Contacts of the helix formed by residues 203 - 220 (chain N) in PDB entry 2QJK
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 203 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191N ASP* 3.7 17.5 - - - -
192N ASP* 5.5 0.9 - - - -
201N ASP* 2.6 25.8 + - - +
202N ALA* 1.3 76.2 - - - +
204N VAL* 1.3 67.1 + - - +
205N HIS* 3.8 11.8 + - - +
206N ALA* 2.6 27.2 + - - +
207N MET* 3.1 8.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 204 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135N LEU 4.9 8.5 - - - +
136N THR* 5.4 5.4 - - - -
189N LEU* 3.4 24.7 - - + +
190N MET* 3.1 20.2 - - - +
191N ASP* 2.9 47.3 + - - +
202N ALA 3.5 2.7 + - - -
203N SER* 1.3 70.9 - - - +
205N HIS* 1.3 62.5 + - - +
207N MET* 4.5 8.5 - - - -
208N ALA* 3.2 23.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 205 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9N VAL* 6.3 0.4 - - - +
132N TYR* 3.1 34.8 + - - +
136N THR* 5.5 3.6 - - - -
201N ASP* 5.6 0.2 + - - -
203N SER* 2.7 14.7 + - - +
204N VAL* 1.3 77.6 - - - +
206N ALA* 1.3 69.3 + - + +
208N ALA* 4.9 1.3 - - - -
209N GLU* 3.2 43.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 206 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200N HIS* 4.9 5.2 - - + +
201N ASP* 3.5 32.3 - - - +
203N SER* 2.6 22.1 + - - +
205N HIS* 1.3 82.2 + - - +
207N MET* 1.3 67.6 + - - +
209N GLU* 2.7 19.0 + - - +
210N ASP* 2.8 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 207 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31N VAL* 4.4 16.8 - - + +
35N VAL* 4.7 3.8 - - + -
189N LEU* 4.3 18.2 - - + -
190N MET 4.5 7.2 - - - +
193N LEU* 4.1 16.6 - - + -
194N VAL* 3.3 46.4 - - + +
196N TYR* 3.9 21.3 + - - +
202N ALA* 3.5 28.3 - - + +
203N SER 3.1 6.5 + - - +
204N VAL* 4.0 11.9 - - - +
206N ALA* 1.3 76.4 - - - +
208N ALA* 1.3 58.6 + - - +
210N ASP* 3.0 2.9 + - - +
211N VAL* 2.8 35.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 208 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132N TYR* 3.8 18.4 - - + +
135N LEU* 3.8 28.7 - - + -
136N THR* 4.4 3.8 - - - +
189N LEU* 3.8 14.7 - - + +
204N VAL* 3.2 16.5 + - + +
205N HIS 3.8 2.0 - - - +
206N ALA 3.2 0.4 - - - -
207N MET* 1.3 77.7 - - - +
209N GLU* 1.3 66.3 + - - +
211N VAL* 3.4 1.6 - - - +
212N SER* 2.8 29.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 209 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9N VAL* 4.0 20.2 - - + +
10N PRO 5.2 3.8 - - - +
11N PHE* 3.1 42.0 - - + -
24N GLN* 3.6 17.5 + - - +
132N TYR* 3.5 14.8 - - + -
205N HIS* 3.2 35.9 + - - +
206N ALA* 2.7 15.5 + - - +
208N ALA* 1.3 75.7 - - - +
210N ASP* 1.3 64.4 + - - +
212N SER* 3.5 0.4 - - - -
213N ALA* 3.3 5.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 210 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24N GLN* 2.8 42.7 + - + +
27N ARG* 3.2 31.7 + - - -
28N GLY* 4.1 17.3 - - - +
196N TYR* 3.5 18.1 + - - +
200N HIS* 4.6 1.7 + - - -
206N ALA* 2.8 22.6 + - - +
207N MET 3.5 5.2 - - - +
209N GLU* 1.3 72.5 - - - +
211N VAL* 1.3 55.7 + - - +
212N SER 2.6 16.1 + - - -
213N ALA* 2.7 16.6 + - - +
214N PHE* 2.8 10.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 211 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28N GLY* 3.8 14.8 - - - +
31N VAL* 3.8 31.0 - - + -
32N TYR* 3.9 16.8 - - + +
36N CYS* 4.1 14.1 - - - -
135N LEU* 3.6 24.9 - - + -
189N LEU* 5.7 0.4 - - + -
207N MET 2.8 16.2 + - - +
208N ALA* 3.4 12.1 - - - +
210N ASP* 1.3 73.2 - - - +
212N SER* 1.3 60.5 + - - +
214N PHE* 3.3 2.3 - - + +
215N LEU* 2.8 39.9 + - + +
301N HEM 4.1 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 212 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11N PHE* 3.8 16.6 - - - -
128N PRO* 3.6 14.2 + - - +
131N ILE* 3.9 11.8 - - - +
132N TYR* 3.5 25.5 + - - +
135N LEU* 4.5 0.5 - - - +
208N ALA 2.8 19.1 + - - -
209N GLU 3.5 5.6 - - - -
210N ASP 2.6 4.8 + - - -
211N VAL* 1.3 73.6 - - - +
213N ALA* 1.3 54.5 + - - -
215N LEU* 2.7 13.4 + - - +
216N MET* 2.6 35.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 213 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11N PHE* 4.2 4.4 - - + -
13N PHE* 3.7 27.8 - - + -
20N PHE* 3.8 2.1 - - - -
24N GLN* 3.7 28.7 - - + +
25N LEU* 3.3 15.2 - - + +
209N GLU 3.3 9.5 + - - +
210N ASP 2.7 12.0 + - - +
212N SER* 1.3 75.4 - - - +
214N PHE* 1.3 61.0 + - - +
216N MET* 3.1 4.3 + - - +
217N TRP 3.0 17.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 214 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25N LEU* 3.6 28.1 - - + +
28N GLY* 3.8 20.2 - - - -
29N LEU* 3.8 31.0 - - + -
32N TYR* 3.5 25.1 - + + -
42N MET* 3.3 39.0 - - + -
45N VAL* 6.3 0.2 - - + -
50N LEU* 4.7 3.1 - - + -
56N PRO* 4.8 2.5 - - + -
89N PHE* 5.0 3.6 - + - -
210N ASP 2.8 5.7 + - - -
211N VAL* 3.3 10.8 - - + +
213N ALA* 1.3 76.2 - - - +
215N LEU* 1.3 64.5 + - + +
217N TRP* 2.8 42.4 + + - +
218N ALA* 2.7 31.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 215 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32N TYR* 5.1 2.9 - - + -
36N CYS* 5.7 0.2 - - - -
42N MET* 4.1 18.6 - - + -
100N LEU* 3.7 56.8 - - + +
103N MET* 5.7 0.2 - - + -
104N ALA* 3.8 6.3 + - + +
131N ILE* 4.4 29.4 - - + -
211N VAL* 2.8 21.5 + - + +
212N SER* 2.7 14.6 + - - +
214N PHE* 1.3 82.2 - - + +
216N MET* 1.3 60.3 + - - -
218N ALA* 3.6 4.5 - - + +
219N ALA* 3.2 22.0 + - - +
301N HEM 4.2 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 216 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431M BGL 5.4 6.3 - - - +
13N PHE* 3.5 42.8 - - + -
20N PHE* 4.0 10.1 - - + -
104N ALA* 3.8 27.8 - - - +
105N LYS* 5.7 3.6 - - + -
128N PRO* 4.4 17.0 - - + -
212N SER 2.6 13.6 + - - +
213N ALA 3.3 9.6 - - - +
214N PHE 3.0 0.2 - - - -
215N LEU* 1.3 71.1 - - - +
217N TRP* 1.3 66.1 + - - +
219N ALA* 3.2 3.7 + - - +
220N GLU* 2.9 31.7 + - + +
223N LEU* 4.4 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 217 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20N PHE* 3.3 30.0 - + + -
25N LEU* 3.9 11.9 - - + -
45N VAL* 4.7 8.7 - - + -
49N SER* 3.5 48.5 - - - -
50N LEU* 4.1 10.5 - - + -
52N GLU* 5.3 2.8 + - + +
53N PRO 5.8 0.2 + - - -
54N GLY 3.9 8.7 + - - -
55N GLY* 3.5 21.9 - - - +
56N PRO* 3.6 21.8 - - + -
213N ALA 3.0 7.2 + - - +
214N PHE* 2.8 41.7 + + - +
216N MET* 1.3 74.0 - - - +
218N ALA* 1.3 89.2 + - + +
220N GLU 2.9 1.9 + - - +
221N PRO* 2.8 62.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 218 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85M ARG* 2.8 30.9 + - - -
42N MET* 3.8 28.7 - - - -
45N VAL* 3.9 8.2 - - + +
101N SER 3.9 4.3 - - - +
214N PHE* 2.7 19.2 + - + +
215N LEU* 3.6 17.3 - - + +
217N TRP* 1.3 94.7 - - + +
219N ALA* 1.3 56.4 + - - +
221N PRO* 3.7 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 219 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81M GLU* 4.5 2.6 - - - +
85M ARG* 3.8 8.2 + - - +
101N SER 3.1 20.9 - - - +
102N LEU* 3.9 24.8 - - + +
104N ALA* 4.7 8.3 - - + +
105N LYS* 3.8 22.9 + - + -
215N LEU 3.2 11.1 + - - +
216N MET* 3.2 4.5 + - - +
217N TRP 3.0 0.6 - - - -
218N ALA* 1.3 80.5 - - - +
220N GLU* 1.3 59.2 + - + +
221N PRO* 3.3 9.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 220 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84M MET* 5.0 3.6 - - - +
91M PHE* 5.5 2.1 - - - +
95M TYR* 2.7 28.9 + - - -
272M ASN* 4.3 2.3 + - - +
20N PHE* 4.1 4.7 - - - -
105N LYS* 3.6 27.5 + - + -
216N MET* 2.9 22.2 + - + +
217N TRP 2.9 6.7 + - - -
219N ALA* 1.3 76.9 - - - +
221N PRO* 1.3 65.6 - - - +
222N LYS* 3.2 10.3 + - - +
223N LEU* 3.0 34.4 + - + +
226N ARG* 2.2 35.3 + - - +
----------------------------------------------------------
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