Contacts of the helix formed by residues 198 - 209 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16C VAL* 5.7 0.2 - - - -
18C GLY 5.3 0.4 - - - -
19C ASN* 4.3 7.9 - - - -
20C ASP* 3.2 15.9 - - - +
60C ILE* 3.8 39.7 - - - -
62C PHE* 3.9 13.9 - - - -
194C PHE* 2.9 28.2 + - + +
197C LYS* 1.3 84.1 - - - +
199C PRO* 1.3 67.2 - - - +
200C TRP 3.3 3.1 + - - -
201C THR* 3.5 3.3 + - - -
202C PHE* 3.0 21.8 + - - +
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Residues in contact with PRO 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C ASP* 3.3 10.8 - - - +
195C LYS* 3.2 23.5 - - + +
196C GLU 3.8 6.1 - - - +
197C LYS 3.5 7.0 - - - +
198C CYS* 1.3 91.1 - - - +
200C TRP* 1.3 69.4 + - + +
202C PHE* 3.6 2.3 + - + +
203C GLU* 3.0 36.2 + - + +
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Residues in contact with TRP 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C ASP* 3.1 28.3 + - + +
21C LEU* 3.8 33.2 - - + -
38C GLU* 3.7 43.1 + - + -
41C ASP* 3.9 11.2 - - + -
42C ARG* 3.1 53.9 - - + +
45C ILE* 3.8 15.8 - - + +
46C GLU* 5.3 1.9 - - - +
199C PRO* 1.3 87.7 - - + +
201C THR* 1.3 61.6 + - - +
203C GLU* 4.0 4.5 - - - +
204C ALA* 3.0 29.1 + - - +
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Residues in contact with THR 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C ASP* 2.9 22.2 + - - -
45C ILE* 3.8 14.8 - - - +
49C MET* 3.4 9.6 - - + +
57C PHE* 3.6 38.7 - - + -
60C ILE* 4.3 8.5 - - + +
164C ALA* 5.3 1.1 - - + -
168C MET* 4.2 4.0 - - + -
194C PHE* 3.9 19.5 - - + -
198C CYS* 3.9 8.1 - - - -
200C TRP* 1.3 76.5 - - - +
202C PHE* 1.3 59.4 + - - +
205C PHE* 2.9 28.2 + - - +
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Residues in contact with PHE 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171C LEU* 4.6 1.3 - - + -
191C ALA* 3.6 31.4 - - + -
194C PHE* 3.7 28.9 - + + -
195C LYS* 3.7 38.4 - - + +
198C CYS 3.0 18.5 + - - +
199C PRO 4.0 2.0 - - - +
201C THR* 1.3 76.5 - - - +
203C GLU* 1.3 70.0 + - + +
205C PHE* 3.3 9.2 - + - +
206C LEU* 3.1 52.4 + - + +
215C LEU* 4.0 18.8 - - + -
220C VAL* 3.8 18.4 - - - -
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Residues in contact with GLU 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C GLU* 5.0 3.8 - - - +
195C LYS* 5.5 7.9 - - - -
199C PRO* 3.0 22.5 + - + +
200C TRP* 4.0 5.2 - - - +
202C PHE* 1.3 84.5 - - + +
204C ALA* 1.3 58.7 + - - +
206C LEU* 3.5 6.4 + - + +
207C LYS* 3.0 29.5 + - - +
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Residues in contact with ALA 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C ILE* 4.0 17.9 - - + -
46C GLU* 4.1 27.9 + - + +
49C MET* 3.6 16.8 - - + -
200C TRP 3.0 18.8 + - - +
201C THR 3.9 3.6 - - - +
203C GLU* 1.3 72.3 - - - +
205C PHE* 1.3 62.4 + - - +
207C LYS* 3.2 1.0 + - - -
208C TYR* 2.8 40.8 + - + +
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Residues in contact with PHE 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C MET* 3.4 15.1 - - + +
168C MET* 3.6 50.3 - - + -
171C LEU* 4.1 21.1 - - + -
172C ASN* 3.7 11.0 - - - -
194C PHE* 4.6 8.1 - + - -
201C THR 2.9 20.7 + - - +
202C PHE* 3.3 13.7 - + - +
204C ALA* 1.3 76.2 - - - +
206C LEU* 1.3 60.2 + - + +
209C ALA* 2.8 20.9 + - + -
210C TYR* 2.7 76.3 + + + -
215C LEU* 4.4 1.3 - - + -
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Residues in contact with LEU 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202C PHE* 3.1 37.8 + - + +
203C GLU* 3.7 7.6 - - + +
205C PHE* 1.3 81.7 - - + +
207C LYS* 1.3 64.3 + - - +
210C TYR* 3.5 40.2 + - + +
215C LEU* 3.6 43.7 - - + +
216C LYS* 3.7 28.8 + - + +
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Residues in contact with LYS 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C GLU* 4.0 20.0 + - - +
203C GLU 3.0 18.0 + - - +
204C ALA* 3.8 4.3 - - - +
206C LEU* 1.3 77.3 - - - +
208C TYR* 1.3 99.5 + - + +
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Residues in contact with TYR 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C GLU* 3.8 38.4 + - + +
49C MET* 3.8 14.2 - - + +
50C LYS* 3.6 53.5 + - + +
204C ALA* 2.8 26.6 + - - +
207C LYS* 1.3 119.4 + - + +
209C ALA* 1.3 58.0 + - - +
210C TYR 3.9 0.2 - - - -
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Residues in contact with ALA 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C MET* 3.7 34.1 - - + +
54C GLU* 6.1 1.6 - - + +
172C ASN* 3.7 8.9 + - - +
205C PHE* 2.8 20.7 + - + +
208C TYR* 1.3 74.0 - - - +
210C TYR* 1.3 67.1 + - - +
211C LYS* 3.5 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