Contacts of the helix formed by residues 194 - 204 (chain C) in PDB entry 5Y1Z
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 ASP 194 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173C PHE* 3.4 16.4 - - - +
174C GLN 3.7 0.3 - - - +
175C LYS 3.8 13.0 - - - +
176C PRO* 3.1 41.9 - - + +
192C PRO* 5.3 1.2 - - - +
193C MET* 1.3 80.5 + - - +
195C LEU* 1.3 65.9 + - - +
196C CYS* 3.2 10.4 - - - +
197C THR* 2.8 40.3 + - - -
198C LEU* 3.0 23.0 + - - +
220C ILE* 3.7 10.1 - - - -
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Residues in contact with LEU 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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162C ILE* 3.9 8.2 - - + +
165C MET* 3.9 36.3 - - + +
166C LYS* 3.7 37.9 - - + -
170C THR* 4.5 7.0 - - - +
173C PHE* 2.9 33.7 + - + +
174C GLN* 4.0 12.6 - - + +
194C ASP* 1.3 72.3 - - - +
196C CYS* 1.3 59.0 + - - +
198C LEU* 3.4 10.5 + - + +
199C GLU* 2.9 30.8 + - - +
220C ILE* 3.8 17.9 - - + +
241C VAL* 4.7 9.4 - - + -
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Residues in contact with CYS 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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174C GLN 3.1 23.1 + - - +
175C LYS* 4.6 4.7 - - + -
176C PRO* 4.8 3.6 - - + -
194C ASP* 3.2 7.4 + - - +
195C LEU* 1.3 76.6 - - - +
197C THR* 1.3 57.2 + - - +
199C GLU* 3.2 12.9 + - - +
200C LYS* 2.9 62.7 + - - +
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Residues in contact with THR 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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176C PRO* 4.2 6.1 - - - +
192C PRO 5.7 0.4 - - - +
193C MET* 3.8 19.5 - - + -
194C ASP* 2.8 35.0 + - - -
196C CYS* 1.3 73.7 - - - +
198C LEU* 1.3 66.2 + - - +
200C LYS* 3.2 7.4 + - + -
201C ASN* 2.8 50.0 + - - +
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Residues in contact with LEU 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 ILE* 3.6 23.1 - - + -
165C MET* 4.1 10.5 - - + -
193C MET* 4.2 9.1 - - - -
194C ASP 3.0 10.4 + - - +
195C LEU* 3.4 18.8 - - + +
197C THR* 1.3 75.0 - - - +
199C GLU* 1.3 57.8 + - - +
201C ASN* 3.7 1.4 - - - +
202C ALA* 2.8 31.9 + - - +
207C TYR* 3.5 25.0 - - - +
213C PHE* 3.5 21.5 - - + -
216C ASP* 4.1 6.1 - - + +
217C ALA* 4.0 41.1 - - + +
220C ILE* 4.1 8.5 - - + -
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Residues in contact with GLU 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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159C LYS* 5.7 11.1 - - + +
162C ILE* 3.4 33.3 - - + +
163C GLN* 4.9 9.2 + - - +
166C LYS* 3.9 19.5 + - - +
195C LEU 2.9 14.2 + - - +
196C CYS* 3.3 15.3 - - - +
198C LEU* 1.3 77.8 - - - +
200C LYS* 1.3 65.8 + - + +
202C ALA* 3.2 5.6 + - - +
203C LYS* 2.9 29.4 + - + +
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Residues in contact with LYS 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 CYS* 2.9 44.2 + - - +
197C THR* 3.9 6.3 - - + +
199C GLU* 1.3 79.3 - - - +
201C ASN* 1.3 61.5 + - - +
203C LYS* 3.1 10.3 + - - +
204C LYS* 2.9 28.9 + - - +
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Residues in contact with ASN 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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193C MET* 4.7 4.4 - - - +
197C THR* 2.8 42.3 + - - +
198C LEU 3.7 0.6 - - - +
200C LYS* 1.3 77.2 - - - +
202C ALA* 1.3 66.7 + - - +
204C LYS* 3.1 11.8 + - - +
205C LYS 3.2 4.2 + - - -
206C MET* 3.1 49.3 + - + +
207C TYR* 3.4 24.1 + - - +
216C ASP* 3.9 7.7 + - - -
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Residues in contact with ALA 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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155C SER* 3.4 20.8 - - - +
158C LEU* 4.2 24.9 - - + -
159C LYS* 4.9 6.3 - - + +
162C ILE* 5.6 0.9 - - + -
198C LEU 2.8 20.1 + - - +
199C GLU* 3.5 7.4 - - - +
201C ASN* 1.3 71.5 - - - +
203C LYS* 1.3 58.5 + - - +
205C LYS* 2.9 21.7 + - - -
206C MET 4.9 0.2 - - - +
207C TYR* 3.4 22.2 - - + -
213C PHE* 4.6 3.4 - - + -
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Residues in contact with LYS 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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155C SER* 5.3 3.9 + - - -
199C GLU* 2.9 15.0 + - + +
200C LYS* 3.1 13.0 + - - +
202C ALA* 1.3 75.1 - - - +
204C LYS* 1.4 56.8 + - - +
205C LYS* 2.9 8.5 + - - +
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Residues in contact with LYS 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 LYS 2.9 15.9 + - - +
201C ASN* 3.1 6.7 + - - +
203C LYS* 1.4 72.0 - - - +
205C LYS* 1.3 68.3 + - - +
206C MET* 3.2 23.8 + - + +
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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