Contacts of the strand formed by residues 231 - 236 (chain C) in PDB entry 3OEE
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 SER 231 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C LEU 3.5 0.7 - - - -
107C GLY* 2.7 32.7 + - - -
108C ARG 3.8 0.9 + - - +
185C ILE* 3.7 12.7 - - - +
203C CYS* 3.0 24.3 - - - +
205C TYR* 5.9 1.3 - - - -
222C LEU* 4.3 17.5 - - - +
227C ALA 2.9 18.3 + - - -
228C MET* 3.2 9.7 + - - +
230C TYR* 1.3 81.5 - - - +
232C ILE* 1.3 62.6 + - - +
233C ILE* 4.5 7.4 - - - -
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Residues in contact with ILE 232 (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 GLY 5.1 1.1 - - - +
105C LEU* 3.4 40.4 - - + +
106C LEU* 3.9 10.8 - - + -
108C ARG 3.5 9.4 - - - +
110C VAL* 4.9 2.2 - - + -
203C CYS 2.9 6.5 + - - +
204C VAL* 3.4 13.0 - - + +
205C TYR 3.0 24.4 + - - +
231C SER* 1.3 77.6 - - - +
233C ILE* 1.3 76.0 + - - +
234C VAL* 4.3 8.7 - - + -
255C ILE* 3.3 42.8 - - + -
259C PHE* 3.9 24.5 - - + -
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Residues in contact with ILE 233 (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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108C ARG 2.9 7.6 + - - +
109C VAL* 3.5 37.1 - - + -
110C VAL* 3.0 27.1 + - - +
205C TYR* 3.5 28.9 - - + +
207C ALA* 5.3 0.4 - - + -
215C VAL* 4.1 23.6 - - + -
218C LEU* 4.8 2.7 - - + -
219C VAL* 3.8 11.4 - - + -
222C LEU* 3.9 28.5 - - + -
228C MET* 4.2 9.4 - - - -
231C SER* 4.5 4.3 - - - -
232C ILE* 1.3 83.2 - - - +
234C VAL* 1.3 73.1 + - - +
235C ALA* 4.1 0.9 - - + -
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Residues in contact with VAL 234 (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 VAL* 3.6 7.0 - - + -
111C ASP 3.9 16.2 - - - +
112C ALA* 4.3 10.8 - - - +
204C VAL* 4.7 6.3 - - + -
205C TYR 2.9 11.6 + - - +
206C VAL* 3.3 6.1 - - + +
207C ALA 2.8 25.8 + - - +
232C ILE* 4.3 5.6 - - + -
233C ILE* 1.3 78.6 - - - +
235C ALA* 1.3 61.9 + - - +
248C ALA* 4.0 25.8 - - + +
251C THR* 4.7 3.1 - - - +
252C ALA* 4.0 16.6 - - + -
255C ILE* 3.7 30.1 - - + -
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Residues in contact with ALA 235 (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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109C VAL* 4.7 4.9 - - + -
110C VAL 3.1 11.9 + - - +
111C ASP* 3.8 18.8 - - - +
112C ALA 4.2 2.3 + - - -
117C ILE* 4.3 17.0 - - + +
207C ALA* 3.4 12.1 - - + -
215C VAL* 4.5 13.2 - - + -
233C ILE* 4.1 0.6 - - + -
234C VAL* 1.3 74.7 - - - +
236C ALA* 1.3 59.2 + - - +
237C THR* 3.6 21.1 - - + -
240C GLU* 3.3 10.2 - - - +
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Residues in contact with ALA 236 (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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112C ALA* 4.7 2.7 - - + +
207C ALA 2.7 10.5 + - - +
208C VAL* 3.2 3.7 - - - -
209C GLY 2.7 28.4 + - - -
234C VAL 4.1 0.8 + - - -
235C ALA* 1.3 72.1 - - - +
237C THR* 1.3 58.6 + - - +
240C GLU* 3.4 6.5 - - - -
244C LEU* 3.2 33.0 - - + +
245C GLN* 3.5 19.9 - - + +
248C ALA* 3.6 14.0 - - + +
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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