Contacts of the helix formed by residues 296 - 305 (chain A) in PDB entry 1CK4
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 THR 296 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A LEU* 3.4 46.8 - - + +
289A TYR* 3.5 31.6 - - + -
290A ASN* 4.1 8.6 + - - +
294A LEU 3.7 4.4 + - - +
295A SER* 1.3 73.5 - - - +
297A GLU* 1.3 59.9 + - - +
298A LYS 3.3 2.5 - - - -
299A PHE* 3.7 8.3 - - + -
300A VAL* 2.8 34.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 297 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A GLU* 5.9 0.2 - - - -
295A SER* 3.2 36.5 - - - +
296A THR* 1.3 81.5 + - - +
298A LYS* 1.3 106.6 + - - +
299A PHE 4.4 0.3 + - - -
300A VAL* 3.4 19.4 - - - +
301A GLU* 3.4 8.8 + - - +
249B LYS* 3.9 10.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 298 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A GLU* 3.4 23.4 - - - +
297A GLU* 1.3 102.5 + - - +
299A PHE* 1.3 60.5 + - - +
301A GLU* 3.4 15.7 + - - +
302A GLU* 3.0 30.1 + - - +
249B LYS* 4.6 16.4 - - - +
277B ASN* 4.9 20.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 299 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A THR 3.9 6.1 - - - -
257A ASP* 3.3 18.2 - - - -
258A GLY* 3.3 31.9 - - - -
259A GLU* 3.7 22.0 + - + -
284A ALA* 3.9 9.0 - - + -
285A ILE 3.3 22.7 - - - -
286A LEU* 3.0 38.8 - - + -
289A TYR* 4.1 17.7 - + + -
295A SER 4.9 0.2 - - - +
296A THR* 3.2 19.0 + - + +
297A GLU* 4.4 0.8 + - - -
298A LYS* 1.3 79.7 - - - +
300A VAL* 1.3 58.3 + - - +
302A GLU* 3.5 1.5 + - - +
303A ILE* 2.9 52.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 300 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A ALA* 5.1 4.0 - - + -
286A LEU* 5.2 7.0 - - + -
296A THR* 2.8 17.0 + - - +
297A GLU* 3.4 15.5 - - - +
299A PHE* 1.3 77.2 - - - +
301A GLU* 1.3 63.9 + - + +
303A ILE* 4.6 2.5 - - - -
304A LYS* 2.8 35.9 + - + +
315A PHE* 3.1 36.1 - - + -
317A ASN* 3.6 23.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 301 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A GLU 3.4 12.8 + - - +
298A LYS* 3.4 15.6 + - - +
299A PHE 3.3 0.8 - - - -
300A VAL* 1.3 82.5 - - + +
302A GLU* 1.3 61.0 + - - +
304A LYS* 3.4 7.7 + - + +
305A SER* 3.0 30.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 302 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A THR* 4.9 2.4 + - - -
258A GLY 4.2 0.5 - - - +
259A GLU* 3.6 16.2 - - - +
260A SER* 2.9 39.7 + - - -
263A ASN* 2.7 32.2 + - - +
266A LEU* 3.8 17.2 - - + +
298A LYS 3.0 17.4 + - - +
299A PHE 4.0 1.3 - - - +
300A VAL 3.4 0.2 - - - -
301A GLU* 1.3 80.2 + - - +
303A ILE* 1.3 73.5 + - + +
305A SER* 2.7 25.2 + - - +
306A ILE* 3.1 12.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 303 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A THR* 5.9 1.6 - - + +
254A ILE 5.9 0.2 - - - +
256A THR* 3.6 25.6 - - + -
258A GLY 4.3 1.6 - - - +
282A SER* 2.7 44.1 + - - +
283A ILE 4.3 2.0 - - - -
284A ALA* 3.6 26.2 - - + +
299A PHE* 2.9 44.3 + - + +
300A VAL 4.0 0.7 - - - +
302A GLU* 1.3 94.9 - - + +
304A LYS* 1.3 65.7 + - - +
306A ILE* 3.0 19.9 + - + +
315A PHE* 3.7 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 304 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A VAL* 2.8 22.6 + - + +
301A GLU* 3.6 9.6 - - - +
303A ILE* 1.3 75.2 - - - +
305A SER* 1.3 57.8 + - - +
306A ILE 2.9 7.6 + - - -
307A ALA* 3.0 22.3 + - - +
311A THR* 2.8 41.9 + - - +
312A GLU* 3.7 22.6 + - - +
315A PHE* 3.3 40.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A LEU* 5.1 6.1 - - - +
270A ILE* 4.1 16.6 - - - +
301A GLU* 3.0 18.3 + - - -
302A GLU* 2.7 19.1 + - - +
303A ILE 3.1 0.2 - - - -
304A LYS* 1.3 74.2 - - - +
306A ILE* 1.3 61.0 + - - +
307A ALA 4.6 2.9 - - - +
----------------------------------------------------------
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