Contacts of the helix formed by residues 211 - 224 (chain E) in PDB entry 4Q9U
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 ILE 211 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156E ILE* 6.4 2.2 - - + -
189E VAL* 6.3 3.1 - - + -
207E ILE* 3.9 21.5 - - + +
208E MET* 4.5 3.1 - - - +
209E ASP 3.1 1.0 + - - -
210E GLN* 1.3 104.9 - - - +
212E GLU* 1.3 77.4 + - + +
213E LYS 3.3 0.9 + - - -
214E TYR* 3.8 9.9 + - - +
215E ILE* 3.5 20.3 + - + +
343E ASN* 6.0 1.3 - - - +
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Residues in contact with GLU 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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186E TYR* 3.6 11.0 + - - -
208E MET 3.7 18.0 - - - +
209E ASP* 3.8 7.0 - - - +
210E GLN 3.4 0.8 - - - -
211E ILE* 1.3 79.8 - - + +
213E LYS* 1.3 64.9 + - - +
215E ILE* 3.1 17.4 - - + +
216E MET* 3.0 27.7 + - + +
283E VAL* 4.0 6.7 - - + -
284E PRO* 3.3 37.3 - - + +
285E ARG* 5.1 2.9 - - + +
341E PHE 3.5 12.1 - - - +
343E ASN* 3.3 33.3 + - - +
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Residues in contact with LYS 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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138E VAL* 6.2 5.6 - - + -
141E GLU* 6.1 2.7 - - - +
209E ASP 4.6 1.4 + - - +
210E GLN* 3.6 16.0 + - - +
211E ILE 3.3 1.2 - - - -
212E GLU* 1.3 77.5 - - - +
214E TYR* 1.3 63.8 + - - +
216E MET* 4.0 0.3 - - - +
217E THR* 3.0 36.5 + - - +
281E LYS* 3.5 25.8 - - - +
283E VAL* 3.8 21.5 - - + +
285E ARG* 3.1 36.8 - - - +
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Residues in contact with TYR 214 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135E THR* 5.6 1.1 + - - -
138E VAL* 3.7 35.9 - - + -
139E SER* 4.6 1.9 + - - -
141E GLU* 5.8 2.2 - - - +
142E PHE* 3.1 48.1 - + + -
160E THR* 5.1 14.6 - - + -
161E LYS* 6.0 0.7 - - - +
164E LEU* 4.9 15.0 - - + +
210E GLN 4.6 1.9 + - - +
211E ILE 3.8 8.5 + - - +
212E GLU 3.5 0.2 - - - -
213E LYS* 1.3 79.4 - - - +
215E ILE* 1.3 72.1 + - + +
217E THR* 3.8 8.6 + - - -
218E ARG* 3.8 46.5 + - + +
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Residues in contact with ILE 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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160E THR* 5.4 4.3 - - + -
163E PHE* 4.4 23.6 - - + -
164E LEU* 4.5 13.9 - - + -
211E ILE* 3.5 19.7 - - + +
212E GLU* 3.1 34.8 - - + +
214E TYR* 1.3 86.0 - - + +
216E MET* 1.3 89.5 + - + +
217E THR 3.2 1.0 + - - -
218E ARG* 3.3 5.5 + - - +
219E LEU* 3.0 26.3 + - + +
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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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212E GLU* 3.0 13.8 + - + +
213E LYS 4.4 1.1 - - - +
215E ILE* 1.3 104.9 - - + +
217E THR* 1.3 56.9 + - - +
219E LEU* 3.4 23.1 - - + -
220E TYR* 2.9 32.7 + - - +
282E ARG* 4.4 4.8 - - - +
283E VAL* 4.3 10.5 - - + -
284E PRO* 3.5 27.8 - - + -
337E TYR* 3.6 19.5 - - + +
341E PHE* 3.4 42.0 - - + +
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Residues in contact with THR 217 (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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630D VAL* 3.7 33.9 - - + +
134E GLU* 3.5 27.6 - - + +
138E VAL* 5.3 9.2 - - + +
213E LYS* 3.0 26.2 + - - +
214E TYR* 4.0 7.9 - - - -
215E ILE 3.2 0.4 + - - -
216E MET* 1.3 78.0 - - - +
218E ARG* 1.3 63.8 + - + +
220E TYR* 4.0 3.1 + - - +
221E LYS 5.0 0.7 + - - -
281E LYS* 6.1 1.0 - - - -
282E ARG* 3.3 30.0 + - - +
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Residues in contact with ARG 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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134E GLU* 4.7 16.4 - - + +
135E THR* 3.2 45.5 + - - +
139E SER* 5.6 1.4 + - - -
161E LYS* 4.2 20.6 - - - +
164E LEU* 3.8 29.4 - - + +
214E TYR* 3.8 35.6 + - + +
215E ILE* 3.3 6.3 + - - +
217E THR* 1.3 83.3 - - + +
219E LEU* 1.3 62.2 + - + +
221E LYS* 3.5 30.9 - - - +
222E TYR* 4.8 2.9 - - - -
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Residues in contact with LEU 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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215E ILE* 3.0 15.0 + - + +
216E MET* 3.4 39.9 - - + -
218E ARG* 1.3 77.0 - - + +
220E TYR* 1.3 58.0 - - - +
221E LYS 3.2 2.7 - - - -
222E TYR* 2.7 14.0 + - + -
223E VAL* 2.7 60.6 + - + -
337E TYR* 3.0 29.2 - - + +
341E PHE* 5.0 6.1 - - + -
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Residues in contact with TYR 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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625C GLN* 5.3 7.2 + - - -
627D GLN* 6.2 0.2 - - - -
216E MET 2.9 18.8 + - - +
217E THR 4.2 3.1 - - - +
218E ARG 3.4 1.0 - - - -
219E LEU* 1.3 74.9 - - - +
221E LYS* 1.3 70.5 + - + +
224E PHE* 3.0 63.8 + + + +
279E ASP 5.3 7.4 + - - -
282E ARG* 3.6 55.2 - - + +
287E LYS* 6.2 1.1 - - - -
330E ARG* 3.2 26.9 + - - -
337E TYR* 3.7 15.7 - + - +
565H ARG* 5.0 10.1 + - - -
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Residues in contact with LYS 221 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134E GLU* 5.7 4.2 + - - -
217E THR 5.0 0.8 + - - +
218E ARG* 3.5 22.4 + - - +
220E TYR* 1.3 88.9 - - + +
222E TYR* 1.3 104.8 + - + +
224E PHE 4.4 5.2 - - - +
227E GLU* 4.9 2.6 - - - +
282E ARG* 5.7 0.6 - - - +
562H LEU* 4.9 15.6 - - - +
565H ARG* 5.8 1.2 + - - -
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Residues in contact with TYR 222 (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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167E MET 5.6 0.2 - - - -
168E HIS* 4.1 27.6 - + + -
171E ARG* 3.8 64.2 + - + +
178E GLN* 4.8 9.7 + - - +
218E ARG 4.8 4.3 - - - -
219E LEU* 2.7 19.9 + - + +
221E LYS* 1.3 121.7 + - + +
223E VAL* 1.3 62.0 + - + +
224E PHE 3.6 2.6 - - - +
226E PRO* 4.6 10.9 - - - +
227E GLU* 4.8 6.8 - - - +
558H LYS* 5.3 2.6 + - - -
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Residues in contact with VAL 223 (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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175E ILE* 6.2 1.6 - - + -
178E GLN* 4.7 22.7 - - + +
219E LEU* 2.7 47.1 + - + -
222E TYR* 1.3 73.1 - - + +
224E PHE* 1.3 63.1 + - - +
226E PRO* 3.1 16.9 - - + +
337E TYR* 3.6 4.0 - - + -
340E ARG* 3.1 18.6 + - - +
341E PHE* 3.2 44.0 - - + -
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Residues in contact with PHE 224 (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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220E TYR* 3.0 66.1 + + + +
221E LYS 4.4 6.1 - - - +
222E TYR 4.4 1.2 - - - +
223E VAL* 1.3 76.5 - - - +
225E CYS* 1.3 73.7 + - + +
226E PRO* 3.4 0.9 - - - +
227E GLU* 4.9 0.5 - - - +
279E ASP* 3.6 7.0 - - - -
287E LYS* 5.7 2.2 - - - -
330E ARG* 3.4 36.1 - - + -
333E SER* 3.8 18.6 - - - -
334E ASN* 3.2 28.5 - - - -
337E TYR* 3.2 34.5 - + + -
565H ARG* 4.3 17.0 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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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