Contacts of the strand formed by residues 337 - 348 (chain B) in PDB entry 1U0C
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 HIS 337 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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327B ILE* 3.8 29.4 - - + -
328B LYS 3.2 8.7 - - - +
329B PRO* 3.4 25.5 - - + +
330B ASN 3.6 2.6 + - - +
333B CYS* 3.5 15.9 - - - +
335B PHE* 2.8 27.6 + - - +
336B LYS* 1.3 93.5 + - + +
338B GLN* 1.3 61.1 + - - +
422B PHE* 3.8 23.2 - - + -
443B THR* 4.2 5.3 - - + +
447B THR* 4.2 14.9 + - - -
448B VAL* 4.3 27.3 - - + +
450B ALA 6.0 2.5 - - - -
451B VAL* 5.9 2.5 - - + -
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Residues in contact with GLN 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B GLN 3.7 0.3 - - - +
327B ILE* 4.0 1.7 - - - -
328B LYS* 2.9 53.3 + - + +
330B ASN* 3.7 12.5 + - + +
333B CYS* 3.7 18.8 - - - -
337B HIS* 1.3 74.7 - - - +
339B LEU* 1.3 74.0 + - - +
340B SER* 4.7 6.7 + - - -
502C C 5.6 0.2 - - - -
503C T 3.4 28.2 + - + +
504C A 2.7 53.1 + - - -
570D T 5.4 0.2 - - - +
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Residues in contact with LEU 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B GLN 3.8 1.6 - - - +
327B ILE* 3.2 33.7 - - + -
338B GLN* 1.3 83.9 + - - +
340B SER* 1.3 60.5 + - - +
341B LEU* 5.5 3.6 - - + -
381B ILE* 5.8 2.8 - - - +
408B ILE* 4.6 8.3 - - + -
412B LEU* 3.6 33.0 - - + -
415B ALA* 4.8 1.6 - - + -
422B PHE* 4.0 34.7 - - + -
425B VAL* 3.7 26.2 - - + -
426B CYS* 4.2 4.5 - - - -
429B VAL* 4.9 5.4 - - + -
503C T 4.0 16.6 + - - +
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Residues in contact with SER 340 (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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324B ILE 4.0 0.2 - - - +
325B ALA* 3.6 4.3 - - - -
326B GLN* 3.0 38.2 + - - +
328B LYS* 3.1 40.7 + - - -
338B GLN* 4.7 7.6 + - - -
339B LEU* 1.3 77.2 - - - +
341B LEU* 1.3 66.0 + - - +
342B THR* 4.3 8.1 + - - -
379B SER* 5.2 2.9 + - - -
381B ILE* 6.0 1.1 - - - -
504C A 6.0 0.9 - - - -
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Residues in contact with LEU 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B ILE 3.5 10.8 - - - +
325B ALA* 3.8 16.6 - - + -
339B LEU* 5.5 2.7 - - + -
340B SER* 1.3 84.9 + - - +
342B THR* 1.3 62.8 + - - +
379B SER* 3.0 31.5 + - - +
381B ILE* 4.1 17.6 - - + +
384B LEU* 3.7 17.3 - - + -
405B VAL* 4.0 20.2 - - + +
408B ILE* 3.6 29.4 - - + -
409B ILE* 3.2 35.0 - - + -
412B LEU* 5.4 2.2 - - + -
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Residues in contact with THR 342 (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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322B SER 3.3 4.2 - - - +
323B ILE* 3.4 5.1 - - - +
324B ILE* 2.7 52.1 + - + +
326B GLN* 4.2 15.2 + - - -
340B SER* 4.3 4.7 + - - -
341B LEU* 1.3 79.0 + - - +
343B PHE* 1.3 73.5 + - - +
344B GLN* 4.1 17.3 - - + +
377B ILE* 4.0 15.5 - - + -
378B LEU 3.7 2.7 - - - -
379B SER* 3.4 14.3 + - - +
384B LEU* 4.3 3.3 - - - +
405B VAL* 5.7 1.9 - - - +
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Residues in contact with PHE 343 (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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313B LEU* 5.0 2.9 - - + -
317B VAL* 3.3 44.0 - - + -
322B SER 3.6 5.6 - - - -
323B ILE* 4.6 9.6 - - + +
342B THR* 1.3 72.8 - - - +
344B GLN* 1.3 65.2 + - - +
345B VAL* 3.8 13.5 - - + -
358B LEU* 5.4 0.7 - - + -
362B ILE* 4.1 3.4 - - + -
376B TYR* 3.6 33.2 - + - -
377B ILE* 3.6 0.7 - - - -
378B LEU* 2.8 38.1 + - + +
384B LEU* 3.7 23.1 - - + +
387B PHE* 3.4 40.2 - + + -
388B LEU* 4.4 12.1 - - + -
391B LEU* 4.2 4.0 - - + -
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Residues in contact with GLN 344 (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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320B ASP 4.3 0.4 + - - +
321B GLY* 3.1 3.1 - - - -
322B SER* 2.7 59.9 + - - +
324B ILE* 4.8 4.0 - - + +
342B THR* 4.1 11.0 - - + +
343B PHE* 1.3 80.7 - - - +
345B VAL* 1.3 65.0 + - - +
346B THR* 3.4 20.2 + - - -
368B ARG* 5.7 1.2 + - - -
370B ARG* 4.6 2.2 - - - +
375B ASP* 3.8 10.4 + - - +
376B TYR 3.1 14.1 - - - +
377B ILE* 3.5 21.1 - - + +
565D G 4.3 5.3 - - - -
566D A 3.5 25.4 + - - +
567D C 4.3 15.9 + - - -
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Residues in contact with VAL 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B LEU* 5.2 0.2 - - + -
316B PHE* 3.0 38.1 - - + -
317B VAL* 4.1 12.8 - - + -
320B ASP 3.7 6.3 - - - +
321B GLY* 4.4 3.1 - - - -
343B PHE* 3.8 26.0 - - + -
344B GLN* 1.3 80.7 - - - +
346B THR* 1.3 66.2 + - - +
355B LEU* 3.7 23.6 - - + +
358B LEU* 4.3 12.3 - - + -
375B ASP* 3.2 5.2 - - - +
376B TYR* 2.8 34.6 + - + +
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Residues in contact with THR 346 (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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320B ASP* 3.1 16.7 + - - +
344B GLN* 3.4 16.3 + - - -
345B VAL* 1.3 72.0 - - - +
347B GLU* 1.3 70.4 + - - +
370B ARG* 3.6 9.4 + - - +
373B VAL* 3.1 35.2 - - + -
374B SER 3.4 2.7 - - - -
375B ASP* 2.5 21.1 + - - +
564D C 2.7 45.8 - - + +
565D G 4.3 3.8 - - - -
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Residues in contact with GLU 347 (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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18A ASP 4.7 0.8 - - - +
97A LEU* 4.1 6.6 - - + +
316B PHE* 3.3 24.4 - - + -
320B ASP* 2.3 31.5 - - - +
346B THR* 1.3 78.6 - - - +
348B LYS* 1.3 71.7 + - - +
351B ARG* 2.7 42.2 + - + +
354B PHE* 4.8 5.8 - - + -
355B LEU* 4.0 22.8 - - + +
373B VAL* 4.5 2.5 - - - -
374B SER* 2.8 34.6 + - - +
601B MG 3.7 0.6 - - - -
564D C 3.1 17.1 + - - -
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Residues in contact with LYS 348 (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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137A ASP* 4.2 5.4 + - - +
347B GLU* 1.3 75.0 + - - +
349B THR* 1.3 57.5 + - - +
350B GLN* 2.9 40.5 - - + +
351B ARG* 2.8 47.9 + - - +
352B ARG 3.6 0.3 + - - -
372B SER* 3.1 35.4 - - - +
373B VAL* 4.3 4.3 - - + -
563D A 3.7 41.8 + - + +
564D C 3.1 24.2 + - - +
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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