - + +
339B TYR* 3.8 32.3 + - + -
342B LEU* 4.0 2.7 - - + -
357B PHE* 5.3 0.4 - - + -
362B GLY 3.8 0.4 + - - -
363B SER 3.4 8.9 + - - -
365B TRP* 1.3 79.0 - - - +
367B MET* 1.3 62.1 + - - +
370B LEU* 3.2 43.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 367 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B PHE* 3.3 57.7 - - + +
358B SER 4.1 2.2 - - - -
359B GLY* 3.5 26.5 - - - +
363B SER* 3.1 14.9 + - - +
364B THR* 3.5 10.8 - - - +
366B THR* 1.3 80.7 - - - +
368B ALA* 1.3 64.1 + - - +
370B LEU* 3.8 2.0 - - - +
371B TYR* 3.0 36.2 + - + +
460B PRO* 4.0 7.2 - - + -
461B LEU 3.5 22.0 - - - +
462B TYR* 3.5 27.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 368 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B THR 2.7 21.7 + - - +
365B TRP 3.9 1.3 - - - +
366B THR 3.4 0.2 - - - -
367B MET* 1.3 73.6 - - - +
369B HIS* 1.3 62.9 + - - +
371B TYR 3.7 1.6 + - - -
372B GLY* 3.4 14.0 + - - -
443B GLN* 4.5 4.5 - - - +
448B GLN* 4.3 7.3 + - - +
462B TYR* 3.9 13.0 + - + -
520B ILE* 4.1 20.7 - - + +
524B GLU* 3.7 31.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 369 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B TYR* 3.4 24.6 + - - +
365B TRP 3.3 11.4 + - - +
367B MET 3.3 0.6 - - - -
368B ALA* 1.3 77.1 - - - +
370B LEU* 1.3 62.2 + - - +
372B GLY* 2.8 22.6 + - - -
373B ASP* 3.9 2.1 + - - +
384B PRO* 4.2 20.3 - - + +
387B TYR* 3.4 50.3 - + + -
437B HIS* 3.8 28.5 - + + -
441B MET* 5.3 8.0 - - + +
443B GLN* 4.9 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 370 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B TYR* 4.0 10.3 - - + -
342B LEU* 3.4 33.2 - - + -
357B PHE* 5.0 3.6 - - + -
366B THR* 3.2 25.9 + - + +
367B MET 3.8 2.9 - - - +
369B HIS* 1.3 79.4 - - - +
371B TYR* 1.3 59.2 + - + +
373B ASP* 3.1 17.3 + - - +
376B TRP* 3.0 51.0 - - + +
381B LEU* 3.4 27.6 - - + -
384B PRO* 3.9 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 371 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B PHE* 3.9 18.6 - + - -
367B MET* 3.0 31.6 + - + +
368B ALA 4.0 1.3 - - - +
370B LEU* 1.3 74.8 - - + +
372B GLY* 1.3 64.3 + - - +
373B ASP 3.2 4.6 - - - +
374B PRO* 4.7 0.5 - - - +
376B TRP* 3.5 43.4 - + - -
448B GLN* 3.5 45.9 - - + +
451B ALA* 3.9 20.8 - - + +
452B LEU* 4.5 2.0 - - + -
457B ASN* 4.0 7.0 - - + -
458B PRO* 2.4 41.8 + - - +
460B PRO* 3.5 36.7 - - + +
462B TYR* 4.1 0.7 - - - -
----------------------------------------------------------
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