Contacts of the helix formed by residues 207 - 215 (chain B) in PDB entry 4H3E
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 207 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200B TYR* 4.6 0.4 - - - -
203B ASP 3.7 7.7 + - - -
204B PHE* 3.0 51.7 + - - +
205B GLU* 3.2 8.9 + - - -
206B ASN* 1.3 93.3 - - - +
208B ARG* 1.3 61.9 + - - +
209B PRO* 3.2 7.4 - - + -
210B ASP* 2.7 64.2 + - - +
211B TYR 3.2 9.2 + - - -
214B GLU* 4.9 3.0 + - - -
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Residues in contact with ARG 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A TRP* 5.6 2.4 - - - -
150B GLY 2.9 27.8 + - - -
151B VAL* 3.8 12.7 + - + +
153B ASN* 2.6 27.5 + - - +
155B GLY* 3.0 27.7 + - - +
195B VAL* 3.2 24.2 + - + +
197B GLU* 4.8 4.9 + - - +
200B TYR* 3.1 47.0 + - + +
206B ASN 2.9 11.8 + - - +
207B ARG* 1.3 72.4 - - - +
209B PRO* 1.3 70.1 - - + +
211B TYR* 3.3 8.5 + - + +
212B LEU* 2.9 34.9 + - + +
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Residues in contact with PRO 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B VAL* 5.0 2.7 - - + +
151B VAL* 4.0 35.9 - - + -
206B ASN 4.4 2.2 - - - +
207B ARG* 3.3 8.3 - - + -
208B ARG* 1.3 95.4 - - + +
210B ASP* 1.3 62.0 + - - +
212B LEU* 3.4 3.0 + - + +
213B LYS* 3.1 31.3 + - + +
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Residues in contact with ASP 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204B PHE* 3.9 7.4 - - + -
207B ARG* 2.7 54.6 + - - +
209B PRO* 1.3 75.9 - - - +
211B TYR* 1.3 60.1 + - - +
213B LYS* 3.3 8.3 + - - +
214B GLU* 2.9 42.4 + - + +
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Residues in contact with TYR 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B PHE* 3.6 36.3 - + - -
113B TYR* 2.8 23.4 + - - -
193B VAL* 3.6 21.4 - - + +
194B ASP 2.7 30.2 + - - -
195B VAL* 4.4 2.0 - - + -
199B ALA* 3.8 8.0 - - + +
200B TYR* 3.4 44.9 - + + -
204B PHE* 3.6 19.3 - + + -
207B ARG 3.2 9.1 + - - +
208B ARG* 3.4 11.7 - - + +
210B ASP* 1.3 77.6 - - - +
212B LEU* 1.3 72.9 + - + +
214B GLU* 3.3 0.5 + - - +
215B ILE* 3.0 32.5 + - + +
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Residues in contact with LEU 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B PHE* 4.9 10.3 - - + -
147B VAL* 3.8 20.2 - - + +
150B GLY* 3.5 12.1 - - - -
151B VAL* 3.4 44.9 - - + +
159B THR* 5.8 0.4 - - - -
193B VAL* 3.7 30.3 - - + -
195B VAL* 4.1 11.9 - - + -
208B ARG* 2.9 26.6 + - + +
209B PRO 3.8 4.9 - - - +
210B ASP 3.3 0.2 - - - -
211B TYR* 1.3 80.7 - - + +
213B LYS* 1.3 60.4 + - - +
215B ILE* 3.4 17.7 - - + +
216B TRP* 3.6 15.4 + - - -
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Residues in contact with LYS 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B VAL* 4.5 25.1 - - + -
209B PRO* 3.1 19.8 + - - +
210B ASP* 3.8 9.2 - - - +
211B TYR 3.3 0.2 - - - -
212B LEU* 1.3 75.7 - - - +
214B GLU* 1.3 65.5 + - + +
216B TRP* 3.1 29.1 + - + +
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Residues in contact with GLU 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B PRO 5.4 0.9 - - - +
50B VAL* 3.4 19.4 - - + +
204B PHE* 3.4 34.9 - - + -
207B ARG* 4.9 3.6 + - - -
210B ASP* 2.9 25.4 + - - +
211B TYR 4.1 2.0 - - - +
213B LYS* 1.3 75.7 - - + +
215B ILE* 1.3 63.3 + - - +
217B SER* 2.7 29.6 + - - +
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Residues in contact with ILE 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B VAL* 4.4 4.4 - - + +
51B PHE* 3.9 8.1 - - + -
113B TYR* 3.8 32.8 - - + +
117B ILE* 4.1 8.3 - - + -
146B PHE* 6.3 0.4 - - + -
193B VAL* 4.2 24.0 - - + -
211B TYR* 3.0 33.6 + - + +
212B LEU* 3.4 24.2 - - + +
214B GLU* 1.3 74.0 - - - +
216B TRP* 1.3 70.8 + - + +
217B SER 3.1 0.2 - - - -
218B VAL* 2.9 31.8 + - + +
219B ILE* 3.3 18.2 + - + +
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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