Contacts of the helix formed by residues 203 - 218 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B PHE* 3.9 13.5 - + - -
127B TYR* 4.5 6.3 + - - -
178B LEU* 3.6 25.9 + - + +
179B LYS* 3.6 35.9 + - + +
197B GLY 3.8 2.0 + - - -
200B CYS 3.0 12.4 + - - +
201B LEU 3.1 1.8 + - - -
202B GLY* 1.3 79.9 - - - +
204B PRO* 1.4 67.4 - - + +
205B LEU* 3.1 43.3 + - + +
206B ASN* 2.8 39.8 + - - +
207B ALA 3.7 0.7 + - - -
90E ASP* 3.6 26.6 + - + +
168E GLY* 5.7 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 204 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B ILE* 3.8 27.4 - - + -
110B LEU* 6.0 0.2 - - + -
178B LEU* 3.3 30.3 - - + +
197B GLY* 3.3 17.9 - - - +
200B CYS* 3.7 18.1 - - + +
203B HIS* 1.4 90.7 - - + +
205B LEU* 1.3 66.1 + - + +
207B ALA* 3.2 14.9 + - - +
208B ALA 3.2 8.5 + - - -
230B THR* 3.7 25.8 - - + +
233B LEU* 4.9 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 205 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B LEU* 3.7 22.0 - - + -
123B PHE* 3.5 24.9 - - + +
126B LEU* 3.8 12.8 - - + -
127B TYR* 3.6 50.7 - - + +
130B ILE* 3.5 25.4 - - + -
178B LEU* 4.2 12.3 - - + -
203B HIS* 3.1 16.8 + - + +
204B PRO* 1.3 75.8 - - + +
206B ASN* 1.3 59.7 + - - +
208B ALA* 3.6 4.8 - - - +
209B VAL* 2.9 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 206 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B PHE* 3.4 22.0 - - - -
201B LEU* 3.0 33.4 + - + +
202B GLY* 4.1 1.0 - - - -
203B HIS* 2.8 19.7 + - - +
205B LEU* 1.3 75.6 - - - +
207B ALA* 1.3 59.8 + - - +
209B VAL* 3.3 5.7 + - - +
210B TRP* 2.9 30.7 + - - +
89E GLY* 3.5 5.7 - - - -
90E ASP 3.0 24.8 + - - -
91E ASN 4.6 0.2 - - - -
92E GLU* 3.4 30.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 207 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B VAL* 3.9 20.0 - - + +
64B THR* 4.5 3.8 - - + -
200B CYS* 4.6 4.3 - - - -
201B LEU* 3.9 17.5 - - + +
203B HIS 3.7 1.6 + - - -
204B PRO* 3.2 9.7 + - + +
206B ASN* 1.3 79.0 - - - +
208B ALA* 1.3 56.6 + - - +
210B TRP* 3.4 4.1 + - - +
211B LEU* 2.9 29.8 + - - +
230B THR* 3.2 31.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 208 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B LEU* 3.7 23.3 - - + -
126B LEU* 3.5 31.1 - - + +
204B PRO 3.2 6.6 + - - +
205B LEU* 3.6 3.1 - - - +
206B ASN 3.3 0.2 - - - -
207B ALA* 1.3 80.4 - - - +
209B VAL* 1.3 56.5 + - - +
211B LEU* 3.3 6.1 + - - +
212B ALA* 2.9 30.5 + - - +
228B ILE* 4.6 17.0 - - + +
230B THR* 4.5 3.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 209 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B ILE* 3.6 13.9 - - + +
122B THR 4.3 0.9 - - - -
123B PHE* 3.8 33.9 - - + +
126B LEU* 4.1 20.4 - - + -
205B LEU 2.9 22.7 + - - +
206B ASN* 3.3 6.7 + - - +
208B ALA* 1.3 72.1 - - - +
210B TRP* 1.3 69.1 + - - +
212B ALA* 3.2 4.7 + - - +
213B ARG* 3.1 56.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 210 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B TYR* 4.4 6.3 - - - -
61B VAL* 4.2 9.0 - - + -
76B GLN* 3.7 30.6 + - - +
77B PRO* 3.5 40.0 - - + +
78B ASP* 3.6 39.3 - - - -
79B PHE* 4.2 12.3 - + + -
201B LEU* 4.5 7.9 - - + -
206B ASN 2.9 17.0 + - - +
207B ALA* 3.6 5.6 - - - +
209B VAL* 1.3 80.0 - - - +
211B LEU* 1.3 90.4 + - + +
213B ARG* 3.4 10.4 + - - +
214B LYS* 3.1 46.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 211 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B ARG* 3.8 26.5 - - + -
61B VAL* 3.8 15.7 - - + -
79B PHE* 3.8 30.1 - - + -
207B ALA 2.9 17.2 + - - +
208B ALA 3.7 3.6 - - - +
210B TRP* 1.3 82.5 - - + +
212B ALA* 1.3 66.6 + - - +
213B ARG 3.2 0.2 + - - -
214B LYS* 3.2 2.0 + - - +
215B MET* 2.9 50.1 + - + +
222B LEU* 4.2 5.6 - - + -
228B ILE* 3.6 40.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 212 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B LEU* 4.0 34.0 - - + +
118B ALA 4.6 0.8 - - - +
121B ILE* 3.8 19.5 - - + -
126B LEU* 4.4 4.0 - - + -
208B ALA 2.9 17.7 + - - +
209B VAL 3.2 4.5 + - - +
211B LEU* 1.3 75.5 - - - +
213B ARG* 1.3 61.1 + - - +
215B MET* 4.0 1.6 - - - +
216B ALA* 3.1 25.1 + - - +
222B LEU* 3.9 14.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 213 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B ALA 4.6 1.3 - - - -
119B THR* 3.4 24.7 - - - +
120B ASP 4.0 0.2 - - - -
121B ILE* 2.8 33.2 + - + +
122B THR* 4.2 4.2 - - - +
123B PHE 5.2 0.6 - - - +
209B VAL* 3.1 32.6 + - - +
210B TRP* 3.6 11.9 - - - +
212B ALA* 1.3 74.5 - - - +
214B LYS* 1.3 64.6 + - - +
216B ALA* 3.2 7.1 + - - +
217B SER* 2.9 24.9 + - - -
87E CYS 4.8 8.3 + - - -
1F MET* 2.6 52.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 214 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B TYR* 4.2 24.7 + - - -
76B GLN* 4.3 20.9 - - - +
79B PHE* 4.5 7.3 - - + -
210B TRP* 3.1 38.2 + - + +
211B LEU* 3.5 9.9 - - - +
213B ARG* 1.3 77.8 - - - +
215B MET* 1.3 68.1 + - + +
217B SER* 3.1 12.1 + - - +
218B LEU* 2.9 52.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B ARG* 3.8 34.1 - - - -
79B PHE* 3.1 47.8 - - + -
211B LEU* 2.9 29.6 + - + +
212B ALA 4.0 3.6 - - - +
214B LYS* 1.3 85.1 - - + +
216B ALA* 1.3 60.7 - - - +
218B LEU* 3.3 12.9 + - + +
220B GLU* 2.9 49.2 + - - +
222B LEU* 3.9 28.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 216 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B LEU 4.0 3.8 - - - +
117B PRO 3.4 28.3 - - - +
118B ALA 3.9 9.6 - - - +
119B THR* 3.8 15.0 - - + +
212B ALA 3.1 19.7 + - - +
213B ARG 3.5 4.0 - - - +
215B MET* 1.3 77.2 - - - +
217B SER* 1.3 57.1 + - - +
219B GLY* 3.1 17.5 + - - -
221B PRO* 4.2 14.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 217 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B THR* 4.0 17.0 - - - -
213B ARG 2.9 15.0 + - - -
214B LYS* 3.1 18.9 + - - +
216B ALA* 1.3 72.9 - - - +
218B LEU* 1.3 67.7 + - - +
219B GLY 3.1 5.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 218 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B TYR* 5.8 2.9 - - + -
79B PHE* 3.9 34.1 - - + -
214B LYS* 2.9 27.0 + - + +
215B MET* 3.7 16.8 - - + +
216B ALA 3.2 0.6 - - - -
217B SER* 1.3 84.7 + - - +
219B GLY* 1.3 60.1 + - - +
220B GLU* 3.5 21.4 + - + +
----------------------------------------------------------
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