Contacts of the helix formed by residues 183 - 193 (chain C) in PDB entry 4GJ0
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 GLN 183 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255A GLN* 3.3 30.4 - - - +
189B TYR* 3.4 27.7 - - + -
192B ASP* 4.4 8.3 + - - +
193B ASP* 2.9 38.6 + - - +
182C LYS* 1.3 76.0 - - - +
184C TRP* 1.3 68.0 + - - +
185C VAL* 4.0 3.7 - - - +
186C HIS* 3.2 12.1 + - + +
187C ALA* 3.0 18.7 + - - +
220C TRP* 3.4 0.9 - - - -
273C CYS 3.4 9.9 - - - +
274C ASP* 3.7 20.9 + - - +
275C ARG 3.1 15.0 - - - +
276C LYS* 4.1 1.4 - - + +
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Residues in contact with TRP 184 (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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272A PHE* 5.1 7.0 - + - -
183C GLN* 1.3 71.8 - - - +
185C VAL* 1.3 81.8 + - + +
187C ALA* 3.1 6.1 + - - +
188C ARG* 2.9 55.5 + - - -
198C LEU* 3.4 14.2 - - + +
220C TRP* 3.4 41.6 - + + +
221C ILE 2.9 22.9 + - - -
222C GLY* 4.4 3.0 - - - -
223C LEU 4.6 3.0 + - - -
224C ARG* 3.3 43.5 - - + -
235C VAL* 3.5 24.5 - - + -
259C CYS* 3.5 27.3 - - + -
260C VAL 4.8 0.4 - - - -
273C CYS* 2.9 23.6 + - + +
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Residues in contact with VAL 185 (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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255A GLN* 5.4 2.9 - - + -
256A GLY* 6.3 3.6 - - - -
189B TYR* 3.3 44.6 - - + +
183C GLN* 4.0 7.2 - - - +
184C TRP* 1.3 98.6 - - + +
186C HIS* 1.3 68.3 + - - +
188C ARG* 3.1 11.6 + - - +
189C TYR* 3.1 57.5 + - + +
273C CYS* 4.7 1.2 + - - +
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Residues in contact with HIS 186 (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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186B HIS* 3.7 11.2 + + - -
189B TYR* 3.8 15.5 + - + -
190B ALA* 3.7 18.1 - - - -
193B ASP* 2.5 34.1 + - + +
181C THR 4.3 2.2 - - - -
182C LYS* 3.4 21.9 + - + +
183C GLN* 3.2 14.3 + - + +
185C VAL* 1.3 82.2 - - - +
187C ALA* 1.3 61.5 + - - +
189C TYR* 3.2 5.8 + - - +
190C ALA* 3.0 19.1 + - - +
301C GOL 2.6 49.9 - - - -
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Residues in contact with ALA 187 (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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182C LYS* 3.9 13.8 - - + +
183C GLN 3.0 12.6 + - - +
184C TRP 3.3 8.5 - - - +
186C HIS* 1.3 77.4 - - - +
188C ARG* 1.3 61.3 + - - +
190C ALA* 3.2 4.1 + - - +
191C CYS* 3.1 26.9 + - - -
198C LEU* 4.0 10.1 - - + -
220C TRP* 4.0 12.3 - - + -
280C TRP* 3.8 31.1 - - + -
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Residues in contact with ARG 188 (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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274A ASP* 3.0 34.8 + - - +
184C TRP* 2.9 30.9 + - + +
185C VAL* 3.2 22.7 - - - +
187C ALA* 1.3 78.5 - - - +
189C TYR* 1.3 68.4 + - + +
191C CYS* 3.3 4.2 + - - +
192C ASP* 3.0 41.5 + - - +
198C LEU* 3.5 23.8 + - + +
224C ARG* 3.5 22.5 - - - +
235C VAL* 4.6 20.9 + - + +
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Residues in contact with TYR 189 (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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183B GLN* 5.7 5.6 - - - -
185B VAL* 3.7 41.1 - - + +
186B HIS* 3.7 37.7 - - + +
189B TYR* 4.2 6.7 - + - -
301B GOL 5.7 1.6 - - - -
185C VAL* 3.1 41.8 + - + +
186C HIS* 3.7 7.0 - - - +
188C ARG* 1.3 86.0 + - + +
190C ALA* 1.3 65.5 + - - +
192C ASP* 3.5 21.8 - - + +
193C ASP* 2.9 30.7 + - - +
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Residues in contact with ALA 190 (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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186B HIS* 3.9 10.4 - - - -
182C LYS* 4.0 8.3 - - + -
186C HIS 3.0 11.2 + - - +
187C ALA* 3.5 9.9 - - - +
189C TYR* 1.3 79.9 - - - +
191C CYS* 1.3 63.5 + - - +
193C ASP* 3.4 8.6 + - - +
194C MET* 3.5 21.1 + - - +
280C TRP* 3.9 24.2 - - + -
301C GOL 3.6 17.7 - - - +
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Residues in contact with CYS 191 (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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187C ALA 3.1 16.1 + - - -
188C ARG 3.5 8.1 - - - +
190C ALA* 1.3 74.2 - - - +
192C ASP* 1.3 65.1 + - - +
194C MET* 2.9 15.8 + - - +
196C GLY* 3.0 17.5 + - - -
197C GLN* 3.7 19.5 - - - -
198C LEU* 3.7 21.1 - - - +
280C TRP* 4.1 4.3 - - - -
282C CYS* 2.0 57.2 - - + -
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Residues in contact with ASP 192 (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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276B LYS* 5.6 0.9 + - - -
188C ARG* 3.0 28.5 + - - +
189C TYR* 3.2 33.0 + - + +
191C CYS* 1.3 75.1 - - - +
193C ASP* 1.3 62.3 + - - +
195C GLU* 3.2 18.5 + - - +
196C GLY 3.4 13.9 - - - +
197C GLN* 4.4 10.6 - - - +
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Residues in contact with ASP 193 (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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181B THR* 3.4 19.7 - - - +
182B LYS* 4.2 3.4 - - - -
183B GLN* 4.8 4.2 + - - +
186B HIS* 2.7 29.9 + - + +
276B LYS* 3.3 28.7 + - - +
189C TYR* 2.9 18.7 + - - +
190C ALA* 3.9 5.6 - - - +
191C CYS 3.0 0.8 + - - -
192C ASP* 1.3 81.2 - - - +
194C MET* 1.3 61.4 + - + +
195C GLU* 3.2 5.5 + - - +
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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