Contacts of the strand formed by residues 193 - 199 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148D ALA* 3.8 22.9 - - - +
150D LEU* 3.7 24.0 - - + -
182D MET* 4.0 20.4 - - + -
183D CYS 3.3 10.5 - - - +
184D ARG* 4.0 9.6 - - - +
189D GLY 3.8 10.5 - - - +
190D PRO* 3.2 10.7 + - + +
191D LYS 3.3 0.2 - - - -
192D GLY* 1.3 82.7 - - - +
194D SER* 1.3 71.8 + - - +
241D GLY* 3.1 14.4 - - - +
243D GLY 2.8 17.7 + - - -
244D PHE* 3.8 39.8 + - + +
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Residues in contact with SER 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161D TYR* 5.9 0.2 - - - -
181D VAL 3.6 0.7 - - - +
182D MET* 3.3 5.0 - - - -
183D CYS* 2.7 35.8 + - - -
185D THR* 2.6 39.0 + - - +
192D GLY 4.1 0.2 + - - -
193D ILE* 1.3 71.7 - - - +
195D CYS* 1.3 60.0 + - - +
196D ILE* 6.0 0.2 - - - -
236D ARG* 4.3 16.6 - - - -
239D SER 4.8 0.9 - - - -
240D GLU* 3.2 7.7 - - - +
241D GLY 3.1 16.7 + - - +
243D GLY* 3.6 9.2 - - - +
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Residues in contact with CYS 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D MET* 4.3 9.9 - - - -
180D VAL* 3.4 32.8 - - - -
181D VAL 3.6 3.4 - - - -
182D MET* 4.0 16.2 - - - -
194D SER* 1.3 72.9 - - - +
196D ILE* 1.3 63.0 + - - +
236D ARG* 3.3 9.1 - - - +
237D ILE* 2.8 58.4 + - + +
239D SER 5.5 0.4 + - - -
243D GLY* 3.7 12.6 - - - +
246D ILE* 4.3 8.3 - - + -
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Residues in contact with ILE 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161D TYR* 3.6 35.4 - - + -
163D LEU* 4.2 12.3 - - + -
179D TYR 3.5 0.5 - - - +
180D VAL* 4.8 1.1 - - - -
181D VAL* 2.8 54.7 + - + +
183D CYS* 3.6 22.0 - - - -
194D SER* 6.0 0.7 - - - -
195D CYS* 1.3 77.5 - - - +
197D VAL* 1.3 72.6 + - - +
198D VAL* 4.4 1.3 - - + -
231D VAL* 3.4 28.7 - - + -
232D PRO 3.9 4.7 - - - +
235D ASN 3.6 15.3 - - - +
236D ARG* 4.1 4.7 - - + +
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Residues in contact with VAL 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D ILE* 3.9 22.0 - - + -
123D PHE* 3.9 29.4 - - + -
178D ILE* 3.8 28.9 - - + -
179D TYR 3.3 5.2 - - - +
180D VAL* 4.8 6.5 - - + -
196D ILE* 1.3 73.1 - - - +
198D VAL* 1.3 65.8 + - - +
199D GLU* 4.6 0.7 - - + -
231D VAL* 3.4 6.6 - - - +
235D ASN* 2.8 44.4 + - + +
237D ILE* 3.9 27.6 - - + -
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Residues in contact with VAL 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163D LEU* 4.0 22.0 - - + -
178D ILE* 3.8 0.7 - - - -
179D TYR* 2.8 44.7 + - + +
181D VAL* 3.7 24.5 - - + -
196D ILE* 4.1 4.7 - - + +
197D VAL* 1.3 78.5 - - - +
199D GLU* 1.3 71.3 + - - +
202D THR* 4.3 9.2 - - - +
205D LEU* 4.1 17.9 - - + -
226D PHE* 4.2 11.0 - - + -
229D CYS* 4.5 2.2 - - - -
231D VAL* 4.1 22.2 - - + -
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Residues in contact with GLU 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122D LYS* 4.1 18.2 + - - -
123D PHE* 3.8 23.6 - - + -
132D LYS* 5.2 9.9 + - - -
177D ASP 3.4 4.3 - - - +
178D ILE* 3.8 21.9 - - + +
197D VAL* 4.3 3.3 + - + -
198D VAL* 1.3 78.1 - - - +
200D LYS* 1.3 68.1 + - - +
202D THR* 2.6 34.6 + - - +
205D LEU* 3.8 6.0 - - - +
231D VAL* 5.7 0.2 - - - +
235D ASN* 4.6 12.4 + - - +
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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