Contacts of the helix formed by residues 191 - 201 (chain A) in PDB entry 3KXK
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 191 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A TYR 4.6 0.2 + - - -
188A THR 5.1 1.2 - - - -
189A ASN* 3.3 4.8 - - - +
190A SER* 1.3 80.0 - - - +
192A LYS* 1.3 64.6 + - - +
193A THR 3.4 2.5 - - - -
194A SER* 3.2 16.1 + - - -
195A LEU* 3.0 19.4 + - - +
264A VAL* 4.5 0.7 - - - -
300A ASN* 3.5 15.1 + - - -
301A LYS* 4.0 11.3 - - - +
336A LEU* 5.9 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A ILE* 3.1 27.6 + - + +
185A VAL* 3.5 11.9 - - - +
186A GLY 3.3 31.2 - - - +
187A TYR 4.0 5.6 + - - +
188A THR* 6.0 1.3 - - - -
190A SER* 3.3 20.8 + - - +
191A GLY* 1.3 74.9 - - - +
193A THR* 1.3 67.0 + - - +
195A LEU* 2.9 15.4 + - - +
196A PHE* 2.9 12.9 + - - +
232A ASP* 3.6 14.1 + - - -
233A THR* 2.5 34.8 + - - -
235A PRO* 3.6 22.9 - - + +
264A VAL* 4.0 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ALA 5.8 0.2 + - - -
22A GLY* 5.6 9.0 - - - -
191A GLY 3.4 0.8 - - - -
192A LYS* 1.3 80.3 - - - +
194A SER* 1.3 57.6 + - - +
196A PHE* 3.1 8.7 + - + +
197A ASN* 2.8 54.8 + - - +
215A SER* 6.6 0.2 - - - -
232A ASP* 4.5 18.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A GLY* 3.2 15.3 + - - -
192A LYS 3.2 0.2 - - - -
193A THR* 1.3 78.2 - - - +
195A LEU* 1.3 57.4 + - - +
197A ASN* 3.4 9.0 + - - +
198A SER* 2.9 33.1 + - - -
335A ALA* 3.6 17.9 - - - -
336A LEU* 3.5 22.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A ILE* 4.6 6.5 - - + -
191A GLY 3.0 11.5 + - - +
192A LYS* 2.9 10.4 + - - +
194A SER* 1.3 75.2 - - - +
196A PHE* 1.3 65.7 + - - +
198A SER* 3.1 3.0 + - - -
199A LEU* 3.0 35.8 + - + +
262A ILE* 4.2 13.7 - - + -
264A VAL* 3.8 25.1 - - + -
298A THR* 4.0 4.0 - - - +
300A ASN* 5.2 0.9 - - - +
333A ILE* 3.8 26.9 - - + -
335A ALA* 3.6 11.1 - - + +
341A LEU* 4.2 11.2 - - + -
344A LEU* 3.6 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A ILE* 4.0 24.4 - - + +
192A LYS 2.9 11.2 + - - +
193A THR* 3.4 11.9 - - + +
195A LEU* 1.3 77.9 - - - +
197A ASN* 1.3 69.0 + - - +
199A LEU* 3.5 3.5 + - - +
200A THR* 2.9 49.5 + - - -
202A LEU* 4.1 12.6 - - + -
215A SER* 4.8 1.3 - - - -
216A PRO 3.2 27.1 - - - -
217A LYS 3.9 8.1 - - - -
219A TYR* 3.9 14.6 - - + -
230A LEU* 3.7 24.2 - - + -
232A ASP* 3.7 41.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A THR* 2.8 42.3 + - - +
194A SER* 3.8 8.0 - - - +
196A PHE* 1.3 87.4 - - - +
198A SER* 1.3 54.4 + - - +
200A THR* 4.4 1.8 - - - -
201A GLY* 2.7 27.5 + - - -
202A LEU* 3.1 40.8 + - - +
215A SER* 4.2 6.0 + - - -
338A ARG* 3.9 4.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A SER 2.9 20.5 + - - -
195A LEU* 3.1 7.4 + - - -
197A ASN* 1.3 76.7 - - - +
199A LEU* 1.3 64.5 + - - +
200A THR 3.4 0.3 + - - -
201A GLY* 3.7 4.5 + - - -
335A ALA 3.0 21.5 + - - -
338A ARG* 3.7 31.4 + - - +
341A LEU* 3.6 29.7 - - - +
345A ARG* 5.5 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A ILE* 4.6 9.4 - - + -
195A LEU* 3.0 38.6 + - + +
196A PHE 4.1 0.7 - - - +
198A SER* 1.3 77.5 - - - +
200A THR* 1.3 59.5 + - - +
221A ILE* 3.4 21.2 - - + +
230A LEU* 3.7 26.7 - - + -
262A ILE* 4.7 11.2 - - + -
341A LEU* 4.8 9.2 - - + +
344A LEU* 3.9 25.6 - - + -
345A ARG* 3.8 44.7 + - + +
348A ILE* 5.2 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A PHE* 2.9 38.9 + - - -
199A LEU* 1.3 81.2 - - - +
201A GLY* 1.3 57.1 + - - +
202A LEU* 3.4 32.9 - - + +
219A TYR* 3.2 47.5 + - + +
221A ILE* 4.0 6.0 - - - +
230A LEU* 4.1 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A ASN 2.7 16.1 + - - -
198A SER 3.7 6.1 + - - -
199A LEU 3.6 0.8 - - - -
200A THR* 1.3 76.5 - - - +
202A LEU* 1.3 63.6 + - - +
338A ARG* 4.4 12.8 - - - -
----------------------------------------------------------
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