Contacts of the strand formed by residues 319 - 329 (chain O) in PDB entry 3H1J
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 319 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168O TYR* 3.1 29.0 + - - -
172O LEU* 4.6 2.7 - - - -
237O ALA* 4.6 3.6 - - - -
260O GLU* 3.1 30.0 + - - +
261O GLY 5.4 0.9 - - - -
263O ALA* 3.5 16.0 - - - +
316O TYR* 2.7 33.8 + - - +
317O SER 3.5 1.6 - - - -
318O ASP* 1.3 86.8 - - - +
320O GLY* 1.3 66.4 + - - +
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Residues in contact with GLY 320 (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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168O TYR* 3.3 15.1 + - - -
260O GLU* 3.4 10.7 - - - +
261O GLY 3.0 20.8 + - - -
262O ALA 3.5 18.8 + - - -
314O VAL 3.5 6.3 - - - -
316O TYR* 4.2 5.4 - - - -
319O SER* 1.3 83.8 + - - +
321O LEU* 1.3 61.5 + - - +
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Residues in contact with LEU 321 (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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163O LEU* 4.3 16.6 - - + -
164O HIS* 4.1 26.5 - - + +
167O ALA* 3.6 35.7 - - + -
168O TYR* 3.7 19.7 - - + +
239O TYR* 4.3 10.1 - - + -
258O VAL* 3.8 14.6 - - + -
259O THR 3.5 7.6 - - - +
261O GLY* 3.9 2.4 - - - +
312O PHE* 4.1 14.8 - - + -
313O ASN* 3.5 2.1 - - - +
314O VAL* 2.9 40.9 + - + +
316O TYR* 5.3 2.9 - - + -
320O GLY* 1.3 81.1 - - - +
322O PHE* 1.3 62.1 + - - +
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Residues in contact with PHE 322 (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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258O VAL* 3.0 6.5 - - - +
259O THR* 2.8 35.5 + - - +
260O GLU 5.1 0.7 - - - +
261O GLY* 4.2 8.7 - - - -
272O PHE* 3.2 52.5 - + + -
275O LEU* 3.6 34.1 - - + -
276O GLN* 4.4 7.4 - - + -
279O LEU* 4.1 11.0 - - + -
311O ALA* 5.2 1.8 - - + -
312O PHE 3.4 18.2 - - - -
313O ASN* 3.6 17.3 - - + +
321O LEU* 1.3 75.9 - - - +
323O GLY* 1.3 70.3 + - - +
344O LEU* 4.4 16.8 - - + -
417O PHE* 3.8 14.9 - + + -
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Residues in contact with GLY 323 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257O VAL 3.0 13.0 - - - -
258O VAL* 3.9 2.7 - - - +
279O LEU* 5.9 0.2 - - - +
311O ALA* 3.5 5.4 - - - +
312O PHE* 2.6 37.5 + - - +
322O PHE* 1.3 86.8 - - - +
324O PHE* 1.3 58.0 + - - +
344O LEU* 5.3 2.9 - - - +
417O PHE* 3.7 14.1 - - - -
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Residues in contact with PHE 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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255O ALA* 5.9 1.3 - - + -
256O ALA* 3.2 2.8 - - - +
257O VAL* 2.9 64.3 + - + -
258O VAL* 5.2 0.2 - - - +
295O LEU* 3.8 15.7 - - + -
310O SER 3.0 15.3 - - - +
312O PHE* 3.9 4.0 - - - +
323O GLY* 1.3 77.6 - - - +
325O TYR* 1.3 57.7 + - - +
326O THR* 3.7 17.5 - - + -
337O ILE* 3.9 20.9 - - + -
340O ALA* 3.5 37.0 - - + -
341O MET* 3.6 32.5 - - + -
344O LEU* 4.5 9.4 - - + -
417O PHE* 3.9 10.8 - + - -
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Residues in contact with TYR 325 (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 PRO 3.8 0.2 + - - -
156O GLN* 3.4 21.8 + - + -
159O VAL* 3.1 36.4 - - + +
160O LEU* 4.1 3.6 - - + -
254O HIS* 2.7 39.1 + + + +
255O ALA 3.2 9.0 - - - -
256O ALA* 3.9 13.9 - - + +
309O ALA* 3.3 0.2 - - - -
310O SER 2.9 23.3 + - - +
312O PHE* 4.4 3.7 - - + +
324O PHE* 1.3 72.7 - - - +
326O THR* 1.3 75.1 + - - +
327O ILE* 3.8 5.8 - - + -
58V ARG 5.3 0.2 - - - -
59V SER* 2.7 26.8 + - - -
60V ALA* 2.9 51.8 - - + +
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Residues in contact with THR 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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253O VAL 4.2 1.6 + - - -
254O HIS* 3.4 4.2 - - - -
255O ALA* 2.7 52.0 + - - +
308O ASP 3.2 7.0 - - - -
309O ALA* 3.7 17.7 - - + -
324O PHE* 3.7 26.9 - - + -
325O TYR* 1.3 81.3 - - - +
327O ILE* 1.3 63.9 + - - +
328O SER* 5.3 1.2 + - - -
336O VAL* 3.9 21.0 - - + +
337O ILE* 4.0 11.5 - - - +
340O ALA* 4.5 5.4 - - + -
59V SER* 3.7 0.2 - - - -
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Residues in contact with ILE 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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252O LEU* 4.1 13.5 - - + -
253O VAL 3.5 3.8 - - - -
254O HIS* 3.5 44.6 - - + +
307O PHE* 3.4 1.4 - - - +
308O ASP* 2.6 37.8 + - + +
325O TYR* 3.8 2.7 - - + -
326O THR* 1.3 78.7 - - - +
328O SER* 1.3 66.7 + - - +
49V LEU* 5.2 2.0 - - + -
55V MET* 3.1 25.4 - - + -
58V ARG* 3.3 46.2 - - + +
59V SER* 3.7 9.4 - - - +
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Residues in contact with SER 328 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252O LEU* 3.4 11.9 - - - +
253O VAL* 2.9 28.2 + - - +
306O PRO 4.2 2.5 - - - -
307O PHE* 4.0 11.2 - - - +
326O THR* 5.3 1.4 + - - -
327O ILE* 1.3 80.0 - - - +
329O GLN* 1.3 76.5 + - - +
332O HIS* 4.5 1.8 - - - -
333O ALA* 3.7 17.5 - - - +
336O VAL* 3.6 30.9 - - - +
337O ILE* 6.0 0.2 - - - +
55V MET* 4.7 0.4 - - - -
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Residues in contact with GLN 329 (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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251O SER 4.5 0.7 - - - -
252O LEU* 4.1 14.1 - - + -
253O VAL* 4.5 0.2 - - - +
305O GLN* 3.3 47.0 - - + +
306O PRO* 3.6 17.2 + - - +
328O SER* 1.3 89.5 + - - +
330O ALA* 1.3 66.8 + - - +
331O ALA* 3.3 4.7 - - - +
332O HIS* 3.4 19.2 + - + +
333O ALA* 3.3 9.4 + - - +
50V LEU* 4.1 11.2 - - - +
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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