Contacts of the strand formed by residues 322 - 328 (chain B) in PDB entry 1UES
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 GLY 322 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318B LEU* 4.4 2.9 - - - -
321B SER* 1.3 78.4 - - - +
323B TRP* 1.3 64.0 + - - -
339B GLU 3.2 11.7 - - - -
340B PRO* 4.1 0.9 - - - -
341B ASN 3.5 6.1 - - - -
358B VAL* 2.8 41.0 + - - +
359B TRP* 3.2 16.9 - - - +
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Residues in contact with TRP 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270B GLN* 2.8 22.3 + - - -
273B ASN* 3.1 52.6 - - + +
274B HIS* 3.4 33.9 - + - -
277B TYR* 4.0 12.3 - + + -
318B LEU* 3.4 8.9 - - - +
322B GLY* 1.3 73.8 - - - -
324B VAL* 1.3 60.1 + - - +
325B TRP* 3.7 11.9 - - + -
339B GLU* 2.8 42.2 + - + +
341B ASN 3.1 18.1 + - - -
343B GLY 3.9 6.1 - - - -
355B THR* 3.4 24.2 - - + +
356B PHE 3.5 5.2 - - - -
357B ASP* 3.3 50.0 - - + -
358B VAL* 4.4 0.7 - - - -
359B TRP* 3.7 3.6 - - - +
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Residues in contact with VAL 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311B PHE* 3.6 35.4 - - + +
314B ALA* 3.8 28.5 - - + +
315B GLY* 3.9 24.7 - - - +
318B LEU* 4.6 1.8 - - + +
323B TRP* 1.3 74.4 - - - +
325B TRP* 1.3 62.9 + - - +
336B ILE* 4.0 4.5 - - + -
337B GLU 3.5 5.2 - - - +
338B LYS* 4.7 1.1 - - - +
355B THR* 3.0 16.7 + - - -
356B PHE* 3.0 48.9 + - + +
358B VAL* 4.7 3.1 - - + +
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Residues in contact with TRP 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273B ASN* 3.0 31.6 + - - -
276B LEU* 3.5 32.3 - - + -
311B PHE* 3.6 5.2 - - - -
323B TRP* 3.7 14.0 - - + +
324B VAL* 1.3 73.5 - - - +
326B LEU* 1.3 67.8 + - - +
327B ALA 3.9 0.2 + - - -
335B SER 3.4 1.0 - - - +
336B ILE* 3.3 5.2 - - - -
337B GLU* 2.7 47.5 + - + +
339B GLU* 3.7 17.3 - - + -
343B GLY 3.9 1.4 + - - -
344B ASN* 3.3 7.6 - - - -
345B PRO* 3.5 34.2 - - + +
352B PRO* 3.3 31.4 - - + -
353B LEU 3.7 2.7 - - - -
354B LEU 3.1 26.5 - - - -
355B THR* 3.3 39.9 + - + -
390B ARG* 5.0 0.7 - - - -
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Residues in contact with LEU 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293B LEU* 4.7 4.7 - - + -
297B ILE* 4.5 14.8 - - + -
301B PHE* 4.7 2.7 - - + -
307B PHE* 3.9 32.1 - - + -
311B PHE* 3.5 16.3 - - + -
325B TRP* 1.3 75.0 - - - +
327B ALA* 1.3 59.0 + - - +
334B LEU* 4.0 28.0 - - + -
335B SER 3.4 15.0 - - - +
336B ILE* 4.9 0.2 - - + -
353B LEU* 2.9 46.4 + - + -
354B LEU* 2.8 27.1 + - + +
384B TRP* 5.0 1.3 - - + -
387B VAL* 5.0 4.5 - - + -
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Residues in contact with ALA 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325B TRP 3.9 0.2 - - - -
326B LEU* 1.3 74.8 - - - +
328B SER* 1.3 61.6 + - - +
334B LEU* 3.2 7.1 - - - +
335B SER* 2.9 39.3 + - - +
337B GLU* 4.3 4.3 - - + -
345B PRO* 3.8 29.4 - - + -
350B LEU* 3.9 18.4 - - + -
351B ASN 3.2 11.7 - - - +
353B LEU* 3.9 4.0 - - - -
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Residues in contact with SER 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327B ALA* 1.3 71.6 - - - +
329B ASP* 1.3 67.1 + - - +
332B GLY* 3.7 5.4 + - - -
333B LYS 3.2 3.1 - - - -
334B LEU* 3.1 11.6 - - - +
350B LEU* 3.5 5.6 - - - -
351B ASN* 2.7 48.8 + - - +
353B LEU* 3.7 11.0 - - - +
391B TYR* 2.7 38.5 - - - -
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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