Contacts of the strand formed by residues 251 - 256 (chain O) in PDB entry 3EXG
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 ILE 251 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17O LEU* 3.9 20.2 - - + -
189O CYS 3.3 2.8 + - - -
190O ILE* 3.6 9.1 - - + +
191O PHE* 3.0 25.9 + - - +
220O ILE* 3.6 6.3 - - - -
221O PRO* 3.3 16.8 - - + +
223O LEU* 3.5 23.3 - - + -
239O PHE* 4.5 4.7 - - + -
240O ALA* 4.3 20.4 - - + +
243O TYR* 4.1 25.1 - - + -
244O CYS* 3.7 24.2 - - - -
250O PRO* 1.3 77.1 - - - +
252O LEU* 1.3 69.8 + - - +
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Residues in contact with LEU 252 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165O TYR* 3.5 22.9 - - - +
179O TYR* 3.6 27.6 - - + +
191O PHE* 3.4 16.6 - - + +
193O CYS* 5.4 2.7 - - + -
213O TYR 3.4 26.2 - - - +
214O TYR* 4.2 10.3 - - - +
217O GLY* 3.9 16.4 - - - +
220O ILE* 3.8 20.0 - - + +
221O PRO 2.8 9.4 + - - +
222O GLY* 2.8 10.4 - - - -
223O LEU* 2.8 35.3 + - - +
251O ILE* 1.3 73.6 - - - +
253O MET* 1.3 59.6 + - - +
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Residues in contact with MET 253 (chain O).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75O LEU* 3.7 30.7 - - + -
190O ILE* 4.7 6.5 - - + -
191O PHE 3.1 9.1 + - - +
192O ILE* 3.3 22.4 - - + +
193O CYS* 2.9 25.7 + - - +
214O TYR* 4.9 1.1 - - - -
223O LEU* 3.3 12.8 - - + +
225O VAL* 3.6 21.3 - - + -
233O VAL* 5.5 0.7 - - + +
236O ALA* 3.8 22.4 - - + -
237O THR* 4.2 13.5 - - + +
240O ALA* 4.3 18.2 - - + -
252O LEU* 1.3 79.7 - - - +
254O GLU* 1.3 58.0 + - - +
255O LEU* 3.7 16.2 - - + -
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Residues in contact with GLU 254 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193O CYS* 3.5 7.2 - - + +
195O ASN* 3.1 35.5 + - + -
211O THR 4.5 0.9 - - - +
212O ASP 3.9 0.3 - - - -
213O TYR* 3.1 29.1 + - + -
214O TYR* 3.0 41.3 + - + +
223O LEU 3.0 8.4 + - - +
224O ARG* 3.3 27.2 + - + +
225O VAL* 2.9 28.4 + - - +
253O MET* 1.3 73.0 - - - +
255O LEU* 1.3 62.1 + - - +
256O GLN* 3.4 8.8 + - + +
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Residues in contact with LEU 255 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71O CYS* 3.5 39.0 - - + +
75O LEU* 4.1 19.7 - - + -
164O LEU* 5.6 0.9 - - + -
192O ILE* 4.0 18.6 - - + -
193O CYS 2.8 13.8 + - - +
194O GLU* 4.5 8.1 - - + -
195O ASN 3.1 21.3 + - - +
225O VAL* 3.8 16.2 - - + -
227O GLY* 4.6 7.0 - - - -
233O VAL* 4.6 8.5 - - + -
253O MET* 3.7 31.4 + - + -
254O GLU* 1.3 75.3 - - - +
256O GLN* 1.3 65.3 + - - +
257O THR* 3.2 5.7 + - - +
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Residues in contact with GLN 256 (chain O).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10O LYS* 5.4 8.0 - - - -
195O ASN* 3.4 15.3 - - - +
197O ARG* 5.1 14.5 - - - +
224O ARG* 3.4 46.6 + - + +
225O VAL 3.0 15.7 + - - +
226O ASP* 4.0 6.2 - - - +
227O GLY* 2.6 27.9 + - - +
228O MET* 4.1 1.7 + - - +
254O GLU* 3.4 20.2 + - - +
255O LEU* 1.3 69.6 - - - +
257O THR* 1.3 57.2 + - - +
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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