Contacts of the helix formed by residues 203 - 218 (chain I) in PDB entry 2WQT
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 HIS 203 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90F ASP* 3.5 33.5 + - + +
168F GLY* 5.5 4.4 - - - -
123I PHE* 3.8 13.9 - + + -
127I TYR* 4.5 6.9 + - - -
178I LEU* 3.7 21.6 + - + +
179I LYS* 3.6 27.6 + - + +
197I GLY 3.9 2.2 + - - -
200I CYS 3.0 10.9 + - - +
201I LEU 3.1 2.2 + - - -
202I GLY* 1.3 79.1 - - - +
204I PRO* 1.3 67.4 - - + +
205I LEU* 3.1 45.4 + - + +
206I ASN* 2.8 39.9 + - - +
207I ALA 3.7 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 204 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108I ILE* 3.9 25.8 - - + -
178I LEU* 3.4 28.9 - - + +
197I GLY* 3.4 19.1 - - - +
200I CYS* 4.0 17.7 - - + +
203I HIS* 1.3 88.6 - - + +
205I LEU* 1.3 66.4 + - + +
207I ALA* 3.2 8.1 + - - +
208I ALA 3.2 15.6 + - - -
230I THR* 3.7 27.4 - - + +
233I LEU* 4.9 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 205 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110I LEU* 3.7 22.0 - - + -
123I PHE* 3.5 25.1 - - + +
126I LEU* 3.7 11.9 - - + -
127I TYR* 3.6 51.6 - - + -
130I ILE* 3.6 24.7 - - + -
178I LEU* 4.2 11.7 - - + -
203I HIS* 3.1 14.6 + - + +
204I PRO* 1.3 75.4 - - + +
206I ASN* 1.3 60.6 + - - +
207I ALA 3.3 0.2 - - - -
208I ALA* 3.7 4.6 - - - +
209I VAL* 2.9 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 206 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89F GLY* 3.6 5.5 - - - -
90F ASP 2.9 25.6 + - - -
91F ASN 4.6 0.4 + - - -
92F GLU* 3.6 29.1 + - + +
123I PHE* 3.4 20.8 - - - -
201I LEU* 3.0 34.5 + - + +
202I GLY* 4.1 0.6 - - - -
203I HIS* 2.8 18.6 + - - +
205I LEU* 1.3 75.8 - - - +
207I ALA* 1.3 59.1 + - - +
209I VAL* 3.3 6.5 + - - +
210I TRP* 2.9 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 207 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61I VAL* 3.9 20.8 - - + +
64I THR* 4.5 4.0 - - + -
200I CYS* 4.6 4.3 - - - -
201I LEU* 3.9 17.5 - - + +
203I HIS 3.7 1.8 + - - -
204I PRO* 3.2 10.2 + - + +
206I ASN* 1.3 78.4 - - - +
208I ALA* 1.3 56.8 + - - +
210I TRP* 3.4 3.3 + - - +
211I LEU* 3.0 29.6 + - - +
230I THR* 3.1 31.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 208 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110I LEU* 3.8 23.3 - - + -
126I LEU* 3.5 30.3 - - + +
204I PRO 3.2 7.6 + - - +
205I LEU* 3.7 3.1 - - - +
206I ASN 3.3 0.2 - - - -
207I ALA* 1.3 76.5 - - - +
209I VAL* 1.3 60.5 + - - +
211I LEU* 3.4 5.6 + - - +
212I ALA* 2.9 31.0 + - - +
228I ILE* 4.5 16.6 - - + +
230I THR* 4.5 3.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 209 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92F GLU* 6.1 0.9 - - - +
121I ILE* 3.7 13.0 - - + +
122I THR 4.3 0.9 - - - -
123I PHE* 3.8 33.7 - - + +
126I LEU* 4.1 19.5 - - + -
205I LEU 2.9 26.9 + - - +
206I ASN* 3.3 6.7 + - - +
208I ALA* 1.3 74.4 - - - +
210I TRP* 1.3 65.2 + - - +
212I ALA* 3.2 5.4 + - - +
213I ARG* 3.1 58.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 210 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39I TYR* 4.3 6.1 - - - -
61I VAL* 4.2 9.2 - - + -
76I GLN* 3.7 30.8 + - - +
77I PRO* 3.5 39.1 - - + +
78I ASP* 3.6 37.9 - - - -
79I PHE* 4.2 12.6 - + + -
201I LEU* 4.5 7.0 - - + -
206I ASN 2.9 17.8 + - - +
207I ALA* 3.7 5.8 - - - +
209I VAL* 1.3 79.5 - - - +
211I LEU* 1.3 90.9 + - + +
213I ARG* 3.5 9.2 + - - +
214I LYS* 3.1 47.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 211 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59I ARG* 3.8 25.1 - - + -
61I VAL* 3.9 14.1 - - + -
79I PHE* 3.8 29.2 - - + -
207I ALA 3.0 18.1 + - - +
208I ALA 3.7 3.4 - - - +
210I TRP* 1.3 82.7 - - + +
212I ALA* 1.3 66.8 + - - +
214I LYS* 3.1 2.9 + - - +
215I MET* 2.9 45.5 + - + +
222I LEU* 4.1 5.6 - - + -
228I ILE* 3.7 40.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 212 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116I LEU* 4.0 34.3 - - + +
118I ALA 4.6 0.8 - - - +
121I ILE* 3.8 18.8 - - + -
126I LEU* 4.4 4.0 - - + -
208I ALA 2.9 18.7 + - - +
209I VAL 3.6 4.0 - - - +
211I LEU* 1.3 76.2 - - - +
213I ARG* 1.3 61.7 + - - +
215I MET* 3.6 1.9 + - - +
216I ALA* 3.1 24.8 + - - +
222I LEU* 3.9 14.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 213 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87F CYS 4.9 6.5 + - - -
92F GLU* 5.8 1.4 + - - -
118I ALA 4.6 0.2 - - - -
119I THR* 3.4 26.2 - - - +
120I ASP* 4.0 2.8 - - - +
121I ILE* 2.8 40.6 + - + +
122I THR* 4.3 4.2 - - - +
123I PHE 5.2 0.4 - - - +
209I VAL* 3.1 32.6 + - - +
210I TRP* 3.6 11.7 - - + +
212I ALA* 1.3 73.5 - - - +
214I LYS* 1.3 66.8 - - - +
216I ALA* 3.2 5.8 + - - +
217I SER* 2.9 25.0 + - - -
1N MET* 2.9 41.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 214 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39I TYR* 4.2 24.4 + - - -
76I GLN* 4.3 20.0 - - - +
79I PHE* 4.5 7.1 - - + -
210I TRP* 3.1 37.5 + - + +
211I LEU* 3.1 9.6 + - - +
213I ARG* 1.3 78.8 - - - +
215I MET* 1.3 68.7 + - + +
217I SER* 3.1 13.1 + - - +
218I LEU* 2.9 52.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 215 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59I ARG* 3.8 32.1 - - - -
79I PHE* 3.1 47.6 - - + -
211I LEU* 2.9 26.6 + - + +
212I ALA 4.0 3.4 - - - +
214I LYS* 1.3 84.2 - - + +
216I ALA* 1.3 60.2 + - - +
218I LEU* 3.3 14.5 + - + +
220I GLU* 2.9 51.8 + - - +
222I LEU* 3.8 31.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 216 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116I LEU 4.0 4.3 - - - +
117I PRO 3.4 28.7 - - - +
118I ALA 3.9 9.4 - - - +
119I THR* 3.8 15.6 - - + +
212I ALA 3.1 19.0 + - - +
213I ARG 3.5 4.3 - - - +
215I MET* 1.3 78.1 - - - +
217I SER* 1.3 60.8 + - - +
219I GLY* 3.2 13.9 + - - -
221I PRO* 4.2 12.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 217 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119I THR* 3.9 16.1 - - - +
213I ARG 2.9 14.7 + - - -
214I LYS* 3.1 18.7 + - - +
216I ALA* 1.3 73.9 - - - +
218I LEU* 1.3 67.9 + - - +
219I GLY 3.2 3.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 218 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39I TYR* 5.9 2.2 - - + -
79I PHE* 3.9 18.2 - - + -
214I LYS* 2.9 28.6 + - + +
215I MET* 3.7 33.4 - - + +
216I ALA 3.3 0.6 - - - -
217I SER* 1.3 84.2 + - - +
219I GLY* 1.3 61.6 + - - +
220I GLU* 3.5 20.9 + - + +
----------------------------------------------------------
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