Contacts of the helix formed by residues 342 - 356 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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340A CYS* 4.2 1.4 - - - +
341A HIS* 1.3 104.3 - - + +
343A ARG* 1.3 63.6 + - - +
344A LYS* 3.2 7.6 + - - +
345A THR* 2.9 30.2 + - - +
346A ALA* 3.0 22.9 + - - +
390A THR* 4.0 4.6 - - - +
204B GLU* 3.6 15.5 - - - +
205B ARG* 3.2 26.0 + - - +
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Residues in contact with ARG 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342A THR* 1.3 74.3 - - - +
344A LYS* 1.3 62.1 + - - +
346A ALA* 3.9 1.0 - - - +
347A SER* 3.1 26.7 + - - -
364A SER* 4.2 8.6 - - - -
365A GLY* 3.1 34.1 + - - +
366A GLU* 3.5 21.7 - - - +
390A THR* 3.7 23.8 + - + +
392A VAL* 5.5 8.5 - - - +
202B LYS* 3.2 31.2 + - - +
203B LEU* 3.8 3.6 - - - +
204B GLU* 3.1 27.9 + - + +
207B GLN* 3.1 35.8 + - + +
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Residues in contact with LYS 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A THR* 3.1 6.3 - - - +
343A ARG* 1.3 77.6 - - - +
345A THR* 1.3 62.1 + - - +
347A SER* 3.3 7.3 + - - -
348A TRP* 3.2 24.4 + - - +
204B GLU* 2.8 19.1 + - - +
205B ARG* 3.7 14.1 - - - +
206B GLY 4.9 4.3 - - - +
207B GLN* 4.9 14.1 - - - +
208B LYS 5.7 0.4 - - - +
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Residues in contact with THR 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317A ARG* 5.6 6.8 - - + +
340A CYS* 3.5 26.5 - - + -
341A HIS* 5.7 0.2 - - - +
342A THR* 2.9 25.5 + - - +
344A LYS* 1.3 75.7 - - - +
346A ALA* 1.3 57.5 + - - +
348A TRP* 3.1 11.8 + - + +
349A LEU* 2.8 29.8 + - + +
408A PHE* 4.1 18.2 - - + -
409A ASP* 4.0 12.7 + - - +
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Residues in contact with ALA 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340A CYS* 3.8 17.9 - - + +
342A THR 3.0 15.0 + - - +
343A ARG 3.9 4.3 - - - +
344A LYS 3.4 0.2 - - - -
345A THR* 1.3 77.6 - - - +
347A SER* 1.3 57.5 + - - +
349A LEU* 3.4 1.6 + - - +
350A ALA* 2.9 30.5 + - - +
362A LEU* 3.9 19.7 - - + -
364A SER* 5.3 1.3 - - - -
388A VAL* 3.7 12.2 - - + +
389A THR 4.5 4.0 - - - -
390A THR* 4.0 17.7 - - + -
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Residues in contact with SER 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343A ARG 3.1 12.1 + - - -
344A LYS* 3.3 11.8 + - - -
346A ALA* 1.3 78.5 - - - +
348A TRP* 1.3 59.9 + - - +
350A ALA* 4.0 1.0 - - - +
351A ALA* 3.0 29.6 + - - +
362A LEU* 3.7 24.5 - - - +
364A SER* 6.0 0.7 - - - -
366A GLU* 5.9 1.1 - - - -
207B GLN* 6.0 0.3 - - - +
208B LYS* 4.2 17.2 + - - +
210B SER* 4.3 17.7 - - - -
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Residues in contact with TRP 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317A ARG* 3.4 65.7 - - + +
318A ASP* 4.0 6.7 - - - -
321A PHE* 3.9 26.2 - + + -
344A LYS 3.2 14.7 + - - +
345A THR* 3.1 11.1 + - + +
347A SER* 1.3 79.7 + - - +
349A LEU* 1.3 99.9 + - + +
351A ALA* 3.3 7.2 + - + +
352A GLU* 2.9 54.7 + - + +
408A PHE* 4.3 6.7 - + - -
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Residues in contact with LEU 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321A PHE* 3.6 29.8 - - + -
324A LEU* 4.1 10.5 - - + -
338A ILE* 3.7 23.3 - - + -
340A CYS* 3.7 24.7 - - - -
345A THR* 2.8 20.8 + - + +
346A ALA 3.6 4.9 - - - +
348A TRP* 1.3 88.4 - - + +
350A ALA* 1.3 57.6 + - - +
352A GLU* 3.2 1.5 + - - +
353A LEU* 2.9 42.0 + - + +
388A VAL* 4.5 5.4 - - + -
408A PHE* 3.8 19.5 - - + -
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Residues in contact with ALA 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346A ALA 2.9 16.8 + - - +
347A SER 4.0 3.4 - - - +
349A LEU* 1.3 77.3 - - - +
351A ALA* 1.3 62.1 + - - +
353A LEU* 3.5 2.2 + - - +
354A SER* 3.0 24.4 + - - -
360A VAL* 3.9 27.8 - - + +
362A LEU* 4.3 26.0 - - + -
388A VAL* 4.5 6.7 - - + +
161B LYS* 5.5 1.0 - - - -
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Residues in contact with ALA 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347A SER 3.0 18.8 + - - +
348A TRP* 3.3 6.9 + - + +
350A ALA* 1.3 76.8 - - - +
352A GLU* 1.3 64.4 + - - +
354A SER* 3.3 7.0 + - - -
355A LYS* 3.0 33.8 + - - +
161B LYS* 4.4 25.9 - - + +
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Residues in contact with GLU 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321A PHE* 3.3 44.9 - - + -
348A TRP* 2.9 45.7 + - + +
349A LEU* 3.6 3.8 - - - +
351A ALA* 1.3 77.6 - - - +
353A LEU* 1.3 62.5 + - - +
355A LYS* 3.3 34.7 + - - +
356A GLU* 3.1 25.5 + - - +
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Residues in contact with LEU 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321A PHE* 3.7 21.3 - - + -
324A LEU* 3.9 15.9 - - + -
325A CYS* 4.7 3.4 - - - -
328A TYR* 3.9 20.9 - - + +
338A ILE* 4.3 9.2 - - + -
349A LEU* 2.9 34.2 + - + +
350A ALA 3.8 3.8 - - - +
352A GLU* 1.3 74.3 - - - +
354A SER* 1.3 63.9 + - - +
356A GLU* 3.0 11.6 + - - +
357A GLY 3.1 0.3 + - - -
358A HIS* 2.8 52.1 + - + +
360A VAL* 3.8 23.8 - - + -
388A VAL* 4.4 5.2 - - + -
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Residues in contact with SER 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350A ALA 3.0 18.7 + - - -
351A ALA 3.3 4.9 + - - -
353A LEU* 1.3 75.8 - - - +
355A LYS* 1.3 58.3 + - - +
357A GLY* 2.9 20.1 + - - -
358A HIS 3.3 14.2 + - - -
360A VAL* 5.6 1.3 - - - -
159B ALA* 6.0 0.2 - - - -
161B LYS* 3.7 27.4 + - - -
191B GLU* 3.8 18.9 + - - -
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Residues in contact with LYS 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351A ALA* 3.0 21.6 + - - +
352A GLU* 3.4 38.3 + - - +
353A LEU 3.2 0.2 - - - -
354A SER* 1.3 76.7 - - - +
356A GLU* 1.3 63.2 + - - +
357A GLY* 3.1 1.4 + - - -
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Residues in contact with GLU 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321A PHE* 4.1 14.1 - - + -
325A CYS* 3.9 25.6 - - + -
352A GLU* 3.1 14.3 + - - +
353A LEU* 3.0 12.1 + - - +
355A LYS* 1.3 79.1 - - - +
357A GLY* 1.3 58.3 + - - +
358A HIS* 3.5 20.8 + - + +
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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