Contacts of the strand formed by residues 228 - 231 (chain C) in PDB entry 1I9R
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 VAL 228 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B ALA* 4.0 13.9 - - + -
124B ALA 5.1 3.4 - - - +
125B HIS* 3.3 14.7 - - + +
147B THR* 3.3 14.3 + - + -
172B TYR* 2.6 19.0 + - + +
258B LEU 5.2 0.7 - - - -
259B LEU* 3.2 43.3 - - + +
168C LEU* 3.4 30.7 - - + -
169C TYR 3.2 13.7 - - - +
170C TYR* 4.1 6.1 - - + -
227C GLY* 1.3 72.6 - - - -
229C PHE* 1.3 69.6 + - - +
261C LEU* 4.5 5.4 - - + -
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Residues in contact with PHE 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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125B HIS* 3.7 23.8 - + - -
145B TYR* 3.9 27.4 - + + -
147B THR* 3.8 5.8 - - - -
167C GLY 3.6 0.2 - - - +
168C LEU* 2.8 10.4 - - - +
169C TYR* 2.7 38.2 + - - +
171C ILE* 4.3 13.7 - - + -
193C LEU* 4.6 3.1 - - + -
205C LEU* 3.7 37.7 - - + -
206C LEU* 3.1 41.3 - - + -
227C GLY* 3.0 32.8 - - - -
228C VAL* 1.3 76.0 - - - +
230C GLU* 1.3 60.8 + - - +
231C LEU* 4.0 14.8 + - + -
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Residues in contact with GLU 230 (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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145B TYR* 2.6 33.4 + - + -
146B TYR 6.1 0.4 - - - +
147B THR* 4.2 8.1 + - - +
149B SER* 6.0 2.3 - - - -
167C GLY* 3.0 16.9 - - - +
168C LEU* 3.5 25.9 - - + +
229C PHE* 1.3 74.5 - - - +
231C LEU* 1.3 66.8 + - - +
232C GLN* 4.2 7.9 + - - +
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Residues in contact with LEU 231 (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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145B TYR* 4.4 0.7 - - - +
163C VAL* 4.0 20.2 - - + -
166C GLN* 3.0 7.1 - - - +
167C GLY 2.4 46.5 + - - +
169C TYR* 3.7 30.7 - - + -
171C ILE* 3.6 32.3 - - + -
195C LEU* 4.2 31.4 - - + -
205C LEU* 5.1 0.9 - - + -
229C PHE* 4.5 8.5 - - + +
230C GLU* 1.3 78.3 - - - +
232C GLN* 1.3 63.6 + - - +
235C ALA* 3.6 11.4 - - + -
236C SER* 6.2 0.2 - - - -
237C VAL* 5.0 6.7 - - + -
258C LEU* 5.3 3.4 - - + -
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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
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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