Contacts of the strand formed by residues 220 - 229 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188C ASN* 3.7 6.1 - - - +
190C TYR 3.3 15.7 - - - +
191C ASP 3.8 2.2 - - - +
193C ILE* 3.8 26.2 - - + +
216C ILE 3.2 16.1 + - - +
218C ASN 3.2 11.2 - - - +
219C ALA* 1.3 78.2 - - - +
221C LYS* 1.3 62.9 + - - +
224C GLY* 3.9 3.6 - - - +
225C TYR 3.2 46.0 - - - +
226C CYS* 4.0 4.7 - - + +
251C PHE* 3.7 35.4 - - + -
276C LYS* 3.0 28.0 + - - +
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Residues in contact with LYS 221 (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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119C ASN* 5.8 0.7 - - - -
188C ASN* 3.3 32.6 + - - +
189C THR* 3.3 21.1 + - - +
190C TYR 3.0 17.6 + - - +
191C ASP* 3.6 26.5 - - - +
220C LEU* 1.3 76.9 - - - +
222C PRO* 1.3 77.9 - - + +
223C ASN 3.3 3.6 - - - +
224C GLY* 2.9 16.1 + - - +
276C LYS* 3.0 9.2 + - - -
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Residues in contact with PRO 222 (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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188C ASN* 3.2 19.5 - - - +
221C LYS* 1.3 90.7 - - + +
223C ASN* 1.3 67.4 + - - +
224C GLY 3.5 0.2 - - - -
276C LYS* 3.3 27.3 - - + +
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Residues in contact with ASN 223 (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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114C SER* 5.7 0.2 + - - -
221C LYS* 3.3 3.1 - - - +
222C PRO* 1.3 87.8 - - - +
224C GLY* 1.3 65.0 + - - +
225C TYR* 3.4 20.9 - - + +
276C LYS* 4.7 1.8 - - - -
277C THR* 3.8 28.2 - - + +
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Residues in contact with GLY 224 (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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190C TYR 4.4 2.7 - - - -
191C ASP* 3.2 18.6 - - - -
220C LEU* 3.9 15.2 - - - +
221C LYS* 2.9 18.6 + - - -
222C PRO 3.5 0.6 + - - -
223C ASN* 1.3 82.4 - - - +
225C TYR* 1.3 62.8 + - - -
274C CYS 4.4 0.2 - - - +
276C LYS* 3.7 25.2 + - - +
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Residues in contact with TYR 225 (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 PRO* 4.6 10.5 - - + -
113C VAL* 3.6 24.9 + - + +
114C SER* 3.8 37.9 - - - -
191C ASP 3.1 8.3 + - - +
192C VAL* 3.2 6.9 - - + +
193C ILE 2.9 23.4 + - - +
220C LEU* 3.2 7.4 - - - +
223C ASN* 3.4 18.3 - - + +
224C GLY* 1.3 76.8 - - - -
226C CYS* 1.4 60.7 + - - +
274C CYS 3.4 7.2 - - - +
275C SER* 3.3 35.7 - - - -
276C LYS 5.1 0.4 - - - -
277C THR* 3.6 20.9 + - + +
279C THR* 4.5 4.7 + - - -
280C GLY 4.0 5.5 + - - -
281C LEU* 3.6 23.1 - - + -
285C ASN* 5.5 0.5 + - - -
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Residues in contact with CYS 226 (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 ILE* 3.2 10.8 - - + +
195C VAL* 4.1 15.5 - - - -
213C TYR* 4.5 11.4 - - - -
216C ILE* 3.6 38.4 - - + -
220C LEU* 4.0 6.2 - - + +
225C TYR* 1.4 76.1 - - - +
227C VAL* 1.3 79.6 + - - +
228C ALA* 4.6 0.9 - - - -
251C PHE* 4.4 0.4 - - + -
272C LEU 3.8 0.3 - - - +
274C CYS* 2.7 45.9 + - + +
281C LEU* 4.3 0.2 - - - +
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Residues in contact with VAL 227 (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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106C MET* 3.4 26.7 - - - +
109C VAL* 4.8 1.1 - - + -
110C PRO* 3.7 29.4 - - + +
193C ILE 3.1 4.0 + - - +
194C ILE* 3.5 17.9 - - + -
195C VAL 2.8 23.4 + - - -
225C TYR 4.4 0.2 - - - -
226C CYS* 1.3 83.8 - - - +
228C ALA* 1.3 61.8 + - - +
271C ILE* 3.5 15.9 - - + -
272C LEU 3.1 4.7 - - - -
273C CYS* 3.9 22.9 - - - -
281C LEU* 4.0 12.3 - - + -
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Residues in contact with ALA 228 (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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106C MET* 4.3 5.4 - - - -
195C VAL* 3.5 23.3 - - + +
213C TYR* 3.2 28.0 - - + +
226C CYS* 4.6 2.2 - - - -
227C VAL* 1.3 78.3 - - - +
229C GLN* 1.3 70.9 + - - +
230C CYS* 3.2 0.4 + - + -
271C ILE* 3.6 1.7 - - - -
272C LEU* 2.9 36.2 + - + +
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Residues in contact with GLN 229 (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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102C TYR* 3.4 32.1 - - + +
106C MET* 3.7 7.5 - - + +
195C VAL 3.0 13.0 + - - +
197C SER* 3.2 38.3 + - - +
198C SER 3.4 15.2 + - - -
208C PHE* 3.8 16.1 - - - -
228C ALA* 1.3 75.9 - - - +
230C CYS* 1.3 61.4 + - - +
231C GLU* 3.3 32.6 + - - +
243C MET* 6.1 0.9 - - - +
269C ILE* 3.5 8.8 - - + +
270C GLY 3.6 5.6 - - - -
501C JFQ 3.7 14.8 - - - +
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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