Contacts of the strand formed by residues 216 - 220 (chain C) in PDB entry 1I0E
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 GLY 216 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173C TYR* 2.9 23.4 + - - -
174C TYR 3.6 9.9 - - - -
176C LEU* 4.0 6.3 - - - -
194C PHE* 3.7 3.4 - - - -
215C ARG* 1.3 75.6 - - - +
217C ILE* 1.3 66.3 + - - -
228C TRP* 3.7 2.8 - - - -
229C VAL* 3.0 32.8 + - - +
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Residues in contact with ILE 217 (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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173C TYR* 3.6 0.8 - - - -
174C TYR* 2.8 45.5 + - + +
176C LEU* 4.6 7.0 - - + -
179C MET* 4.9 4.5 - - + -
187C LEU* 5.3 5.6 - - + -
192C PHE* 3.9 9.4 - - + +
193C LEU* 3.0 28.3 - - + +
194C PHE* 3.1 51.4 - - + +
216C GLY* 1.3 76.0 - - - -
218C TRP* 1.3 67.9 + - - +
219C HIS* 5.2 2.7 - - - +
226C LEU* 4.7 8.7 - - + -
227C VAL 3.6 2.9 - - - +
228C TRP* 3.2 18.8 - - + +
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Residues in contact with TRP 218 (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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159C VAL* 5.2 0.4 - - - -
162C LEU* 3.1 65.9 - - + +
163C ASN* 4.1 8.3 - - - +
165C LEU* 4.1 14.4 - - + -
169C PHE* 3.5 27.6 - - - -
171C GLY* 3.8 12.0 - - - -
172C LYS 3.3 27.7 - - - +
173C TYR* 3.9 17.0 - - + -
217C ILE* 1.3 75.7 - - - +
219C HIS* 1.3 72.9 + - - +
220C ASN* 3.7 9.2 - - + -
225C PHE* 3.4 38.6 - + - -
226C LEU* 3.4 1.4 - - - +
227C VAL* 2.9 44.9 + - + +
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Residues in contact with HIS 219 (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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171C GLY* 3.1 4.7 - - - -
172C LYS* 3.0 24.2 + - - +
174C TYR* 3.4 38.8 - + - -
187C LEU* 4.1 21.6 - - + +
192C PHE* 4.4 9.8 - + - -
217C ILE* 5.2 3.6 - - + +
218C TRP* 1.3 92.4 + - - +
220C ASN* 1.3 85.7 + - - +
221C ASP* 4.8 1.5 - - - +
223C LYS* 3.5 36.3 - - + +
225C PHE 3.5 10.3 - - - +
226C LEU* 4.0 13.9 - - + -
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Residues in contact with ASN 220 (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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168C GLU 3.7 25.2 + - - +
169C PHE* 4.5 5.9 - - - -
170C LYS 3.3 15.5 - - - +
171C GLY* 3.4 3.4 - - - -
218C TRP* 3.7 5.1 - - + -
219C HIS* 1.3 93.8 + - - +
221C ASP* 1.3 62.1 + - - +
222C ASN* 3.8 5.1 - - - +
223C LYS* 2.5 32.9 + - - -
224C SER* 2.7 31.0 + - - -
225C PHE* 3.1 29.9 + - - +
252C ARG* 4.9 2.8 - - - +
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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