Contacts of the helix formed by residues 354 - 364 (chain D) 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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314D GLN* 3.8 17.3 - - - +
317D ASP* 2.6 42.6 + - - +
350D ILE* 4.2 4.0 - - - -
351D GLY 3.2 13.0 + - - -
352D GLN 3.1 6.1 + - - +
353D LYS* 1.3 78.2 - - - +
355D PRO* 1.3 69.2 - - - +
356D VAL* 3.3 7.4 + - - +
357D PHE* 3.0 22.8 + - - +
358D LYS* 4.2 1.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 355 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311D LYS* 6.0 1.3 - - - -
314D GLN* 3.7 18.2 - - - +
317D ASP* 4.1 1.6 - - - +
319D GLU* 6.0 2.5 - - + -
353D LYS 3.8 4.7 - - - +
354D SER* 1.3 90.7 - - - +
356D VAL* 1.3 63.9 + - + +
357D PHE 3.4 0.3 + - - -
358D LYS* 3.6 13.3 + - - +
359D GLU* 4.0 6.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 356 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317D ASP* 3.7 29.6 - - + +
319D GLU* 4.4 12.3 - - + +
350D ILE* 4.2 1.8 - - + -
354D SER* 3.1 6.7 - - - +
355D PRO* 1.3 80.9 - - + +
357D PHE* 1.3 65.5 + - - +
359D GLU* 3.0 19.0 + - - +
360D LEU* 2.9 32.6 + - + +
397D TRP* 3.3 39.9 - - + -
401D LYS* 6.0 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 357 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350D ILE* 3.7 21.0 - - + +
351D GLY 3.3 25.1 - - - +
352D GLN* 3.5 20.4 - - + +
354D SER* 3.0 19.1 + - - +
356D VAL* 1.3 78.7 - - - +
358D LYS* 1.3 63.2 + - - +
360D LEU* 3.5 4.4 + - - +
361D GLN* 3.0 37.5 + - - +
366D LEU* 4.2 2.8 - - + +
374D LEU* 3.9 24.0 - - + -
376D GLN* 3.2 23.8 - - - -
383D GLY 3.5 13.7 - - - -
385D ALA* 3.5 21.8 - - + -
73E GLN* 4.4 14.1 - - + -
74E GLY 5.0 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 358 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354D SER 4.2 1.0 + - - +
355D PRO* 3.6 10.1 + - + +
356D VAL 3.2 0.6 - - - -
357D PHE* 1.3 81.0 - - + +
359D GLU* 1.3 59.6 + - - +
361D GLN* 3.3 15.7 + - - +
362D GLU* 2.9 57.2 + - + +
73E GLN* 5.9 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 359 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355D PRO 4.0 3.4 + - - +
356D VAL* 3.0 34.7 + - - +
358D LYS* 1.3 79.4 - - - +
360D LEU* 1.3 66.0 + - + +
362D GLU* 3.3 6.6 + - - +
363D LYS* 2.8 62.7 + - + +
397D TRP* 3.6 18.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 360 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350D ILE* 3.6 28.3 - - + -
356D VAL* 2.9 20.6 + - + +
357D PHE* 3.8 3.4 - - - +
359D GLU* 1.3 78.3 - - + +
361D GLN* 1.3 59.0 + - - +
363D LYS* 3.1 5.8 + - - -
364D GLY 2.9 24.6 + - - -
365D TYR* 3.1 27.0 + - + -
366D LEU* 3.9 23.3 - - + -
387D TYR* 3.6 29.2 - - + +
397D TRP* 3.6 40.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 361 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357D PHE* 3.0 28.0 + - + +
358D LYS* 3.4 17.4 - - - +
360D LEU* 1.3 77.4 - - - +
362D GLU* 1.3 67.4 + - + +
364D GLY* 3.3 12.6 + - - -
366D LEU* 4.0 8.0 - - - +
368D LYS* 5.7 0.9 - - - -
374D LEU* 4.0 31.7 - - + +
73E GLN* 3.5 27.5 + - - +
74E GLY* 3.7 15.0 + - - -
75E ALA 4.9 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 362 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358D LYS* 2.9 57.4 + - + +
359D GLU* 3.9 6.0 - - - +
361D GLN* 1.3 81.4 - - + +
363D LYS* 1.3 61.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 363 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359D GLU* 2.8 53.5 + - + +
360D LEU 3.1 3.8 + - - +
362D GLU* 1.3 79.8 - - + +
364D GLY* 1.3 62.2 + - - +
365D TYR* 3.4 48.9 + - + +
391D ASN* 5.4 0.5 + - - -
397D TRP* 4.2 12.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 364 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360D LEU 2.9 4.9 + - - -
361D GLN* 3.3 11.4 + - - -
362D GLU 3.3 0.6 - - - -
363D LYS* 1.3 80.0 - - - +
365D TYR* 1.3 59.8 + - - +
366D LEU 3.3 11.0 + - - +
368D LYS* 4.1 26.2 + - - -
374D LEU* 6.3 0.9 - - - -
388D ASP* 5.2 1.4 - - - +
391D ASN* 3.3 18.9 + - - -
428D PHE* 5.4 1.0 - - - -
----------------------------------------------------------
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