Contacts of the strand formed by residues 340 - 349 (chain B) in PDB entry 5DQE
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 THR 340 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338B HIS* 5.4 0.5 - - - -
339B MET* 1.3 76.9 + - - +
341B LEU* 1.3 64.0 + - - +
360B THR* 4.5 5.8 - - - -
361B GLU 3.7 15.0 - - - +
362B ARG* 3.9 25.2 + - + +
414B ASN* 3.6 7.5 + - - +
415B ARG* 2.8 73.4 + - - +
416B ASP* 4.4 15.5 + - - -
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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
----------------------------------------------------------
228B LEU* 4.2 15.5 - - + -
333B TYR* 4.3 12.1 - - + -
339B MET* 4.4 8.3 - - + -
340B THR* 1.3 76.5 - - - +
342B THR* 1.3 61.7 + - - +
343B CYS* 4.3 13.2 - - - -
359B GLU 3.8 0.2 - - - +
360B THR* 3.0 9.4 - - - -
361B GLU* 2.9 37.4 + - + +
372B TYR* 3.5 48.9 - - + -
412B VAL* 4.1 15.9 - - + -
413B THR 3.5 3.1 - - - +
415B ARG* 4.5 0.7 - - - -
421B LEU* 3.5 31.9 - - + -
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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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359A GLU* 5.4 0.2 + - - -
341B LEU* 1.3 73.9 - - - +
343B CYS* 1.3 63.4 + - - +
344B SER* 4.0 3.4 - - - +
358B VAL* 3.7 27.4 - - + -
359B GLU 3.4 5.4 - - - +
360B THR* 3.8 9.0 - - + +
411B VAL 3.5 2.3 - - - +
412B VAL* 3.3 4.5 - - - +
413B THR* 2.9 46.7 + - - +
415B ARG* 3.3 30.1 - - - +
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Residues in contact with CYS 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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333B TYR* 4.3 16.2 - - - +
341B LEU* 4.3 13.5 - - - -
342B THR* 1.3 77.4 - - - +
344B SER* 1.3 61.4 + - - +
345B SER* 5.2 2.7 - - - +
357B LYS 3.5 2.3 - - - +
358B VAL* 3.4 2.4 - - - -
359B GLU* 2.8 43.4 + - - +
361B GLU* 5.5 1.1 - - - -
374B LEU* 4.0 28.7 - - + -
410B GLN* 6.3 1.6 - - - +
411B VAL 3.6 3.6 - - - -
412B VAL* 4.1 26.5 - - + -
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Residues in contact with SER 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A GLU* 5.0 3.4 - - - -
342B THR* 4.0 3.3 - - - -
343B CYS* 1.3 72.4 - - - +
345B SER* 1.3 61.1 + - - +
346B LYS* 3.5 18.2 + - - +
356B GLU* 3.0 29.9 + - - +
357B LYS 3.3 4.9 - - - -
358B VAL* 4.2 9.9 - - - +
409B LEU 3.5 1.4 - - - +
410B GLN* 3.3 4.8 - - - +
411B VAL* 2.8 46.9 + - - +
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Residues in contact with SER 345 (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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343B CYS* 4.1 3.0 + - - +
344B SER* 1.3 73.1 + - - +
346B LYS* 1.3 61.6 + - - +
356B GLU* 3.3 3.6 - - - +
357B LYS* 2.8 44.5 + - - -
359B GLU* 5.2 4.7 + - - -
408B ILE* 4.9 0.4 - - - -
409B LEU 3.5 4.7 - - - -
410B GLN* 3.1 31.9 + - - +
501B 5E4 3.4 33.9 - - - -
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Residues in contact with LYS 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A GLU* 2.8 37.8 + - - -
279B PRO* 4.3 5.6 - - + -
283B GLY* 3.9 24.1 + - - +
288B LEU* 5.2 0.2 - - - +
344B SER* 3.5 15.7 + - - +
345B SER* 1.3 78.1 - - - +
347B VAL* 1.3 62.3 + - - +
348B CYS* 3.9 6.0 + - - -
353B GLN* 3.7 24.5 - - + +
355B VAL 3.4 7.9 - - - +
356B GLU* 3.7 24.5 - - + -
407B THR 3.8 0.3 - - - +
408B ILE* 3.3 5.7 - - - +
409B LEU* 2.8 52.1 + - + +
411B VAL* 4.1 17.4 - - - +
501B 5E4 4.2 0.9 - - - -
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Residues in contact with VAL 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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346B LYS* 1.3 71.4 - - - +
348B CYS* 1.3 68.5 + - - +
353B GLN* 3.5 4.3 - - - -
354B VAL* 2.9 44.2 + - + -
355B VAL* 3.0 18.6 + - + +
382B TYR* 4.4 17.5 - - + -
383B LEU* 4.5 12.1 - - + -
406B PHE* 4.5 9.9 - - + -
407B THR 3.5 8.1 - - - +
408B ILE* 4.2 13.2 - - + -
501B 5E4 3.3 33.4 - - + -
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Residues in contact with CYS 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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277B LYS 3.8 9.4 - - - +
278B PHE* 4.2 2.9 - - - -
279B PRO* 3.4 42.2 - - - -
346B LYS* 4.7 7.2 - - - -
347B VAL* 1.3 79.3 - - - +
349B SER* 1.3 61.0 + - - +
350B PHE 4.2 0.4 - - - -
351B GLY 4.2 4.9 - - - -
352B LYS 3.3 7.6 - - - +
353B GLN* 3.9 14.1 - - - -
405B ASN 3.6 0.4 - - - +
406B PHE* 3.3 11.4 - - - -
407B THR* 2.8 48.8 + - - +
409B LEU* 5.8 0.4 - - - -
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Residues in contact with SER 349 (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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348B CYS* 1.3 72.2 - - - +
350B PHE* 1.3 91.2 + - - +
352B LYS* 2.8 24.5 + - - +
354B VAL* 3.7 22.7 - - - +
405B ASN 3.3 4.0 - - - -
406B PHE* 3.3 29.9 - - - -
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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