Contacts of the helix formed by residues 195 - 203 (chain C) in PDB entry 5I94
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 195 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143C PHE* 3.9 0.4 - - - -
152C LYS* 4.1 21.8 - - + +
193C MET 4.4 0.2 - - - -
194C LEU* 1.3 73.6 - - - +
196C LYS* 1.3 59.8 + - - +
197C ASP* 3.6 14.4 - - + +
198C LEU* 2.9 31.6 + - - +
199C PHE* 2.7 27.7 + - - +
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Residues in contact with LYS 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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140C ASP* 3.1 44.6 + - - +
143C PHE* 3.4 42.5 - - + -
144C TYR* 3.7 30.2 + - + +
152C LYS* 5.3 2.6 - - - +
195C ASP* 1.3 69.9 - - - +
197C ASP* 1.3 54.4 - - - +
199C PHE* 3.7 0.9 - - - +
200C LYS* 2.9 36.3 + - + +
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Residues in contact with ASP 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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195C ASP* 3.6 15.6 - - + +
196C LYS* 1.3 80.8 - - - +
198C LEU* 1.3 69.6 + - - +
200C LYS* 3.5 10.3 + - - +
201C LYS* 3.6 12.8 + - - +
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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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184C THR* 3.5 43.1 - - + +
185C LEU* 5.2 0.4 - - + -
187C THR* 5.5 5.8 - - + +
193C MET 3.4 26.2 - - - +
194C LEU* 3.6 11.0 - - + -
195C ASP* 2.9 30.7 + - - +
197C ASP* 1.3 79.1 + - - +
199C PHE* 1.3 69.0 + - - +
201C LYS* 3.4 15.5 + - + +
202C CYS* 3.5 12.2 + - - -
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Residues in contact with PHE 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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139C GLU 3.8 3.8 - - - -
142C LEU* 3.5 20.6 - - + -
143C PHE* 3.7 41.7 - + + -
146C ILE* 3.9 12.6 - - + -
153C ILE* 4.0 11.0 - - + -
158C PHE* 3.9 22.7 - + - -
181C LEU* 6.2 0.7 - - + -
194C LEU* 3.8 29.7 - - + +
195C ASP 2.7 19.0 + - - +
196C LYS 3.7 2.0 - - - +
198C LEU* 1.3 72.5 - - - +
200C LYS* 1.3 59.4 + - + +
202C CYS* 2.7 33.1 + - + +
203C VAL* 3.2 46.0 + - + -
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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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139C GLU* 3.6 43.8 + - + +
140C ASP* 3.9 19.0 + - - +
143C PHE* 6.3 0.4 - - + -
196C LYS* 2.9 24.6 + - + +
197C ASP* 3.9 5.4 - - - +
199C PHE* 1.3 80.7 - - + +
201C LYS* 1.3 58.4 + - - +
203C VAL* 3.9 5.9 - - - +
204C GLN* 3.0 42.3 + - + +
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Residues in contact with LYS 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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180C MET* 4.0 40.9 - - + +
197C ASP 3.6 7.9 + - - +
198C LEU* 3.4 13.6 + - + +
199C PHE 2.8 1.4 + - - -
200C LYS* 1.3 79.5 - - - +
202C CYS* 1.3 63.6 + - - +
204C GLN* 3.5 27.3 - - - +
205C SER* 6.0 0.2 - - - -
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Residues in contact with CYS 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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176C GLU 5.1 0.2 - - - -
177C CYS* 3.6 23.8 + - - +
180C MET* 3.6 34.3 - - + +
181C LEU* 3.8 37.5 - - + -
184C THR* 3.9 13.9 - - - -
198C LEU* 3.5 13.9 + - - +
199C PHE* 2.7 17.5 + - + +
201C LYS* 1.3 71.8 - - - +
203C VAL* 1.3 61.9 + - + +
204C GLN 3.0 8.5 + - - -
205C SER* 4.1 6.9 + - - -
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Residues in contact with VAL 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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139C GLU* 4.2 4.9 - - + -
142C LEU* 3.7 19.7 - - + -
158C PHE* 4.1 11.9 - - + -
177C CYS* 4.6 4.3 - - - -
181C LEU* 6.3 0.2 - - + -
199C PHE* 3.5 53.8 - - + +
200C LYS* 3.9 12.1 - - - +
202C CYS* 1.3 75.2 - - + +
204C GLN* 1.3 66.8 + - - +
205C SER 3.4 1.1 - - - -
206C ASN 3.5 2.5 + - - -
207C ILE* 3.2 28.2 + - + +
210C LEU* 3.8 22.0 - - + -
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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