Contacts of the helix formed by residues 298 - 308 (chain A) in PDB entry 4KIK
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 GLY 298 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A GLY 3.2 1.2 + - - -
291A ASP* 3.6 12.3 - - - +
294A TYR* 3.8 23.6 - - - -
295A GLY 3.1 17.1 + - - -
296A PRO 3.1 0.6 - - - -
297A ASN* 1.3 74.7 - - - +
299A CYS* 1.3 57.6 + - - +
300A PHE 3.3 2.7 - - - -
301A LYS* 3.5 6.4 + - - -
302A ALA* 3.1 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 299 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A TYR* 3.9 36.1 - - - -
276A TRP* 2.8 24.9 + - - +
279A LEU* 4.0 15.5 - - + -
280A MET* 3.5 34.8 - - - -
289A GLY* 3.1 20.8 + - - +
297A ASN 4.4 1.3 - - - -
298A GLY* 1.3 75.1 - - - +
300A PHE* 1.4 75.1 + - - +
302A ALA* 4.1 0.7 - - - -
303A LEU* 3.2 9.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 300 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A ALA* 3.8 27.6 - - + -
133A LEU* 3.8 28.5 - - + -
134A ARG* 3.6 51.6 + - + +
137A HIS* 4.2 9.2 - - + -
205A TYR* 3.7 34.5 - + - -
208A PHE* 4.4 13.0 - + - -
276A TRP* 5.9 1.3 - + - -
280A MET* 5.3 0.9 - - + -
297A ASN* 4.3 11.4 - - + +
298A GLY 3.3 0.8 - - - -
299A CYS* 1.4 83.3 - - - +
301A LYS* 1.4 59.9 + - - +
303A LEU* 3.5 6.4 + - + +
304A ASP* 3.0 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 301 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A ARG* 5.1 1.3 - - - +
294A TYR* 3.4 47.3 - - + -
297A ASN 5.3 0.2 + - - -
298A GLY* 3.5 7.3 + - - +
300A PHE* 1.4 74.2 - - - +
302A ALA* 1.3 64.3 + - - +
304A ASP* 3.3 31.2 + - + +
305A ASP* 3.2 46.1 + - - +
308A ASN* 5.0 4.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 302 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A ARG* 3.9 4.9 + - - +
276A TRP* 3.9 14.4 - - + -
279A LEU* 4.3 2.7 - - + -
291A ASP* 3.2 26.2 - - - +
294A TYR* 3.8 10.7 - - - -
298A GLY 3.1 13.9 + - - +
299A CYS* 3.5 9.2 - - - +
301A LYS* 1.3 74.4 - - - +
303A LEU* 1.4 60.2 + - - +
305A ASP* 3.3 20.7 + - - +
306A ILE* 3.5 12.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 303 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A LEU* 3.9 25.6 - - + +
130A ALA* 3.7 29.6 - - + -
134A ARG* 6.1 0.2 - - - +
208A PHE* 4.6 0.7 - - + -
273A LEU* 3.9 24.5 - - + -
276A TRP* 3.6 42.3 - - + +
299A CYS 3.2 7.1 + - - +
300A PHE* 3.8 5.8 - - + +
302A ALA* 1.4 73.6 - - - +
304A ASP* 1.4 56.3 + - - +
306A ILE* 3.1 7.6 + - + +
307A LEU* 2.8 61.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 304 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A ARG* 2.7 36.8 + - - -
300A PHE 3.0 14.1 + - - +
301A LYS* 3.3 32.4 + - - +
303A LEU* 1.4 76.4 - - - +
305A ASP* 1.4 56.2 + - - +
307A LEU* 3.4 11.3 + - - +
308A ASN* 2.9 45.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A ARG* 4.0 19.6 + - - +
294A TYR* 2.6 32.8 + - - -
301A LYS* 3.2 32.8 + - - +
302A ALA* 3.4 8.8 - - - +
303A LEU 3.2 0.2 - - - -
304A ASP* 1.4 75.1 - - - +
306A ILE* 1.4 62.0 + - - +
308A ASN* 3.2 16.0 + - - +
309A LEU* 3.2 14.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 306 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A LEU* 5.6 0.3 - - - +
269A LEU* 3.8 29.8 - - + +
272A ARG* 3.3 62.1 - - + +
273A LEU* 4.1 15.9 - - + -
275A LYS* 5.7 0.2 - - - -
276A TRP* 3.6 25.1 - - + -
302A ALA* 3.6 11.2 - - + +
303A LEU* 3.1 8.9 + - - +
305A ASP* 1.4 73.7 - - - +
307A LEU* 1.3 66.9 + - + +
309A LEU* 3.2 30.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 307 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A LEU* 4.3 28.8 - - + +
126A LEU* 4.5 10.5 - - + -
127A SER* 3.7 37.7 - - - +
130A ALA* 5.8 0.7 - - + -
273A LEU* 5.4 0.2 - - + -
303A LEU* 2.8 52.7 + - + +
304A ASP* 3.7 13.0 - - - +
306A ILE* 1.3 77.2 - - + +
308A ASN* 1.3 64.6 + - - +
309A LEU 3.2 5.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 308 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A LYS* 5.0 4.3 + - - -
304A ASP* 2.9 33.0 + - - +
305A ASP* 3.2 7.3 + - - +
307A LEU* 1.3 80.4 + - - +
309A LEU* 1.4 62.1 + - - +
310A LYS* 3.6 21.9 + - - +
----------------------------------------------------------
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