Contacts of the strand formed by residues 323 - 328 (chain O) in PDB entry 2V10
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 PHE 323 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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277O TYR* 3.6 45.5 - + + -
278O THR 4.1 15.0 - - - -
279O LEU* 5.6 1.1 - - + -
319O PHE* 3.3 33.5 + + + +
320O ILE* 3.1 15.5 - - - +
322O LYS* 1.3 98.2 - - + +
324O TYR* 1.3 64.8 + - - +
325O THR* 3.4 7.8 + - - -
336O PHE* 4.2 17.5 - - + -
337O ALA 3.2 20.4 - - - +
338O LEU* 3.6 24.9 - - + -
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Residues in contact with TYR 324 (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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159O SER* 3.6 30.5 - - - -
160O PHE 3.6 12.3 - - - -
161O TYR* 3.8 18.2 - + + +
175O GLN* 3.8 12.0 + - - -
177O VAL* 4.3 1.2 - - - +
181O SER* 3.6 7.1 - - - -
182O ASP 2.8 31.7 + - - -
185O HIS* 3.5 40.2 - - + -
186O TYR* 3.9 21.1 - + + -
190O PHE* 3.9 21.4 - + - -
320O ILE 4.2 2.9 - - - -
323O PHE* 1.3 73.3 - - - +
325O THR* 1.4 57.2 + - - +
335O GLY 3.9 0.3 - - - +
336O PHE* 3.5 4.9 - - - -
337O ALA 2.9 28.4 + - - +
339O ALA* 3.4 14.6 - - + +
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Residues in contact with THR 325 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159O SER* 3.0 6.3 + - - -
160O PHE* 2.9 43.0 + - - -
225O VAL* 4.4 2.7 - - + -
320O ILE* 4.3 14.4 - - - +
323O PHE 3.4 5.7 + - - -
324O TYR* 1.4 70.3 - - - +
326O GLU* 1.3 69.3 + - - +
327O PHE* 3.3 38.4 + - + -
334O ILE* 4.2 4.0 - - + -
335O GLY 3.4 3.6 - - - +
336O PHE* 3.2 36.0 - - + -
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Residues in contact with GLU 326 (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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155O GLU* 5.7 0.5 - - - +
157O VAL* 4.0 34.1 - - + +
159O SER* 3.2 16.6 - - - +
180O GLY 4.9 0.2 - - - -
181O SER* 3.8 11.4 + - - -
190O PHE* 3.1 39.8 - - + -
192O TYR* 2.9 30.4 + - - -
325O THR* 1.3 79.3 - - - +
327O PHE* 1.3 63.3 + - - +
328O ASP* 3.8 3.1 + - - +
334O ILE* 3.2 5.9 - - - -
335O GLY 2.7 38.6 + - - +
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Residues in contact with PHE 327 (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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39O THR* 4.0 9.4 - - + -
157O VAL* 3.2 5.8 - - - +
158O PHE* 2.8 71.8 + + + +
160O PHE* 3.7 23.6 - + - -
201O TRP* 3.5 39.3 - + + -
225O VAL* 3.6 36.8 - - + -
227O THR* 3.8 17.9 - - + -
325O THR* 3.3 26.2 - - + -
326O GLU* 1.3 74.1 - - - +
328O ASP* 1.3 60.5 + - - +
329O ARG 4.0 0.4 + - - -
333O ARG 4.2 0.9 - - - -
334O ILE* 4.0 7.9 - - + +
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Residues in contact with ASP 328 (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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156O ASP 3.5 6.7 - - - +
157O VAL* 3.7 15.0 - - + +
192O TYR* 4.2 8.1 - - + -
201O TRP* 3.5 7.0 - - - -
326O GLU* 4.6 7.2 - - - +
327O PHE* 1.3 74.0 - - - +
329O ARG* 1.3 62.9 + - - +
330O ARG* 3.1 17.0 + - - +
331O ASN* 3.3 16.3 + - - +
332O ASN* 2.8 25.6 + - - -
333O ARG* 3.0 47.1 + - + +
334O ILE* 5.0 0.2 - - - -
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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