Contacts of the strand formed by residues 351 - 357 (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 ASN 351 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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327B ALA* 3.2 8.0 - - - -
328B SER* 2.7 48.7 + - - +
329B ASP 5.4 3.3 + - - +
349B GLY 4.2 2.2 + - - -
350B LEU* 1.3 72.9 - - - +
352B PRO* 1.3 66.9 - - - +
353B LEU* 3.3 6.0 + - + +
390B ARG* 2.9 24.1 - - - +
391B TYR* 4.9 3.0 - - - +
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Residues in contact with PRO 352 (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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254B ASN* 5.5 2.9 - - - +
276B LEU* 3.8 19.0 - - + +
325B TRP* 3.3 34.2 - - + -
326B LEU 4.2 0.9 - - - +
344B ASN* 4.3 8.5 - - - +
345B PRO* 4.4 8.3 - - + -
346B VAL* 3.8 22.7 - - + +
350B LEU 3.4 10.0 - - - +
351B ASN* 1.3 84.5 - - + +
353B LEU* 1.3 63.3 + - - +
390B ARG* 3.7 16.8 + - - +
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Residues in contact with LEU 353 (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 2.2 - - + -
325B TRP* 3.7 0.6 - - - -
326B LEU* 2.9 24.0 + - + +
327B ALA 3.9 5.8 - - - -
328B SER* 3.6 26.2 - - - +
334B LEU* 3.6 19.5 - - + -
351B ASN* 3.4 18.8 - - + +
352B PRO* 1.3 74.4 - - - +
354B LEU* 1.3 59.5 + - - +
387B VAL* 3.6 21.4 - - + +
390B ARG* 2.8 69.5 + - + +
391B TYR* 3.5 15.9 - - + +
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Residues in contact with LEU 354 (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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280B GLN* 3.7 23.3 - - - +
307B PHE* 4.4 7.2 - - + -
311B PHE* 3.8 21.2 - - + -
325B TRP* 3.1 6.7 - - - -
326B LEU* 2.8 36.1 + - + -
353B LEU* 1.3 80.6 - - - +
355B THR* 1.3 66.5 + - - +
356B PHE* 4.1 4.5 - - + -
379B TRP* 3.8 29.4 - - + -
382B VAL* 4.0 29.6 - - + -
384B TRP* 3.9 15.9 - - + -
387B VAL* 4.2 13.9 - - + -
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Residues in contact with THR 355 (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 4.2 1.1 - - - +
277B TYR* 3.6 24.3 - - + -
280B GLN* 2.6 37.8 + - - +
311B PHE* 4.5 0.7 - - - -
323B TRP* 3.4 25.0 - - + +
324B VAL 3.0 13.9 + - - -
325B TRP* 3.3 52.0 + - + -
354B LEU* 1.3 72.5 - - - +
356B PHE* 1.3 68.0 + - - +
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Residues in contact with PHE 356 (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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277B TYR* 4.4 2.9 - - - -
280B GLN* 4.7 1.1 - - - -
281B PHE* 4.7 2.9 - + - -
311B PHE* 3.7 17.7 - + - -
312B ASN* 4.2 2.7 - - - -
323B TRP* 3.5 3.5 - - - -
324B VAL* 3.0 42.1 + - + +
354B LEU* 4.1 21.3 - - + -
355B THR* 1.3 85.8 + - - +
357B ASP* 1.3 62.2 + - - +
358B VAL* 3.5 1.3 + - + +
375B LEU* 3.7 39.3 - - + -
378B LEU* 3.4 39.9 - - + -
379B TRP* 3.6 45.5 - + - -
382B VAL* 4.1 8.3 - - + -
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Residues in contact with ASP 357 (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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227B HIS* 2.9 11.1 + - - -
277B TYR* 3.6 22.1 - - + -
322B GLY 3.5 1.2 - - - +
323B TRP* 3.3 29.8 - - + -
356B PHE* 1.3 71.3 - - - +
358B VAL* 1.3 62.1 + - - +
359B TRP* 3.2 29.4 + - - -
362B ALA* 3.5 23.1 - - + +
363B TYR* 4.4 5.5 - - - -
374B HIS* 4.5 8.8 + - - -
378B LEU* 5.3 0.2 - - - +
392B MN 2.1 34.1 + - - -
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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