Contacts of the helix formed by residues 210 - 218 (chain H) in PDB entry 3GHG
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 GLU 210 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208H GLY 3.2 0.4 - - - -
209H LYS* 1.3 83.0 - - + +
211H CYS* 1.3 64.3 + - - +
212H GLU* 2.1 45.4 + - - +
213H GLU* 2.4 40.3 + - - +
214H ILE* 3.1 14.6 + - - +
216H ARG* 4.4 2.6 + - - -
227H ILE* 3.9 20.9 - - + -
229H PRO* 5.6 0.2 - - + -
248H GLY 4.2 0.9 - - - +
250H THR* 4.3 7.2 + - + +
302H LEU* 5.5 9.4 - - + -
305H MET* 4.2 19.7 - - + -
456H PRO* 3.7 26.1 - - + +
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Residues in contact with CYS 211 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210H GLU* 1.3 75.1 + - - +
212H GLU* 1.3 55.0 + - - +
214H ILE* 3.9 4.7 - - - -
215H ILE 3.4 4.0 + - - -
227H ILE* 4.8 0.9 - - - -
238H VAL* 3.6 9.0 - - - -
239H TYR 3.4 7.9 - - - -
240H CYS* 2.0 48.2 - - + -
242H MET* 3.1 26.2 - - - +
248H GLY* 3.3 8.3 - - - +
249H TRP 3.4 11.7 - - - +
250H THR* 3.1 38.8 + - - +
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Residues in contact with GLU 212 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210H GLU* 2.1 34.2 + - - +
211H CYS* 1.3 66.1 - - - +
213H GLU* 1.3 63.7 + - - +
214H ILE 3.0 1.3 - - - -
215H ILE* 2.9 39.7 - - - +
216H ARG* 3.2 37.9 + - - +
246H ASN 4.8 2.4 - - - +
247H GLY 4.0 4.5 - - - +
248H GLY* 3.4 20.4 + - - +
455H ARG* 4.3 12.3 + - + -
456H PRO* 4.0 13.2 - - + -
458H PHE* 4.4 17.5 - - + -
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Residues in contact with GLU 213 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208H GLY* 3.9 0.4 - - - -
209H LYS* 2.6 57.5 + - + +
210H GLU* 2.4 30.6 + - - +
212H GLU* 1.3 73.9 - - - +
214H ILE* 1.3 56.5 + - - +
216H ARG* 3.7 32.6 + - - +
217H LYS* 3.0 50.0 + - - +
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Residues in contact with ILE 214 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206H VAL* 3.8 17.9 - - + -
207H SER* 4.0 9.0 - - - -
208H GLY 3.3 31.0 - - - +
210H GLU 3.1 9.2 + - - +
211H CYS 3.7 9.0 - - - +
212H GLU 3.0 0.4 - - - -
213H GLU* 1.3 74.9 - - - +
215H ILE* 1.3 61.7 + - - +
217H LYS* 2.8 12.4 + - - +
218H GLY 2.8 22.9 + - - -
219H GLY 3.5 5.2 + - - +
225H TYR* 3.7 44.0 - - + -
226H LEU 4.0 4.7 - - - +
227H ILE* 4.1 8.1 - - + -
240H CYS* 4.8 3.6 - - - -
242H MET* 3.5 16.2 - - + -
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Residues in contact with ILE 215 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211H CYS 3.4 1.7 + - - +
212H GLU* 2.9 50.5 - - - +
214H ILE* 1.3 78.9 - - - +
216H ARG* 1.3 56.1 + - + +
218H GLY* 3.0 16.1 + - - -
219H GLY 3.3 22.0 - - - +
220H GLU* 3.3 21.9 - - - +
242H MET* 3.4 28.5 - - + +
246H ASN 5.0 8.5 - - - +
247H GLY* 4.7 2.5 - - - -
248H GLY* 3.9 7.4 - - - +
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Residues in contact with ARG 216 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210H GLU* 4.4 2.0 + - - -
212H GLU* 3.2 41.7 + - - +
213H GLU* 3.7 37.1 + - - +
215H ILE* 1.3 73.9 - - + +
217H LYS* 1.3 63.5 + - - +
218H GLY* 3.0 2.8 + - - -
458H PHE* 3.3 37.7 - - - -
209I ILE* 4.3 9.2 - - - +
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Residues in contact with LYS 217 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206H VAL* 4.3 18.2 - - + -
207H SER 3.5 28.2 + - - +
208H GLY* 3.7 7.1 - - - -
209H LYS* 3.7 9.8 - - - +
213H GLU* 3.0 35.2 + - - +
214H ILE* 2.8 15.3 + - - +
216H ARG* 1.3 75.3 - - - +
218H GLY* 1.3 59.1 + - - +
219H GLY 3.9 0.2 - - - -
209I ILE* 3.5 22.5 - - - +
210I GLN* 4.2 9.9 + - - -
213I GLU* 3.1 51.4 + - + +
232I LYS* 6.3 0.8 - - - +
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Residues in contact with GLY 218 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206H VAL* 6.1 0.2 - - - -
214H ILE 2.8 6.7 + - - -
215H ILE 3.0 13.3 + - - -
216H ARG 3.0 1.5 - - - -
217H LYS* 1.3 80.4 - - - +
219H GLY* 1.3 56.8 + - - -
220H GLU* 3.8 11.9 + - - +
206I LYS* 5.6 0.5 + - - -
207I ASN* 5.9 0.2 - - - -
209I ILE* 5.6 0.4 - - - -
210I GLN* 3.5 34.1 + - - +
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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