Contacts of the helix formed by residues 342 - 355 (chain B) in PDB entry 3EWS
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 342 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340B CYS* 4.2 2.1 - - - +
341B HIS* 1.3 102.5 - - + +
343B ARG* 1.3 65.9 + - - +
344B LYS* 3.3 37.1 - - - +
345B THR* 3.2 21.3 + - - -
346B ALA* 3.2 22.2 + - - +
390B THR* 4.0 6.6 - - - +
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Residues in contact with ARG 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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203A LEU* 3.5 29.6 - - - +
204A GLU 3.6 12.9 + - - -
206A GLY* 3.6 4.8 - - - -
207A GLN* 2.8 47.5 + - + +
208A LYS 3.8 12.9 + - - -
209A ILE* 4.1 14.3 - - - +
230A PHE* 3.8 4.4 - - - -
342B THR* 1.3 74.0 - - - +
344B LYS* 1.3 58.7 + - - +
346B ALA* 3.1 3.8 + - - +
347B SER* 2.9 38.2 + - - +
364B SER* 3.6 22.9 - - - -
365B GLY* 4.4 6.3 - - - +
366B GLU* 3.7 19.3 + - - -
390B THR* 4.1 13.3 - - + +
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Residues in contact with LYS 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A ARG 5.9 0.2 + - - -
206A GLY* 5.5 8.5 - - - -
207A GLN* 4.6 23.9 - - + +
342B THR* 3.3 33.2 - - - +
343B ARG* 1.3 80.2 - - - +
345B THR* 1.3 59.7 + - - +
347B SER* 3.4 7.6 + - - -
348B TRP* 3.1 26.2 + - - +
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Residues in contact with THR 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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317B ARG* 5.5 11.8 - - + +
340B CYS* 3.6 24.9 - - + -
341B HIS* 5.6 0.7 - - - +
342B THR* 3.2 23.3 + - - -
343B ARG 3.3 0.2 - - - -
344B LYS* 1.3 78.1 - - - +
346B ALA* 1.3 60.5 + - - +
348B TRP* 3.6 6.5 - - + +
349B LEU* 2.9 32.8 + - + +
408B PHE* 4.3 17.7 - - + -
409B ASP* 4.0 13.6 + - - +
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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
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340B CYS* 3.9 17.7 - - + -
342B THR 3.2 10.1 + - - +
343B ARG* 3.1 9.1 + - + +
345B THR* 1.3 80.6 - - - +
347B SER* 1.3 56.4 + - - +
349B LEU 3.3 0.9 + - - -
350B ALA* 2.9 31.4 + - - +
362B LEU* 4.0 14.6 - - + -
388B VAL* 3.7 18.9 - - + +
389B THR 4.5 4.0 - - - -
390B THR* 4.3 13.0 - - - +
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Residues in contact with SER 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A SER* 5.5 7.9 - - - -
343B ARG* 2.9 28.5 + - - +
344B LYS* 3.4 10.4 + - - -
346B ALA* 1.3 70.4 - - - +
348B TRP* 1.3 61.9 + - - +
350B ALA* 3.8 1.1 - - - +
351B ALA* 2.9 32.2 + - - +
362B LEU* 4.1 22.8 - - - +
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Residues in contact with TRP 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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317B ARG* 3.2 52.2 - - - +
318B ASP* 4.0 18.6 - - - -
321B PHE* 3.6 31.2 - + + -
344B LYS 3.1 20.5 + - - +
345B THR* 3.6 6.7 - - + +
347B SER* 1.3 76.9 + - - +
349B LEU* 1.3 99.2 + - + +
351B ALA* 3.7 4.0 - - - +
352B GLU* 2.8 57.8 + - + +
408B PHE* 4.5 8.3 - + - -
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Residues in contact with LEU 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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321B PHE* 3.8 21.5 - - + -
324B LEU* 3.8 22.9 - - + -
338B ILE* 3.7 22.0 - - + -
340B CYS* 3.8 14.1 - - - -
345B THR* 2.9 19.1 + - + +
346B ALA 3.8 3.1 - - - +
348B TRP* 1.3 91.7 - - + +
350B ALA* 1.3 57.4 + - - +
352B GLU* 4.1 0.8 - - - -
353B LEU* 3.1 34.8 + - + +
388B VAL* 4.4 7.4 - - + -
408B PHE* 3.6 33.9 - - + -
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Residues in contact with ALA 350 (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 ALA 2.9 18.5 + - - +
347B SER* 3.8 5.8 - - - +
349B LEU* 1.3 77.7 - - - +
351B ALA* 1.3 65.6 + - - +
353B LEU 3.7 0.2 + - - -
354B SER* 3.5 14.0 + - - -
360B VAL* 3.4 35.3 - - + +
362B LEU* 4.4 17.0 - - + -
388B VAL* 4.3 14.4 - - + -
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Residues in contact with ALA 351 (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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347B SER 2.9 17.3 + - - +
348B TRP* 3.7 4.5 - - - +
350B ALA* 1.3 73.8 - - - +
352B GLU* 1.3 53.3 + - - +
353B LEU 2.9 4.9 + - - -
354B SER* 2.9 10.3 + - - -
355B LYS* 2.7 38.3 + - + +
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Residues in contact with GLU 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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318B ASP* 5.7 1.3 - - - +
321B PHE* 3.5 29.9 - - + -
348B TRP* 2.8 51.9 + - + +
349B LEU* 4.3 2.2 - - - +
351B ALA* 1.3 73.2 - - - +
353B LEU* 1.3 56.6 + - - +
355B LYS* 3.3 37.8 + - - +
356B GLU* 3.1 39.7 + - - +
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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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321B PHE* 3.8 19.7 - - + -
324B LEU* 4.4 9.4 - - + -
325B CYS* 5.0 2.9 - - - -
328B TYR* 4.4 13.2 - - + -
338B ILE* 4.4 17.7 - - + -
349B LEU* 3.1 38.6 + - + +
350B ALA 3.8 5.8 - - - +
351B ALA 2.9 2.2 + - - -
352B GLU* 1.3 75.2 - - - +
354B SER* 1.3 59.4 + - - +
356B GLU* 3.0 5.5 + - - +
357B GLY 3.0 9.9 + - - -
358B HIS* 2.9 53.5 + - + +
360B VAL* 3.6 24.0 - - + -
386B VAL* 5.0 0.4 - - + -
388B VAL* 4.5 4.3 - - + -
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Residues in contact with SER 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A GLU* 5.9 2.7 - - - -
350B ALA 3.5 10.5 + - - -
351B ALA* 2.9 16.7 + - - -
353B LEU* 1.3 72.0 - - - +
355B LYS* 1.3 56.5 + - - +
356B GLU 2.9 8.9 + - - -
357B GLY* 3.1 13.2 + - - -
358B HIS 3.1 19.2 + - - -
359B GLN* 4.7 6.5 - - - -
360B VAL* 5.3 2.9 - - - -
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Residues in contact with LYS 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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351B ALA* 2.7 19.1 + - + +
352B GLU* 3.3 38.0 + - - +
354B SER* 1.3 77.5 + - - +
356B GLU* 1.3 61.7 + - - +
357B GLY 3.6 0.2 - - - -
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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