Contacts of the helix formed by residues 194 - 204 (chain C) in PDB entry 1EQR
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 PRO 194 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162C THR* 3.8 20.6 - - + +
164C MET* 5.7 0.2 - - + -
191C PRO* 5.4 5.4 - - + -
193C SER* 1.4 84.9 - - - +
195C GLN* 1.3 54.3 + - - +
196C LEU 3.6 1.8 - - - -
197C PHE* 3.5 11.7 + - + +
198C LYS* 3.1 34.0 + - - +
209C TYR* 3.9 7.0 - - - +
211C GLN* 4.4 0.2 - - - +
213C VAL* 3.4 39.7 - - + -
214C LYS 5.0 1.1 - - - +
215C CYS* 4.2 9.0 - - - -
231C GLN* 4.9 4.9 - - - +
233C ASP* 3.2 24.0 - - - +
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Residues in contact with GLN 195 (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 GLU* 2.4 38.0 + - - +
192C GLN* 5.0 3.3 - - - +
193C SER* 2.9 40.8 + - - +
194C PRO* 1.3 77.0 - - - +
196C LEU* 1.3 84.3 + - + +
198C LYS* 3.4 22.3 - - - +
199C GLN* 3.4 18.6 + - - +
449C HIS* 5.7 5.2 - - + +
451C PHE* 5.2 5.6 - - + -
514C PHE* 5.8 2.2 - - - -
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Residues in contact with LEU 196 (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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194C PRO 3.6 0.4 - - - -
195C GLN* 1.3 104.3 - - + +
197C PHE* 1.3 65.7 + - + +
198C LYS 3.3 0.4 - - - -
199C GLN* 3.3 12.7 + - - +
200C LEU* 2.9 34.4 + - + +
451C PHE* 3.5 35.0 - - + -
513C LYS 5.3 0.2 - - - +
514C PHE* 4.2 24.5 - - + -
516C PHE* 4.1 34.8 - - + -
517C LEU* 4.5 13.5 - - + -
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Residues in contact with PHE 197 (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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162C THR* 4.0 21.8 - - + -
163C PRO* 3.8 41.7 - - + -
166C THR* 3.9 27.6 - - + -
167C LYS 5.9 0.7 - - - -
191C PRO* 6.5 0.2 - - + -
193C SER 5.3 2.5 - - - -
194C PRO* 3.5 15.0 + - + +
196C LEU* 1.3 80.1 - - + +
198C LYS* 1.3 60.9 + - - +
200C LEU* 3.4 21.5 - - + +
201C LEU* 2.9 35.0 + - + +
516C PHE* 5.9 5.6 - + - -
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Residues in contact with LYS 198 (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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162C THR* 5.2 0.4 - - - +
194C PRO 3.1 19.7 + - - +
195C GLN* 3.4 15.9 - - - +
197C PHE* 1.3 73.6 - - - +
199C GLN* 1.3 70.0 + - + +
201C LEU* 3.1 21.3 + - - +
202C MET* 3.3 17.3 + - - +
209C TYR* 3.7 21.1 - - + -
233C ASP* 3.1 33.2 + - - +
234C VAL 2.9 24.3 + - - -
235C GLU* 3.1 31.5 - - + +
489C ARG* 3.3 19.3 - - - +
531C LEU 3.7 6.3 + - - -
532C ALA* 4.8 2.0 - - - +
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Residues in contact with GLN 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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195C GLN* 3.4 18.2 + - - +
196C LEU* 3.3 21.2 + - + +
198C LYS* 1.3 81.6 - - + +
200C LEU* 1.3 57.9 + - - +
202C MET* 2.9 22.2 + - - +
203C MET* 3.2 21.5 + - + +
235C GLU* 3.5 22.2 - - - +
449C HIS* 4.3 3.8 + - - -
451C PHE* 3.6 30.8 - - - +
489C ARG* 3.7 22.6 - - + +
490C ILE 4.7 3.5 - - - +
496C GLN* 5.4 0.3 - - - +
517C LEU* 4.7 12.6 - - + +
521C LEU* 6.0 0.2 - - - +
528C HIS* 3.5 24.0 + - + +
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Residues in contact with LEU 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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196C LEU 2.9 20.7 + - - +
197C PHE* 3.4 27.4 - - + +
199C GLN* 1.3 76.1 - - - +
201C LEU* 1.3 57.0 + - + +
203C MET* 3.0 15.4 + - + +
204C SER* 2.9 32.0 + - - +
516C PHE* 4.4 28.5 - - + +
517C LEU* 4.6 13.5 - - + -
520C ALA* 4.2 24.5 - - + -
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Residues in contact with LEU 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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160C ILE* 4.0 25.4 - - + -
161C GLU 5.5 0.4 - - - +
162C THR* 4.7 8.1 - - + -
197C PHE* 2.9 25.5 + - + +
198C LYS* 3.1 9.8 + - - +
200C LEU* 1.3 77.9 - - + +
202C MET* 1.3 69.2 + - + +
204C SER* 3.3 8.8 + - - +
206C PHE* 3.2 54.3 + - + +
209C TYR* 3.6 35.2 - - + -
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Residues in contact with MET 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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198C LYS 3.3 15.4 + - - +
199C GLN 2.9 9.4 + - - +
201C LEU* 1.3 80.7 - - + +
203C MET* 1.3 60.5 + - + +
204C SER 2.9 4.7 - - - -
205C GLY* 3.0 19.4 + - - -
206C PHE* 3.4 22.2 - - + +
207C ASP 3.4 14.4 - - - +
209C TYR* 3.8 27.8 - - + -
235C GLU* 3.5 20.4 - - + +
236C THR* 3.6 14.6 - - - -
237C SER* 3.0 25.8 + - - +
526C PRO* 4.0 16.4 - - + +
528C HIS* 4.0 19.7 - - + +
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Residues in contact with MET 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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199C GLN* 3.2 27.8 + - + +
200C LEU* 3.0 16.7 + - + +
202C MET* 1.3 80.5 - - - +
204C SER* 1.3 55.7 + - - +
205C GLY 3.3 1.9 + - - -
517C LEU* 4.5 10.5 - - + -
520C ALA* 3.7 39.7 - - + +
521C LEU* 4.0 16.4 - - + -
523C TYR 5.7 1.0 - - - +
524C GLY 6.2 0.4 - - - -
525C THR* 3.9 23.8 - - - -
526C PRO* 4.3 8.3 - - + -
528C HIS* 3.8 26.0 - - + +
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Residues in contact with SER 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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200C LEU* 2.9 18.2 + - - +
201C LEU* 3.6 11.7 - - - +
202C MET 2.9 0.6 - - - -
203C MET* 1.3 78.9 - - - +
205C GLY* 1.3 58.3 + - - +
206C PHE* 3.4 24.3 + - - -
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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