Contacts of the helix formed by residues 203 - 220 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191E ASP* 3.8 17.3 - - - -
192E ASP* 5.2 1.1 + - - -
201E ASP* 2.6 26.6 + - - +
202E ALA* 1.3 76.8 - - - +
204E VAL* 1.3 68.0 + - - +
205E HIS* 3.9 11.9 + - - +
206E ALA* 2.6 26.9 + - - +
207E MET* 3.1 8.7 + - - -
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Residues in contact with VAL 204 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135E LEU 4.9 10.3 - - - +
136E THR* 5.4 5.8 - - - +
189E LEU* 3.4 27.5 - - + +
190E MET* 3.2 19.7 - - - +
191E ASP* 2.9 46.9 - - - +
202E ALA 3.5 3.2 + - - -
203E SER* 1.3 69.8 - - - +
205E HIS* 1.3 64.1 + - - +
207E MET* 4.5 3.8 - - - -
208E ALA* 3.2 24.7 + - + +
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Residues in contact with HIS 205 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132E TYR* 3.1 35.6 + - - +
136E THR* 5.4 3.6 - - - -
203E SER* 2.7 15.1 + - - +
204E VAL* 1.3 78.6 - - - +
206E ALA* 1.3 69.7 + - + +
208E ALA* 4.9 1.3 - - - -
209E GLU* 3.2 43.4 + - + +
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Residues in contact with ALA 206 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196E TYR* 5.3 0.2 - - + -
200E HIS* 5.2 3.6 - - + +
201E ASP* 3.5 31.2 - - - +
203E SER* 2.6 21.6 + - - +
205E HIS* 1.3 80.2 + - + +
207E MET* 1.3 70.0 + - - +
209E GLU* 2.7 20.4 + - - +
210E ASP* 2.8 22.7 + - - +
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Residues in contact with MET 207 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E VAL* 4.4 18.7 - - + +
35E VAL* 4.7 1.8 - - + -
189E LEU* 3.7 26.2 - - + -
190E MET 4.6 5.6 - - - +
193E LEU* 4.2 15.7 - - + -
194E VAL* 3.4 46.0 - - + +
196E TYR* 3.8 20.8 + - + +
202E ALA* 3.6 28.7 - - + +
203E SER 3.1 7.4 + - - +
204E VAL* 3.9 6.1 - - - +
206E ALA* 1.3 77.2 - - - +
208E ALA* 1.3 60.0 + - - +
210E ASP* 3.0 3.1 + - - +
211E VAL* 2.8 34.7 + - - +
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Residues in contact with ALA 208 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132E TYR* 3.8 17.3 - - + +
135E LEU* 3.9 28.7 - - + -
136E THR* 4.4 4.7 - - - +
189E LEU* 3.7 4.8 - - + +
204E VAL* 3.2 15.6 + - + +
205E HIS 3.7 4.0 - - - +
206E ALA 3.1 0.4 - - - -
207E MET* 1.3 78.0 - - - +
209E GLU* 1.3 63.6 + - - +
211E VAL* 3.3 9.9 - - - +
212E SER* 2.8 31.1 + - - -
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Residues in contact with GLU 209 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E VAL* 4.0 19.8 - - + +
10E PRO* 5.2 4.3 - - - +
11E PHE* 3.1 42.1 - - + -
24E GLN* 3.6 16.6 + - - +
132E TYR* 3.5 15.2 - - + -
205E HIS* 3.2 33.6 + - - +
206E ALA* 2.7 16.4 + - - +
208E ALA* 1.3 75.7 - - - +
210E ASP* 1.3 62.7 + - - +
212E SER* 3.5 0.2 - - - -
213E ALA* 3.3 5.9 + - - +
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Residues in contact with ASP 210 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E GLN* 2.8 44.0 + - + +
27E ARG* 3.2 30.5 + - - -
28E GLY* 4.2 14.1 - - - +
196E TYR* 3.2 23.1 + - - +
200E HIS* 4.8 1.4 - - - -
206E ALA* 2.8 21.5 + - - +
207E MET 3.0 6.4 + - - +
209E GLU* 1.3 73.7 - - - +
211E VAL* 1.3 55.0 + - - +
212E SER 2.6 5.3 + - - -
213E ALA* 2.6 28.4 + - - +
214E PHE* 2.8 9.4 + - - +
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Residues in contact with VAL 211 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28E GLY* 3.8 14.2 - - - +
31E VAL* 3.8 31.6 - - + +
32E TYR* 4.0 16.4 - - + +
36E CYS* 4.0 15.3 - - - -
135E LEU* 3.6 26.5 - - + -
207E MET 2.8 15.8 + - - +
208E ALA* 3.3 11.7 - - - +
210E ASP* 1.3 72.6 - - - +
212E SER* 1.3 60.2 + - - +
214E PHE* 3.4 2.9 - - + +
215E LEU* 2.8 41.6 + - + +
301E HEM 4.1 8.3 - - + -
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Residues in contact with SER 212 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E PHE* 3.8 16.2 - - - -
104E ALA* 5.2 0.3 - - - +
128E PRO* 3.9 14.9 - - - +
131E ILE* 3.8 11.3 - - - +
132E TYR* 3.5 25.8 + - - +
135E LEU* 4.5 0.2 - - - +
208E ALA 2.8 19.0 + - - -
209E GLU 3.5 5.8 - - - -
210E ASP 2.6 4.4 + - - -
211E VAL* 1.3 74.9 - - - +
213E ALA* 1.3 53.7 + - - -
215E LEU* 2.6 30.7 + - - +
216E MET* 2.6 18.9 + - - +
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Residues in contact with ALA 213 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E PHE* 4.2 4.6 - - + -
13E PHE* 3.8 27.6 - - + -
20E PHE* 3.8 2.4 - - - -
24E GLN* 3.7 29.2 - - + +
25E LEU* 3.2 14.7 - - + +
209E GLU 3.3 9.0 + - - +
210E ASP 2.6 11.7 + - - +
212E SER* 1.3 75.6 - - - +
214E PHE* 1.3 63.2 + - - +
216E MET* 3.1 3.8 + - - +
217E TRP 3.0 17.3 + - - -
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Residues in contact with PHE 214 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E LEU* 3.6 26.3 - - - +
28E GLY* 3.8 19.3 - - - -
29E LEU* 3.8 30.1 - - + -
32E TYR* 3.5 26.0 - + + -
42E MET* 3.2 38.4 - - + -
50E LEU* 4.7 3.1 - - + -
56E PRO* 4.8 2.9 - - + -
89E PHE* 5.0 3.4 - + - -
210E ASP 2.8 5.5 + - - -
211E VAL* 3.4 10.8 - - + +
213E ALA* 1.3 76.7 - - - +
215E LEU* 1.3 60.5 + - + +
217E TRP* 2.8 41.2 + + - +
218E ALA* 2.7 32.9 + - + -
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Residues in contact with LEU 215 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E TYR* 5.1 2.9 - - + -
36E CYS* 5.6 0.2 - - - -
42E MET* 4.1 19.3 - - + -
100E LEU* 3.8 55.0 - - + +
103E MET* 5.4 0.4 - - + -
104E ALA* 3.3 11.9 + - + +
131E ILE* 4.4 28.5 - - + -
211E VAL* 2.8 20.5 + - + +
212E SER* 2.6 15.6 + - - +
214E PHE* 1.3 82.6 - - + +
216E MET* 1.3 59.5 + - - -
218E ALA* 3.6 4.5 - - + +
219E ALA* 3.1 17.3 + - - +
301E HEM 4.3 18.2 - - + -
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Residues in contact with MET 216 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431D BGL 4.9 8.5 - - - +
13E PHE* 3.5 43.1 - - + -
20E PHE* 4.0 9.9 - - + -
104E ALA* 3.4 28.4 - - + +
105E LYS* 5.5 4.3 - - + -
128E PRO* 4.4 15.0 - - + -
212E SER 2.6 14.4 + - - +
213E ALA 3.3 9.6 - - - +
215E LEU* 1.3 74.1 - - - +
217E TRP* 1.3 57.8 + - - +
219E ALA* 3.2 3.3 + - - +
220E GLU* 2.9 38.0 + - + +
223E LEU* 4.4 15.0 - - + -
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Residues in contact with TRP 217 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85D ARG* 6.3 0.4 - - - -
20E PHE* 3.3 30.0 - + + -
25E LEU* 3.9 12.6 - - + -
45E VAL* 4.7 9.9 - - + -
49E SER* 3.5 47.3 - - - -
50E LEU* 4.1 10.8 - - + -
52E GLU* 5.7 0.6 + - + -
53E PRO 5.8 0.2 + - - -
54E GLY 3.9 8.4 + - - -
55E GLY* 3.5 22.3 - - - +
56E PRO* 3.6 22.2 - - + -
213E ALA 3.0 7.2 + - - +
214E PHE* 2.8 39.1 + + - +
216E MET* 1.3 74.4 - - - +
218E ALA* 1.3 91.7 + - + +
219E ALA 2.9 0.7 + - - -
220E GLU 2.9 0.6 + - - +
221E PRO* 2.8 60.5 + - + +
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Residues in contact with ALA 218 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D ARG* 2.9 29.8 + - - -
42E MET* 3.9 26.9 - - + -
45E VAL* 3.9 8.2 - - + +
101E SER 3.9 4.9 - - - +
214E PHE* 2.7 19.4 + - + +
215E LEU* 3.6 17.9 - - + +
217E TRP* 1.3 94.0 - - + +
219E ALA* 1.3 57.7 + - - +
221E PRO* 3.7 0.3 - - - +
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Residues in contact with ALA 219 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D GLU* 4.5 2.9 - - - +
85D ARG* 3.8 7.4 + - - +
101E SER 3.1 20.6 - - - +
102E LEU* 3.8 28.5 - - + +
104E ALA* 4.3 7.6 - - + -
105E LYS* 3.9 20.3 + - + +
215E LEU 3.1 13.6 + - - +
216E MET* 3.8 2.7 - - - +
217E TRP 2.9 1.6 + - - -
218E ALA* 1.3 77.0 - - - +
220E GLU* 1.3 59.2 + - + +
221E PRO* 3.2 13.0 - - - +
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Residues in contact with GLU 220 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D MET* 4.9 3.5 - - - +
91D PHE* 5.6 2.3 - - - +
95D TYR* 2.6 28.8 + - - -
272D ASN* 4.1 3.1 + - - +
20E PHE* 4.1 4.7 - - - -
105E LYS* 3.6 30.1 + - + +
216E MET* 2.9 27.6 + - + +
217E TRP 2.9 5.2 + - - -
219E ALA* 1.3 71.3 - - - +
221E PRO* 1.3 65.5 - - - +
222E LYS* 3.2 9.5 + - - +
223E LEU* 2.9 35.1 + - + +
226E ARG* 2.4 35.0 + - - +
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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) + - + + + + + -
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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