Contacts of the strand formed by residues 334 - 347 (chain B) in PDB entry 3HO5
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 VAL 334 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265B TYR* 2.9 53.4 + - + +
266B LEU* 3.9 13.0 - - + -
299B LEU* 3.8 12.1 - - + -
324B TYR* 3.9 21.5 - - + -
325B THR 3.7 14.1 - - - +
326B VAL* 3.8 2.7 - - - +
327B SER* 4.0 1.8 - - - -
333B GLN* 1.3 80.3 + - - +
335B ASP* 1.3 60.8 + - - +
336B LEU* 3.3 29.9 + - + +
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Residues in contact with ASP 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B TYR* 3.9 2.1 - - - -
325B THR 2.9 15.1 + - - +
326B VAL 4.5 0.9 - - - +
327B SER* 3.5 22.6 - - - +
328B ARG* 4.9 8.8 + - - +
334B VAL* 1.3 69.2 - - - +
336B LEU* 1.3 58.7 + - - +
337B ARG* 3.0 59.8 + - - +
338B THR* 2.6 50.2 + - + +
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Residues in contact with LEU 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B LEU* 3.6 30.7 - - + -
267B ASP* 3.8 24.2 - - + +
268B ILE* 4.9 3.1 - - + -
324B TYR* 3.6 25.6 + - + +
334B VAL* 3.3 16.3 + - + +
335B ASP* 1.3 72.5 + - - +
337B ARG* 1.3 63.1 + - + +
338B THR 3.2 0.8 + - - -
339B ALA* 3.8 6.2 + - - +
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Residues in contact with ARG 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B ARG* 5.9 2.4 - - - +
329B LYS* 5.9 2.4 - - - +
335B ASP* 3.0 39.1 + - - +
336B LEU* 1.3 77.3 - - + +
338B THR* 1.3 57.8 + - - +
339B ALA* 3.3 8.0 + - - +
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Residues in contact with THR 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B GLU* 3.5 6.9 - - - +
324B TYR* 3.9 1.6 - - - -
325B THR* 2.9 49.2 + - + -
326B VAL 5.6 0.2 - - - +
328B ARG* 4.8 12.8 - - - +
335B ASP* 2.6 42.2 + - + +
337B ARG* 1.3 78.6 - - - +
339B ALA* 1.3 65.3 + - - +
340B ARG* 3.3 13.8 + - - +
616B TYR* 6.0 0.2 - - - +
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Residues in contact with ALA 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B LEU* 6.2 0.2 - - + -
322B VAL* 4.0 8.3 - - + -
323B GLU 3.2 8.5 - - - -
324B TYR* 3.5 33.3 - - + +
336B LEU 3.8 6.6 + - - +
337B ARG 3.3 5.8 + - - +
338B THR* 1.3 77.7 + - - +
340B ARG* 1.3 61.3 + - - +
341B VAL* 4.1 3.8 + - + +
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Residues in contact with ARG 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B LYS* 4.2 0.4 - - - +
322B VAL* 3.9 2.9 - - - -
323B GLU* 2.6 74.6 + - + +
338B THR 3.6 13.9 - - - +
339B ALA* 1.3 74.8 - - - +
341B VAL* 1.3 65.2 + - - +
342B PHE* 3.3 24.3 - - + -
397B VAL 5.5 0.4 + - - -
405B PRO* 3.4 28.9 + - + +
616B TYR* 3.3 58.6 - - + +
617B CYS 4.0 10.9 + - - -
618B THR* 4.5 6.3 - - - +
619B PRO* 4.8 7.3 - - - +
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Residues in contact with VAL 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B ARG* 4.5 20.6 - - + +
321B VAL 4.0 5.2 - - - +
322B VAL* 4.0 17.5 - - + -
339B ALA* 5.6 3.1 - - + +
340B ARG* 1.3 74.8 - - - +
342B PHE* 1.3 68.3 + - - +
343B LEU 3.8 8.7 - - - +
344B GLU* 3.5 36.8 - - + +
405B PRO* 3.9 12.3 - - - +
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Residues in contact with PHE 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B TYR* 3.7 31.6 - + - -
321B VAL* 2.8 23.8 + - + +
323B GLU* 3.6 20.2 - - + -
340B ARG* 3.3 45.8 - - + -
341B VAL* 1.3 78.3 - - - +
343B LEU* 1.3 67.9 + - + +
365B LEU* 5.1 3.8 - - + -
395B LEU* 4.5 9.4 - - + -
397B VAL* 4.1 22.2 - - + -
405B PRO* 3.8 24.8 - - + +
406B TYR* 3.4 39.1 - + + -
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Residues in contact with LEU 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B LEU 4.3 0.2 - - - -
320B ARG* 3.4 3.5 - - - -
321B VAL* 3.1 50.6 + - + +
341B VAL* 3.8 2.1 - - - +
342B PHE* 1.3 87.1 - - + +
344B GLU* 1.3 69.0 + - - +
345B VAL* 4.1 13.2 - - + -
367B ILE* 4.1 16.6 - - + -
369B LEU* 5.7 0.2 - - + -
388B PHE* 4.0 24.2 - - + -
393B LEU* 3.8 24.9 - - + -
395B LEU* 4.2 8.1 - - + -
406B TYR* 3.4 29.4 - - + +
423B GLU* 4.9 3.1 - - + -
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Residues in contact with GLU 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B GLU* 3.7 9.5 - - - +
310B TRP* 3.9 24.0 - - + -
312B ILE* 5.7 1.7 - - - +
318B ILE* 3.4 29.6 - - + +
319B LEU 3.6 4.5 - - - -
320B ARG* 3.6 19.6 + - + -
341B VAL* 3.5 21.3 - - + +
343B LEU* 1.3 79.3 - - - +
345B VAL* 1.3 62.5 + - - +
346B ALA 3.7 3.3 + - - -
386B SER* 5.0 2.9 - - - -
388B PHE* 5.8 3.6 - - - -
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Residues in contact with VAL 345 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B ILE* 3.4 2.7 - - - +
319B LEU* 2.8 51.2 + - + +
321B VAL* 5.8 0.2 - - + -
343B LEU* 4.6 11.0 - - + -
344B GLU* 1.3 76.6 - - - +
346B ALA* 1.3 65.7 + - - +
347B GLU* 3.3 17.4 - - - +
369B LEU* 3.9 28.0 - - + -
386B SER* 3.4 29.4 - - - +
388B PHE* 4.6 6.7 - - + -
389B THR* 3.7 17.5 - - + -
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Residues in contact with ALA 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B TRP* 3.8 17.3 - - + -
314B PRO 4.5 12.8 - - - +
315B HIS* 4.7 0.9 - - + -
318B ILE* 3.9 12.1 - - + +
344B GLU 3.7 4.8 + - - -
345B VAL* 1.3 76.3 - - - +
347B GLU* 1.3 70.4 + - - +
374B ILE* 4.6 9.5 - - - +
384B GLY 3.6 23.6 - - - +
385B LEU* 4.5 7.8 - - + +
386B SER* 4.2 15.6 + - - +
389B THR* 4.7 1.4 - - - +
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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
----------------------------------------------------------
315B HIS* 3.4 3.7 - - - +
316B ASP 2.7 31.5 + - - -
317B HIS* 2.9 55.4 + - + +
318B ILE* 4.6 0.2 - - - -
319B LEU* 4.3 10.8 - - - +
345B VAL* 3.3 22.6 - - - +
346B ALA* 1.3 87.4 - - - +
348B LEU* 1.3 56.3 + - - +
349B HIS 3.5 9.6 - - - +
353B LEU* 3.7 21.1 - - + +
369B LEU* 6.1 0.3 - - - +
370B GLY 5.1 0.2 - - - +
372B GLY* 3.5 25.3 + - - -
374B ILE* 4.8 2.0 - - - -
389B THR* 4.2 9.5 - - - +
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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