Contacts of the helix formed by residues 214 - 228 (chain T) in PDB entry 3EXG
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 ARG 214 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148T TRP* 4.0 12.5 + - - -
172T ASN* 3.7 35.2 - - - +
174T LEU* 3.6 37.3 + - - +
175T MET* 4.0 21.2 - - + +
178T VAL* 6.2 1.2 - - - +
213T SER* 1.3 79.2 + - - +
215T PRO* 1.3 70.1 - - + +
216T VAL 2.6 6.9 + - - -
217T GLY* 3.0 14.6 + - - -
218T HIS* 3.6 33.9 + - + +
313T ILE* 5.6 8.7 - - - +
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Residues in contact with PRO 215 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211T SER* 3.9 9.9 - - - +
212T HIS* 3.5 10.1 - - - +
213T SER* 3.5 6.3 - - - -
214T ARG* 1.3 97.0 - - + +
216T VAL* 1.3 60.8 + - - -
217T GLY 3.2 0.4 - - - -
218T HIS* 3.0 27.2 + - + +
219T CYS* 3.2 15.8 + - - -
262T VAL* 4.3 14.8 - - + -
263T GLU* 4.2 4.0 - - - -
264T GLY* 3.8 29.8 - - - +
313T ILE* 6.0 1.8 - - + -
314T PRO* 4.5 10.5 - - + -
319T ILE* 4.8 0.5 - - - +
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Residues in contact with VAL 216 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148T TRP* 3.6 35.4 - - + -
201T GLU* 4.4 6.5 - - + -
211T SER* 3.6 31.3 + - - +
212T HIS* 3.7 9.4 - - - -
213T SER 2.8 22.8 + - - +
214T ARG 2.6 5.7 + - - -
215T PRO* 1.3 73.5 - - - +
217T GLY* 1.3 61.7 + - - +
218T HIS 3.2 0.3 + - - -
219T CYS* 3.3 9.9 + - - +
220T LEU* 3.2 20.5 + - + +
235T VAL* 4.7 8.5 - - + -
236T ILE 4.7 0.4 - - - +
237T ASN* 3.9 24.0 - - + +
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Residues in contact with GLY 217 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148T TRP* 3.5 26.1 - - - +
214T ARG 3.0 9.5 + - - -
216T VAL* 1.3 81.3 - - - +
218T HIS* 1.3 60.5 + - - +
220T LEU* 3.3 7.0 + - - +
221T GLU* 3.0 30.0 + - - +
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Residues in contact with HIS 218 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214T ARG* 3.6 48.9 + - + +
215T PRO* 3.0 19.4 + - + +
217T GLY* 1.3 76.2 - - - +
219T CYS* 1.3 60.3 + - - +
221T GLU* 3.3 16.3 - - - +
222T ALA* 2.9 15.6 + - - +
313T ILE* 6.5 1.1 - - + -
314T PRO* 5.2 2.4 - - - +
315T GLN* 4.3 20.9 + - - -
316T VAL* 2.8 38.7 - - + +
319T ILE* 4.1 12.3 - - + -
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Residues in contact with CYS 219 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209T VAL* 3.5 32.5 - - + +
210T VAL 5.3 0.2 - - - -
211T SER* 3.6 24.0 - - - -
215T PRO 3.2 18.2 + - - -
216T VAL* 3.3 8.1 - - - +
218T HIS* 1.3 74.8 - - - +
220T LEU* 1.3 53.8 + - - +
222T ALA* 2.9 6.0 + - - +
223T ALA* 2.6 36.6 + - - +
235T VAL* 4.2 16.5 - - + +
262T VAL* 3.7 14.6 - - - -
319T ILE* 4.0 9.8 - - - +
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Residues in contact with LEU 220 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148T TRP* 3.5 36.8 - - + -
201T GLU* 4.1 13.7 - - + +
202T ARG* 3.9 21.0 - - + -
216T VAL 3.2 9.5 + - - +
217T GLY* 3.5 8.7 - - - +
219T CYS* 1.3 77.4 - - - +
221T GLU* 1.3 57.7 + - - +
223T ALA* 3.4 4.0 + - - +
224T ALA* 2.9 29.1 + - - +
235T VAL* 3.7 28.7 - - + -
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Residues in contact with GLU 221 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217T GLY 3.0 10.9 + - - +
218T HIS* 3.3 38.3 - - - +
220T LEU* 1.3 76.5 - - - +
222T ALA* 1.3 58.0 - - - +
224T ALA* 3.4 6.0 + - - +
225T VAL* 3.1 31.0 + - - +
316T VAL* 3.4 15.5 - - + +
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Residues in contact with ALA 222 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218T HIS 2.9 13.2 + - - +
219T CYS* 2.9 11.3 + - - +
221T GLU* 1.3 75.6 - - - +
223T ALA* 1.3 60.9 + - - +
225T VAL* 3.1 3.5 + - - +
226T LEU* 2.8 34.1 + - - +
233T CYS* 5.6 0.2 - - - -
316T VAL* 4.1 9.2 - - - +
319T ILE* 4.4 14.1 - - + -
320T ILE* 3.8 31.6 - - + +
323T ILE* 5.3 4.7 - - + -
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Residues in contact with ALA 223 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202T ARG* 3.6 34.2 + - - +
219T CYS 2.6 19.0 + - - +
220T LEU 3.7 4.0 - - - +
222T ALA* 1.3 74.7 - - - +
224T ALA* 1.3 61.6 + - - +
226T LEU* 3.9 1.9 - - - +
227T SER* 3.0 25.5 + - - -
231T VAL 4.7 1.4 - - - +
233T CYS* 4.0 30.0 - - + -
235T VAL* 4.1 5.8 - - + -
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Residues in contact with ALA 224 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202T ARG* 4.9 3.3 - - - +
220T LEU 2.9 16.5 + - - +
221T GLU* 3.7 7.0 - - - +
222T ALA 3.1 0.2 - - - -
223T ALA* 1.3 79.6 - - - +
225T VAL* 1.3 64.0 + - + +
226T LEU 3.1 0.5 + - - -
227T SER* 3.3 16.5 + - - -
228T LYS* 3.6 12.2 + - - +
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Residues in contact with VAL 225 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221T GLU 3.1 15.8 + - - +
222T ALA 3.1 8.6 + - - +
224T ALA* 1.3 76.5 - - + +
226T LEU* 1.3 64.5 + - + +
228T LYS* 3.4 22.8 - - - +
229T GLU* 3.9 17.5 - - - +
316T VAL* 5.3 3.6 - - + -
320T ILE* 3.9 26.9 - - + -
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Residues in contact with LEU 226 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222T ALA 2.8 17.4 + - - +
223T ALA* 4.0 4.5 - - - +
224T ALA 3.1 0.4 - - - -
225T VAL* 1.3 78.1 - - + +
227T SER* 1.3 63.6 + - - +
229T GLU* 2.9 46.7 + - - +
231T VAL* 3.3 41.5 + - + +
233T CYS* 4.4 4.7 - - - -
320T ILE* 4.3 21.5 - - + +
323T ILE* 3.6 43.3 - - + -
324T LYS* 4.1 17.7 - - + -
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Residues in contact with SER 227 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202T ARG* 3.7 20.6 + - - -
223T ALA 3.0 8.6 + - - -
224T ALA* 3.3 11.1 + - - -
226T LEU* 1.3 72.9 - - - +
228T LYS* 1.3 56.5 + - - +
229T GLU 2.6 15.6 + - - -
230T GLY* 2.7 14.3 + - - +
231T VAL 3.3 8.7 + - - -
232T GLU* 3.2 22.7 - - - +
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Residues in contact with LYS 228 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224T ALA 3.6 14.1 + - - +
225T VAL* 3.4 15.4 - - - +
227T SER* 1.3 77.6 + - - +
229T GLU* 1.3 59.2 + - + +
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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