Contacts of the strand formed by residues 220 - 230 (chain A) in PDB entry 3RIE
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 LEU 220 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189A THR* 3.9 7.5 - - - +
190A TYR 3.3 12.3 - - - +
191A ASP 4.3 0.2 - - - +
192A VAL 4.3 0.7 - - - -
193A ILE* 3.6 26.5 - - + +
216A ILE 3.3 15.5 - - - +
217A TYR 3.1 8.8 + - - +
218A ASN 3.9 5.2 - - - +
219A ALA* 1.4 81.1 - - - +
221A LYS* 1.3 66.7 + - - +
222A PRO* 4.6 0.7 - - - +
224A GLY* 4.1 5.6 - - - +
225A TYR 3.3 41.1 - - - +
226A CYS* 4.0 5.4 - - + +
251A PHE* 3.7 31.9 - - + -
276A LYS* 3.3 20.8 + - - -
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Residues in contact with LYS 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A ASN* 5.3 3.2 - - - +
189A THR* 3.0 44.7 + - - +
190A TYR 2.7 21.4 + - - +
191A ASP* 3.2 30.0 + - - +
220A LEU* 1.3 76.5 - - - +
222A PRO* 1.4 78.7 - - + +
223A ASN* 3.2 16.4 - - - +
224A GLY* 3.1 15.1 + - - +
276A LYS* 3.2 10.4 + - - +
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Residues in contact with PRO 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A THR* 5.7 0.2 - - - +
220A LEU 4.6 0.9 - - - +
221A LYS* 1.4 92.6 - - + +
223A ASN* 1.3 59.8 + - + +
224A GLY 3.5 0.4 - - - -
276A LYS* 3.2 28.7 - - + +
277A THR* 5.1 1.7 - - - +
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Residues in contact with ASN 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A SER* 5.5 1.0 + - - -
191A ASP* 5.1 3.1 + - - +
221A LYS* 3.4 18.7 - - - +
222A PRO* 1.3 75.7 - - + +
224A GLY* 1.3 62.2 + - - +
225A TYR* 3.4 23.0 - - - +
276A LYS* 4.9 1.8 - - - -
277A THR* 4.8 18.4 - - + -
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Residues in contact with GLY 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A ASP* 3.3 18.4 - - - -
220A LEU* 4.1 14.2 - - - +
221A LYS* 3.1 20.2 + - - -
222A PRO 3.5 0.8 + - - -
223A ASN* 1.3 82.2 - - - +
225A TYR* 1.3 62.8 + - - -
275A SER* 4.4 0.7 - - - -
276A LYS* 3.7 25.0 + - - +
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Residues in contact with TYR 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A PRO* 4.5 12.1 - - + -
113A VAL* 3.7 26.2 + - + +
114A SER* 4.0 35.7 - - - -
191A ASP 3.1 8.3 + - - +
192A VAL* 3.2 6.5 - - + +
193A ILE 3.0 23.4 + - - +
220A LEU* 3.3 7.1 - - - +
223A ASN* 3.4 20.2 + - - +
224A GLY* 1.3 74.9 - - - -
226A CYS* 1.3 60.2 + - - +
227A VAL 4.4 0.2 - - - -
274A CYS 3.4 4.0 - - - +
275A SER* 3.3 37.2 - - - -
276A LYS 5.2 0.4 - - - -
277A THR* 4.1 15.4 + - - +
279A THR* 4.8 3.8 + - - -
280A GLY 4.1 5.3 + - - -
281A LEU* 3.5 24.7 - - + -
285A ASN* 5.4 0.7 + - - -
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Residues in contact with CYS 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A ILE* 3.1 11.2 - - + +
195A VAL* 3.9 17.5 - - - -
213A TYR* 4.8 8.1 - - - -
216A ILE* 3.6 35.9 - - + -
220A LEU* 4.0 6.3 - - + +
225A TYR* 1.3 74.9 - - - +
227A VAL* 1.3 78.9 + - - +
228A ALA* 4.6 4.7 - - - -
272A LEU 3.7 1.2 - - - +
273A CYS* 3.7 1.0 - - - -
274A CYS* 2.8 49.1 + - + +
281A LEU* 4.2 0.5 - - - +
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Residues in contact with VAL 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A MET* 3.4 28.3 - - - +
109A VAL* 4.6 2.2 - - + -
110A PRO* 3.8 32.9 - - + +
193A ILE 3.1 4.6 + - - +
194A ILE* 3.5 17.5 - - + -
195A VAL 2.9 23.9 + - - +
226A CYS* 1.3 79.0 - - - +
228A ALA* 1.3 62.6 + - - +
271A ILE* 3.5 16.4 - - + -
272A LEU 3.2 3.1 - - - -
273A CYS* 3.7 25.8 - - - -
281A LEU* 4.2 6.5 - - + -
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Residues in contact with ALA 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A MET* 4.2 3.8 - - - -
195A VAL* 3.6 24.5 - - + -
213A TYR* 3.3 28.3 - - + +
226A CYS* 4.7 2.5 - - - -
227A VAL* 1.3 77.8 - - - +
229A GLN* 1.3 67.3 + - - +
230A CYS* 3.8 0.2 - - - +
271A ILE* 3.4 3.1 - - - -
272A LEU* 2.8 40.2 + - + +
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Residues in contact with GLN 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A TYR* 3.3 34.3 - - + +
106A MET* 3.6 6.6 - - + +
195A VAL* 3.1 15.5 + - - +
197A SER* 3.2 43.8 + - - +
198A SER 3.5 7.5 + - - -
199A ASP* 4.3 8.6 + - - +
208A PHE* 3.5 29.1 - - - -
228A ALA* 1.3 77.3 - - - +
230A CYS* 1.3 67.2 + - - +
269A ILE* 3.4 17.5 - - + +
270A GLY 3.5 5.6 - - - +
501A JFQ 4.0 10.5 - - + +
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Residues in contact with CYS 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A PHE* 5.5 3.6 - - - -
228A ALA* 5.7 0.2 - - + -
229A GLN* 1.3 81.5 + - - +
231A GLU* 1.3 76.2 + - - +
239A THR* 5.9 0.4 - - - -
240A ILE* 4.4 10.1 - - - -
243A MET* 4.1 29.8 - - - -
256A TYR* 3.9 21.1 - - + -
269A ILE* 3.3 10.0 - - - +
270A GLY 2.8 22.3 + - - +
272A LEU* 3.6 37.7 - - + +
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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