Contacts of the helix formed by residues 198 - 209 (chain B) in PDB entry 3G4C
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 CYS 198 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16B VAL* 5.6 0.2 - - - -
18B GLY 5.2 0.7 - - - -
19B ASN* 4.2 10.5 - - - -
20B ASP* 3.3 18.0 - - - +
60B ILE* 3.6 40.6 - - - -
62B PHE* 3.9 13.7 - - - -
194B PHE* 2.8 31.4 + - + +
197B LYS* 1.3 79.8 - - - +
199B PRO* 1.3 60.6 - - - +
200B TRP 3.4 0.2 + - - -
201B THR* 4.1 3.1 - - - -
202B PHE* 2.9 27.2 + - - +
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Residues in contact with PRO 199 (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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20B ASP* 3.2 11.7 - - - +
42B ARG* 4.8 2.0 - - - +
195B LYS* 3.3 22.9 - - + +
196B GLU 4.0 6.3 - - - +
197B LYS 3.5 8.1 - - - +
198B CYS* 1.3 88.5 - - - +
200B TRP* 1.3 68.3 + - + +
202B PHE* 3.9 2.4 - - + +
203B GLU* 3.0 37.6 + - + +
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Residues in contact with TRP 200 (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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20B ASP* 3.2 29.4 + - + +
21B LEU* 3.7 31.2 - - + -
41B ASP* 4.0 15.3 - - + -
42B ARG* 3.2 68.8 + - + +
45B ILE* 3.9 21.6 - - + +
46B GLU* 5.7 0.7 - - - +
199B PRO* 1.3 85.6 - - + +
201B THR* 1.3 58.9 + - - +
203B GLU* 3.9 1.4 - - - +
204B ALA* 3.0 30.1 + - - +
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Residues in contact with THR 201 (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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20B ASP* 2.8 20.9 + - - -
45B ILE* 3.8 14.4 - - - +
49B MET* 3.3 18.3 - - + +
57B PHE* 3.6 28.6 - - + -
60B ILE* 4.2 8.7 - - + +
164B ALA* 5.2 0.7 - - + -
168B MET* 4.2 4.3 - - + -
194B PHE* 3.7 22.4 - - + -
198B CYS* 3.8 8.1 - - - -
200B TRP* 1.3 75.5 - - - +
202B PHE* 1.3 62.0 + - - +
205B PHE* 2.9 26.9 + - - +
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Residues in contact with PHE 202 (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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171B LEU* 4.4 2.5 - - + -
191B ALA* 3.6 41.3 - - + -
194B PHE* 3.6 29.4 - + + +
195B LYS* 3.6 44.6 - - + +
198B CYS 2.9 19.1 + - - +
199B PRO 3.9 2.7 - - - +
201B THR* 1.3 76.0 - - - +
203B GLU* 1.3 71.7 + - - +
205B PHE* 3.3 12.2 + + - +
206B LEU* 3.0 50.1 + - + +
215B LEU* 4.3 16.8 - - + -
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Residues in contact with GLU 203 (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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42B ARG* 4.2 17.9 - - - +
195B LYS* 3.3 36.4 + - - +
199B PRO* 3.0 23.2 + - + +
200B TRP 4.0 2.9 - - - +
202B PHE* 1.3 85.3 - - + +
204B ALA* 1.3 56.7 + - - +
206B LEU* 3.5 15.3 + - - +
207B LYS* 3.0 29.0 + - - +
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Residues in contact with ALA 204 (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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45B ILE* 3.9 20.0 - - + -
46B GLU* 4.1 18.6 - - + -
49B MET* 3.3 23.4 - - + +
200B TRP 3.0 18.2 + - - +
201B THR 4.0 2.5 - - - +
203B GLU* 1.3 74.1 - - - +
205B PHE* 1.3 60.2 - - - +
207B LYS* 3.1 3.0 + - - -
208B TYR* 2.8 36.6 + - + -
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Residues in contact with PHE 205 (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 MET* 3.6 10.0 - - - +
168B MET* 3.6 53.8 - - + -
171B LEU* 4.2 21.5 - - + -
172B ASN* 3.4 22.9 - - - -
194B PHE* 4.6 7.2 - + - -
201B THR 2.9 20.8 + - - +
202B PHE* 3.3 14.8 - + - +
204B ALA* 1.3 73.5 - - - +
206B LEU* 1.3 64.8 + - + +
209B ALA* 2.8 36.0 + - + -
210B TYR* 2.9 45.6 + + + -
215B LEU* 4.7 4.7 - - + -
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Residues in contact with LEU 206 (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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195B LYS* 6.0 0.7 - - - +
202B PHE* 3.0 42.7 + - + +
203B GLU* 3.7 20.6 - - - +
205B PHE* 1.3 78.5 - - + +
207B LYS* 1.3 59.8 + - - +
210B TYR* 3.4 38.7 + - + +
215B LEU* 3.7 39.3 - - + +
216B LYS* 4.0 26.4 - - + +
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Residues in contact with LYS 207 (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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46B GLU* 4.2 9.2 + - - +
203B GLU 3.0 18.2 + - - +
204B ALA* 3.1 5.8 + - - +
206B LEU* 1.3 79.0 - - - +
208B TYR* 1.3 100.6 + - + +
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Residues in contact with TYR 208 (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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46B GLU* 2.9 54.4 + - + +
49B MET* 3.9 6.5 - - + +
50B LYS* 3.7 58.6 + - + +
204B ALA* 2.8 29.7 + - - +
207B LYS* 1.3 114.3 + - + +
209B ALA* 1.3 57.2 + - - +
210B TYR 3.9 0.7 - - - -
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Residues in contact with ALA 209 (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 MET* 3.8 34.8 - - + +
54B GLU* 6.2 0.4 - - + +
172B ASN* 3.9 4.3 + - - +
205B PHE* 2.8 17.9 + - + -
208B TYR* 1.3 74.8 - - - +
210B TYR* 1.3 65.4 + - - +
211B LYS* 3.4 21.0 + - - +
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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