Contacts of the strand formed by residues 193 - 199 (chain C) in PDB entry 1RX0
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 ILE 193 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148C ALA* 3.8 19.7 - - - +
150C LEU* 3.6 28.5 - - + -
182C MET* 4.0 20.0 - - + -
183C CYS 3.3 11.4 - - - +
184C ARG* 3.9 10.1 - - - +
189C GLY 3.8 12.1 - - - +
190C PRO* 3.3 10.1 + - + +
191C LYS 3.3 0.4 - - - -
192C GLY* 1.3 80.5 - - - +
194C SER* 1.3 72.0 + - - +
241C GLY* 3.1 14.4 - - - +
243C GLY 2.8 18.4 + - - -
244C PHE* 3.8 37.2 + - + +
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Residues in contact with SER 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181C VAL 3.6 0.9 - - - +
182C MET* 3.4 4.0 - - - -
183C CYS* 2.8 33.2 + - - +
185C THR* 2.7 39.9 + - - +
193C ILE* 1.3 70.5 - - - +
195C CYS* 1.3 61.9 + - - +
196C ILE* 4.7 3.1 - - - -
236C ARG* 4.3 16.6 - - - -
239C SER 4.7 0.9 - - - -
240C GLU* 3.2 7.7 - - - +
241C GLY 3.0 17.4 + - - +
243C GLY* 3.6 9.4 - - - +
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Residues in contact with CYS 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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110C MET* 4.3 9.6 - - - -
180C VAL* 3.5 33.0 - - - -
181C VAL 3.5 3.1 - - - -
182C MET* 4.1 16.4 - - - -
194C SER* 1.3 72.0 - - - +
196C ILE* 1.3 63.6 + - - +
236C ARG* 3.4 8.0 - - - +
237C ILE* 2.8 58.8 + - + +
239C SER 5.5 0.6 + - - -
243C GLY* 3.7 11.1 - - - -
246C ILE* 4.3 9.9 - - + -
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Residues in contact with ILE 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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154C ALA* 4.0 4.5 - - + -
161C TYR* 3.6 36.1 - - + -
163C LEU* 4.5 5.4 - - + -
179C TYR 3.4 0.5 - - - +
180C VAL* 4.7 0.4 - - - -
181C VAL* 2.8 45.6 + - + +
183C CYS* 3.2 28.9 - - - -
185C THR* 4.7 3.4 - - + -
194C SER 4.7 0.4 - - - -
195C CYS* 1.3 82.5 - - - +
197C VAL* 1.3 77.3 + - - +
198C VAL* 4.1 5.6 - - + +
231C VAL* 3.7 21.8 - - + -
232C PRO 4.7 2.2 - - - +
235C ASN* 3.7 12.6 - - + +
236C ARG* 4.1 12.8 - - + +
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Residues in contact with VAL 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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111C ILE* 3.9 21.5 - - + -
123C PHE* 3.7 32.5 - - + -
178C ILE* 3.7 26.7 - - + -
179C TYR 3.3 4.9 - - - +
180C VAL* 4.7 8.7 - - + -
196C ILE* 1.3 73.2 - - - +
198C VAL* 1.3 64.1 + - - +
199C GLU* 4.6 0.4 - - + -
231C VAL* 3.4 6.8 - - - +
235C ASN* 2.9 41.5 + - + +
237C ILE* 3.9 26.5 - - + -
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Residues in contact with VAL 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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163C LEU* 4.0 22.9 - - + -
178C ILE* 3.8 1.0 - - - -
179C TYR* 2.8 44.8 + - + +
181C VAL* 3.6 24.7 - - + -
196C ILE* 4.1 4.3 - - + +
197C VAL* 1.3 77.8 - - - +
199C GLU* 1.3 66.3 + - - +
202C THR* 4.4 3.4 - - - +
205C LEU* 4.1 23.1 - - + -
226C PHE* 4.1 11.4 - - + -
229C CYS* 4.4 7.4 - - - -
231C VAL* 4.1 22.7 - - + -
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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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122C LYS* 4.2 19.4 + - - -
123C PHE* 3.7 25.5 - - + -
132C LYS* 4.0 15.2 + - - -
177C ASP 3.4 4.7 - - - +
178C ILE* 3.8 21.9 - - + +
197C VAL* 4.3 2.4 + - + -
198C VAL* 1.3 76.9 - - - +
200C LYS* 1.3 69.6 + - - +
202C THR* 2.6 34.6 + - - +
205C LEU* 3.8 6.1 - - - +
231C VAL* 5.7 0.4 - - - +
235C ASN* 4.5 12.3 + - - +
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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
------------------------------------------------------------
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