Contacts of the helix formed by residues 185 - 200 (chain E) in PDB entry 3KHU
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 185 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155E GLN* 5.3 0.3 + - - -
183E ASP* 3.0 19.0 + - + +
184E GLU* 1.3 83.0 - - - +
186E PRO* 1.3 77.6 - - + +
187E GLU* 3.8 5.3 + - - +
188E GLY* 3.0 21.1 + - - -
189E GLN* 2.9 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 186 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184E GLU 4.7 0.9 - - - +
185E THR* 1.3 88.5 - - + +
187E GLU* 1.3 62.3 + - + +
189E GLN* 3.4 6.1 + - + +
190E ARG* 3.1 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 187 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123E TYR* 4.0 10.9 + - - -
153E ASN* 2.7 32.0 + - - +
155E GLN* 3.5 24.3 + - - +
185E THR* 3.3 5.0 + - - +
186E PRO* 1.3 77.6 - - + +
188E GLY* 1.3 66.7 + - - +
190E ARG* 3.2 22.2 + - - +
191E ALA* 3.1 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 188 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155E GLN* 3.9 9.1 + - - -
157E LEU* 4.2 3.1 - - - +
183E ASP* 3.7 23.8 - - - -
185E THR* 3.0 19.9 + - - -
187E GLU* 1.3 77.3 - - - +
189E GLN* 1.3 56.4 + - - +
191E ALA* 3.2 6.4 + - - +
192E VAL* 3.0 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 189 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182E GLY 4.3 3.8 + - - -
183E ASP 2.9 24.8 + - - +
184E GLU* 4.1 12.1 - - - +
185E THR 2.9 18.1 + - - +
186E PRO* 4.0 6.3 - - + +
187E GLU 3.2 0.2 - - - -
188E GLY* 1.3 72.1 - - - +
190E ARG* 1.3 59.7 + - - +
192E VAL* 3.4 23.1 + - - +
193E GLN* 2.9 30.0 + - - +
210E THR* 5.1 6.1 + - - -
211E THR 5.3 3.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 190 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1E MET* 3.3 33.9 - - - +
2E PHE* 3.4 43.0 - - + +
123E TYR* 4.6 15.5 + - - +
186E PRO 3.1 14.0 + - - +
187E GLU* 3.4 26.9 + - - +
188E GLY 3.2 0.2 - - - -
189E GLN* 1.3 75.8 - - - +
191E ALA* 1.3 63.9 + - - +
193E GLN* 3.5 6.0 + - - +
194E ALA* 3.1 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 191 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123E TYR* 3.8 17.9 + - - +
125E ILE* 4.0 14.1 - - + +
155E GLN* 3.9 20.9 - - + -
157E LEU* 3.7 21.5 - - + +
187E GLU 3.1 12.5 + - - +
188E GLY* 3.2 8.9 + - - +
190E ARG* 1.3 75.6 - - - +
192E VAL* 1.3 65.2 + - - +
194E ALA* 3.1 4.3 + - - +
195E LEU* 3.1 17.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 192 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157E LEU* 3.7 23.6 - - + -
180E ILE* 4.0 13.1 - - + +
182E GLY* 3.9 19.5 - - - +
188E GLY 3.0 18.1 + - - +
189E GLN* 3.7 24.9 - - - +
190E ARG 3.4 0.2 - - - -
191E ALA* 1.3 75.0 - - - +
193E GLN* 1.3 64.3 + - - +
195E LEU* 3.1 4.9 + - - +
196E CYS* 2.9 23.6 + - - -
210E THR* 3.7 35.2 - - + -
211E THR 5.3 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 193 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1E MET 5.9 4.7 - - - +
189E GLN 2.9 17.6 + - - +
190E ARG* 3.8 6.5 - - - +
191E ALA 3.3 0.2 - - - -
192E VAL* 1.3 76.4 - - - +
194E ALA* 1.3 64.7 + - - +
196E CYS* 3.1 12.4 + - + +
197E ALA* 2.9 25.1 + - + +
200E GLU* 6.0 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 194 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2E PHE* 3.8 36.1 - - + +
4E ILE* 3.5 16.8 + - + +
125E ILE* 3.8 19.3 - - + -
190E ARG 3.1 14.2 + - - +
191E ALA 3.1 8.5 + - - +
193E GLN* 1.3 78.4 - - - +
195E LEU* 1.3 60.6 + - - +
197E ALA* 3.4 12.3 + - - +
198E VAL* 3.4 9.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 195 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4E ILE* 4.0 6.0 - - + +
23E ILE* 6.2 0.2 - - + -
84E LEU* 3.9 30.5 - - + -
86E PHE* 4.2 8.1 - - + -
125E ILE* 5.7 0.2 - - + -
127E THR* 4.1 8.5 - - + +
157E LEU* 3.9 23.8 - - + -
159E ASN* 4.0 20.2 - - + +
180E ILE* 3.8 27.6 - - + -
191E ALA 3.1 12.0 + - - +
192E VAL 3.7 6.5 - - - +
194E ALA* 1.3 73.6 - - - +
196E CYS* 1.3 67.3 + - - +
198E VAL* 3.1 21.8 + - + +
199E TYR* 3.3 25.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 196 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180E ILE* 3.8 15.6 - - - +
192E VAL* 2.9 22.5 + - - -
193E GLN* 3.3 12.1 - - + +
195E LEU* 1.3 76.4 - - - +
197E ALA* 1.3 57.1 + - - +
199E TYR* 3.0 7.9 + - - +
200E GLU* 2.8 41.2 + - - +
205E ARG* 4.6 10.8 - - - +
208E ILE* 3.9 15.4 - - + +
210E THR* 3.7 29.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 197 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2E PHE 5.6 3.1 - - - +
3E GLU* 6.5 1.6 - - + -
193E GLN* 2.9 14.9 + - + +
194E ALA* 3.6 13.0 - - - +
195E LEU 3.2 0.2 - - - -
196E CYS* 1.3 74.9 - - - +
198E VAL* 1.3 63.4 + - + +
200E GLU* 3.5 21.1 + - - +
201E HIS* 2.9 23.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 198 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4E ILE* 3.8 30.7 - - + +
7E ILE* 4.7 6.5 - - + -
23E ILE* 3.9 33.7 - - + -
27E CYS* 3.8 7.8 - - - -
30E ILE* 4.3 12.8 - - + -
194E ALA 3.7 13.7 - - - +
195E LEU* 3.1 16.1 + - + +
196E CYS 3.1 0.8 - - - -
197E ALA* 1.3 77.5 - - - +
199E TYR* 1.3 68.4 + - + +
201E HIS* 2.9 30.8 + - + +
202E TRP* 3.7 6.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 199 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19E THR* 4.5 5.9 - - + +
23E ILE* 4.8 8.9 - - + +
86E PHE* 4.6 2.5 - + - -
129E LYS* 3.7 7.3 + - - -
159E ASN* 2.6 31.9 + - - -
161E GLN* 3.2 20.0 + - - -
172E LEU* 6.2 2.0 - - + -
178E VAL* 3.7 40.8 - - + -
180E ILE* 4.2 5.8 - - + -
195E LEU* 3.3 34.2 + - + -
196E CYS* 3.0 7.4 + - - +
198E VAL* 1.3 81.7 - - + +
200E GLU* 1.3 58.9 + - - +
201E HIS 3.0 0.2 - - - -
202E TRP* 3.0 39.3 + + - -
203E VAL* 2.8 30.2 + - + +
208E ILE* 4.0 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 200 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193E GLN* 5.2 1.4 - - - +
196E CYS* 2.8 25.4 + - - +
197E ALA* 3.8 19.4 + - - +
198E VAL 3.1 1.0 + - - -
199E TYR* 1.3 75.5 - - - +
201E HIS* 1.3 62.2 + - - +
202E TRP* 3.1 1.3 + - - -
203E VAL 3.6 14.4 + - - +
205E ARG* 3.7 33.3 + - - +
208E ILE* 3.6 16.6 - - + -
----------------------------------------------------------
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