Contacts of the helix formed by residues 354 - 364 (chain B) in PDB entry 1XSK
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 354 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B GLN* 3.5 18.5 - - - +
317B ASP* 2.6 42.7 + - - +
350B ILE* 4.5 3.6 - - - -
351B GLY 3.3 12.4 + - - -
352B GLN 3.1 5.4 - - - +
353B LYS* 1.3 77.3 - - - +
355B PRO* 1.3 69.7 - - - +
356B VAL* 3.2 9.8 + - - +
357B PHE* 3.0 23.0 + - - +
358B LYS* 4.3 1.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 355 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B GLN* 3.6 17.9 - - - +
317B ASP* 4.5 0.7 - - - +
319B GLU* 6.6 0.4 - - + -
353B LYS 3.6 5.4 - - - +
354B SER* 1.3 90.2 - - - +
356B VAL* 1.3 63.1 + - + +
357B PHE 3.4 0.3 + - - -
358B LYS* 3.6 14.0 + - + +
359B GLU* 3.9 6.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 356 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B ASP* 3.8 27.8 - - + +
319B GLU* 4.9 9.9 - - + +
350B ILE* 4.1 3.6 - - + -
354B SER* 3.1 7.8 - - - +
355B PRO* 1.3 80.9 - - + +
357B PHE* 1.3 64.4 + - - +
358B LYS 3.3 0.2 - - - -
359B GLU* 3.0 17.0 + - - +
360B LEU* 2.9 29.9 + - + +
397B TRP* 3.3 40.2 - - + -
401B LYS* 5.5 2.5 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
350B ILE* 3.7 22.6 - - + +
351B GLY 3.3 16.2 - - - +
352B GLN* 3.3 33.0 - - + +
354B SER 3.0 15.6 + - - +
356B VAL* 1.3 78.0 - - - +
358B LYS* 1.3 63.5 + - + +
360B LEU* 3.2 5.8 + - - +
361B GLN* 2.9 36.0 + - + -
366B LEU* 4.2 3.1 - - + +
374B LEU* 3.8 28.7 - - + -
376B GLN* 3.4 22.9 - - - -
383B GLY 3.3 20.2 - - - -
385B ALA* 3.6 17.5 - - + -
73F GLN* 4.9 7.9 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
354B SER 4.3 1.2 + - - +
355B PRO 3.6 9.0 + - - +
356B VAL 3.3 0.6 - - - -
357B PHE* 1.3 80.6 - - + +
359B GLU* 1.3 63.1 + - - +
361B GLN* 3.7 18.1 - - - +
362B GLU* 3.0 45.0 + - + +
73F GLN* 5.9 6.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 359 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B PRO 3.9 3.8 + - - +
356B VAL* 3.0 23.4 + - - +
358B LYS* 1.3 80.1 - - - +
360B LEU* 1.3 63.1 + - + +
362B GLU* 3.3 8.6 + - - +
363B LYS* 3.1 57.5 + - + +
397B TRP* 3.6 32.5 + - - +
401B LYS* 5.1 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 360 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B ILE* 3.3 35.2 - - + -
356B VAL* 2.9 20.3 + - + +
357B PHE* 3.6 5.8 - - - +
359B GLU* 1.3 73.5 - - + +
361B GLN* 1.3 60.6 + - - +
363B LYS* 3.3 3.1 + - - +
364B GLY 2.9 23.9 + - - -
365B TYR* 3.0 41.4 + - + -
366B LEU* 3.7 23.3 + - + -
387B TYR* 3.6 21.1 - - + -
397B TRP* 3.7 31.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 361 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B PHE* 2.9 26.8 + - + +
358B LYS* 3.7 19.3 - - - +
359B GLU 3.3 0.2 - - - -
360B LEU* 1.3 77.4 - - - +
362B GLU* 1.3 64.1 + - + +
364B GLY* 3.4 11.4 + - - -
366B LEU* 4.2 7.1 - - + +
368B LYS* 5.9 0.3 - - - -
374B LEU* 3.7 38.0 - - + +
73F GLN* 3.0 31.3 + - - +
74F GLY* 3.7 6.5 + - - -
75F ALA 5.1 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 362 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B LYS* 3.0 50.6 + - + +
359B GLU* 3.7 7.3 - - - +
360B LEU 3.2 0.2 - - - -
361B GLN* 1.3 81.2 - - + +
363B LYS* 1.3 61.6 + - + +
364B GLY* 3.4 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 363 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B GLU* 3.1 49.3 + - + +
360B LEU 3.3 2.4 + - - +
362B GLU* 1.3 78.5 - - + +
364B GLY* 1.3 62.2 + - - +
365B TYR* 3.4 49.1 + - + +
391B ASN* 5.3 0.7 + - - -
397B TRP* 4.3 10.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 364 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B LEU 2.9 6.0 + - - -
361B GLN* 3.4 6.9 + - - -
362B GLU 3.2 5.6 - - - -
363B LYS* 1.3 79.1 - - - +
365B TYR* 1.3 61.0 + - - +
366B LEU 3.5 4.1 - - - +
368B LYS* 4.2 29.3 - - - -
374B LEU* 6.3 1.1 - - - -
388B ASP* 5.5 1.2 - - - +
391B ASN* 3.4 20.8 + - - +
428B PHE* 5.3 0.9 - - - -
----------------------------------------------------------
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