Contacts of the helix formed by residues 210 - 225 (chain A) in PDB entry 2WK6
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 210 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ILE* 3.9 6.6 + - - +
79A ARG* 3.9 19.2 - - - +
207A THR 4.2 2.5 - - - -
208A VAL 2.8 8.1 + - - -
209A ASP* 1.3 74.4 - - - +
211A LEU* 1.3 65.6 + - - +
212A PRO* 3.4 21.0 - - - +
213A LEU* 3.0 32.8 + - - +
214A ILE* 2.8 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A LEU* 6.2 0.9 - - + -
210A SER* 1.3 69.7 - - - +
212A PRO* 1.3 69.5 - - + +
214A ILE* 3.8 2.9 - - - +
215A THR* 2.8 37.1 + - - +
242A PHE* 3.7 22.2 - - + -
247A GLN* 4.5 2.7 - - + +
250A GLU* 3.9 13.9 - - + +
251A LEU* 3.4 43.4 - - + +
254A THR* 3.7 24.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ILE* 4.1 14.8 - - + -
82A GLY* 4.7 4.0 - - - -
83A MET* 3.8 32.3 - - + +
88A THR* 3.3 34.6 - - + +
91A LEU* 4.2 2.4 - - - +
210A SER* 3.4 15.3 - - - +
211A LEU* 1.3 98.6 - - + +
213A LEU* 1.3 55.4 + - - +
215A THR* 3.8 0.7 - - - +
216A ALA* 3.1 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LEU* 3.9 39.7 - - + +
78A ILE* 4.0 19.5 - - + -
91A LEU* 3.7 24.7 - - + -
95A LEU* 5.6 0.9 - - - +
198A LEU* 5.4 6.1 - - + -
202A ARG* 3.6 26.8 + - + +
207A THR* 3.5 22.7 - - - +
210A SER* 3.0 25.3 + - - +
212A PRO* 1.3 75.1 - - - +
214A ILE* 1.3 66.6 + - - +
216A ALA* 4.3 0.5 - - - +
217A SER* 3.0 26.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A THR* 4.8 0.4 - - + -
202A ARG* 3.3 6.3 - - - +
208A VAL 3.2 26.7 - - - +
210A SER 2.8 16.1 + - - +
211A LEU 3.8 2.9 - - - +
213A LEU* 1.3 76.5 - - - +
215A THR* 1.3 55.2 + - - +
217A SER* 3.3 0.7 + - - -
218A ILE* 2.8 64.4 + - + +
241A VAL* 3.5 26.9 - - + -
242A PHE* 3.6 23.1 - - + -
251A LEU* 4.1 19.3 - - + -
1482A IUR 3.4 22.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A THR* 3.9 20.4 - - + -
211A LEU* 2.8 21.1 + - - +
212A PRO 3.8 4.0 - - - -
214A ILE* 1.3 73.7 - - - +
216A ALA* 1.3 65.5 + - - +
219A LEU* 3.0 53.5 + - + +
251A LEU* 3.9 12.1 - - - +
254A THR* 3.7 27.0 - - + +
255A LEU* 4.1 15.0 - - - +
258A VAL* 4.2 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A THR* 4.3 1.5 - - - +
91A LEU* 3.7 22.4 - - + -
92A THR* 3.1 37.0 - - - +
95A LEU* 4.1 6.5 - - + -
212A PRO 3.1 16.4 + - - +
213A LEU 4.3 0.9 - - - +
215A THR* 1.3 79.9 - - - +
217A SER* 1.3 52.0 + - - +
220A SER* 2.6 42.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A LEU* 4.2 3.8 - - - +
195A ASP* 2.3 30.5 + - - -
199A TYR* 3.8 3.1 - - - -
202A ARG* 3.5 16.2 + - - -
213A LEU 3.0 21.4 + - - -
214A ILE 3.5 2.9 - - - -
216A ALA* 1.3 77.7 - - - +
218A ILE* 1.3 57.7 + - - +
220A SER* 2.9 14.3 + - - -
221A LYS* 2.6 33.6 + - - +
1482A IUR 3.1 11.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A HIS* 3.9 24.2 - - + -
118A THR* 4.1 17.0 - - + -
214A ILE* 2.8 45.2 + - + +
217A SER* 1.3 72.0 - - - +
219A LEU* 1.3 68.4 + - + +
221A LYS* 3.2 15.3 + - - +
222A LYS* 3.2 15.8 + - + +
232A VAL* 4.2 16.4 - - + -
255A LEU* 4.0 23.8 - - + -
1482A IUR 3.4 36.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A THR* 3.7 11.7 - - + -
215A THR* 3.0 37.5 + - + +
218A ILE* 1.3 77.7 - - + +
220A SER* 1.3 56.9 + - - +
222A LYS* 3.0 5.4 + - + +
223A LEU* 2.6 45.7 + - + +
230A LEU* 5.4 1.8 - - + -
232A VAL* 5.3 3.8 - - + -
255A LEU* 3.6 33.7 - - + +
258A VAL* 3.7 12.3 - - + -
259A GLY* 3.5 33.7 - - - +
262A LEU* 5.0 0.7 - - + -
264A LEU* 5.0 6.3 - - + -
266A VAL* 5.0 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A THR* 3.6 10.4 - - - +
95A LEU* 3.7 11.4 - - - +
96A ALA* 3.5 35.7 - - - +
192A VAL* 3.6 3.5 - - - +
195A ASP* 4.1 7.6 + - - +
216A ALA 2.6 29.6 + - - -
217A SER* 2.9 17.3 + - - -
219A LEU* 1.3 73.7 - - - +
221A LYS* 1.3 62.6 + - - +
224A VAL* 3.3 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 221 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A HIS* 4.2 5.8 - - + -
143A ILE* 3.4 41.8 - - + +
144A SER 4.1 10.1 - - - +
187A GLN* 3.3 19.5 - - - +
192A VAL* 4.2 21.3 - - + -
195A ASP* 2.8 25.0 + - - +
199A TYR* 4.1 2.2 - - - -
217A SER* 2.6 32.5 + - - +
218A ILE 3.2 6.5 + - - +
220A SER* 1.3 85.8 + - - +
222A LYS* 1.3 66.3 + - - +
224A VAL* 3.5 4.9 + - - +
225A GLU* 3.3 19.2 - - - +
1482A IUR 2.6 27.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ASP* 2.7 28.8 + - - +
115A LYS 4.3 0.6 + - - -
116A HIS* 3.0 35.8 + - + -
142A MET* 4.0 4.0 - - - +
143A ILE 3.0 26.0 + - - +
218A ILE* 3.2 17.2 + - + +
219A LEU* 3.0 8.8 + - + +
221A LYS* 1.3 78.0 - - - +
223A LEU* 1.3 64.4 + - - +
225A GLU* 3.0 33.9 + - - +
226A GLY 3.9 2.9 + - - -
227A LEU* 3.9 13.7 + - + +
230A LEU* 3.8 22.7 - - + -
264A LEU* 4.0 19.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A THR* 3.5 32.3 - - + -
93A GLN* 5.3 1.6 - - + +
96A ALA* 4.6 11.9 - - + -
101A GLN* 5.9 1.6 - - - +
219A LEU* 2.6 23.3 + - + +
220A SER* 4.0 5.8 - - - +
222A LYS* 1.3 72.7 - - - +
224A VAL* 1.3 62.3 + - - +
225A GLU 3.1 1.3 + - - -
226A GLY* 3.4 11.6 + - - -
259A GLY* 5.0 1.6 - - - +
262A LEU* 3.6 42.0 - - + +
263A GLY 5.2 0.7 - - - -
264A LEU* 4.0 27.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ALA* 3.2 31.6 - - + +
100A GLN 3.4 24.0 - - - +
101A GLN* 4.8 6.1 - - + +
102A LEU* 2.8 46.3 + - + +
143A ILE* 4.1 9.4 - - + -
191A LEU* 4.5 7.4 - - + -
192A VAL* 3.9 12.6 - - + +
220A SER 3.3 16.4 + - - +
221A LYS 3.7 4.9 - - - +
222A LYS 3.2 0.4 - - - -
223A LEU* 1.3 76.8 - - - +
225A GLU* 1.3 58.0 + - - +
226A GLY 3.4 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A LEU* 4.0 7.9 - - + -
104A TRP* 2.7 29.7 + - - -
112A LEU* 4.6 0.7 - - - +
114A ASP* 2.5 31.3 - - - +
141A PRO* 2.9 32.0 - - + +
143A ILE* 3.3 23.9 + - + +
221A LYS 3.3 14.9 - - - +
222A LYS* 3.0 39.5 + - - +
223A LEU 3.1 1.0 - - - -
224A VAL* 1.3 77.4 - - - +
226A GLY* 1.3 58.6 + - - +
227A LEU* 3.6 13.9 - - + +
----------------------------------------------------------
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