Contacts of the helix formed by residues 343 - 354 (chain B) in PDB entry 3EIJ
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 ASP 343 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338B TYR* 3.7 10.7 - - - +
341B SER* 3.0 22.6 + - - +
342B GLY* 1.3 72.4 - - - +
344B ILE* 1.3 65.8 + - - +
345B SER* 3.2 14.1 + - - -
346B GLU* 3.1 36.2 + - + +
347B ALA* 3.2 15.8 + - - +
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Residues in contact with ILE 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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338B TYR* 3.6 29.6 - - + +
342B GLY 3.0 19.9 + - - +
343B ASP* 1.3 71.2 + - - +
345B SER* 1.3 64.9 + - - +
347B ALA* 3.2 6.8 + - - +
348B GLU* 3.1 24.8 + - + +
385B ASP* 4.4 15.7 - - + +
386B LEU* 4.5 17.1 - - + +
389B SER* 3.2 33.7 - - - +
390B LEU* 5.9 1.3 - - + -
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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
----------------------------------------------------------
343B ASP* 3.2 10.6 + - - -
344B ILE* 1.3 82.6 - - - +
346B GLU* 1.3 60.6 + - - +
348B GLU* 3.3 7.6 + - - +
349B HIS* 2.9 46.7 + - - -
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Residues in contact with GLU 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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256B ARG* 2.7 41.1 + - - +
259B GLN* 3.4 18.1 - - - +
297B LYS* 3.1 20.7 - - + -
337B GLU* 3.8 21.3 - - - +
341B SER* 5.6 1.1 - - - +
343B ASP* 3.1 35.7 + - + +
345B SER* 1.3 75.0 - - - +
347B ALA* 1.3 62.3 + - - +
349B HIS* 3.5 2.6 + - - +
350B CYS* 3.1 38.8 + - - -
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Residues in contact with ALA 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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334B LEU* 3.8 26.2 - - + +
338B TYR* 4.2 12.6 - - + -
343B ASP 3.2 10.0 + - - +
344B ILE 3.2 10.2 + - - +
346B GLU* 1.3 80.2 - - - +
348B GLU* 1.3 55.5 + - - +
350B CYS* 3.3 4.5 + - - +
351B LEU* 3.0 28.9 + - - +
386B LEU* 3.9 22.4 - - + -
390B LEU* 5.4 1.8 - - + -
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Residues in contact with GLU 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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344B ILE* 3.1 14.5 + - + +
345B SER* 3.3 11.0 + - - +
346B GLU 3.3 0.2 - - - -
347B ALA* 1.3 74.4 - - - +
349B HIS* 1.3 78.8 + - - +
351B LEU* 3.4 3.7 + - - +
352B LYS* 3.1 49.0 + - - +
389B SER* 4.7 8.7 + - - -
390B LEU* 3.7 22.2 - - + +
393B SER* 3.5 29.9 + - - -
395B THR* 3.7 13.0 + - + +
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Residues in contact with HIS 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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256B ARG* 3.3 55.4 - - + +
345B SER* 2.9 36.0 + - - -
346B GLU 3.9 5.2 - - - +
348B GLU* 1.3 86.9 - - + +
350B CYS* 1.3 58.9 + - - +
352B LYS* 3.2 10.4 + - + +
353B GLU* 2.9 33.4 + - + +
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Residues in contact with CYS 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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256B ARG* 4.3 6.1 - - - -
263B GLN* 4.6 13.5 - - - -
297B LYS* 4.7 6.1 - - - -
334B LEU* 3.6 15.7 - - + -
337B GLU* 5.2 4.0 - - - -
346B GLU* 3.1 48.4 + - - +
347B ALA* 3.7 5.4 - - - +
348B GLU 3.1 0.2 - - - -
349B HIS* 1.3 75.1 - - - +
351B LEU* 1.3 60.8 + - - +
352B LYS 3.1 1.6 - - - -
353B GLU* 4.1 9.0 - - - +
354B LEU* 3.1 30.3 + - - +
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Residues in contact with LEU 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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331B ILE* 3.9 27.6 - - + -
334B LEU* 3.4 10.7 - - + +
347B ALA 3.0 15.9 + - - +
348B GLU* 3.8 7.0 - - - +
349B HIS 3.4 0.2 - - - -
350B CYS* 1.3 77.3 - - - +
352B LYS* 1.3 59.2 + - - +
354B LEU* 3.6 16.5 + - + +
355B GLU* 3.7 4.2 + - - -
356B VAL* 4.6 3.0 + - + -
360B HIS* 3.6 48.9 + - + +
363B LEU* 4.2 24.2 - - + -
390B LEU* 4.5 15.0 - - + -
395B THR* 4.1 13.0 - - + -
396B ILE* 4.6 3.8 - - + -
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Residues in contact with LYS 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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348B GLU* 3.1 40.3 + - + +
349B HIS* 3.2 12.8 + - + +
350B CYS 3.1 0.6 - - - -
351B LEU* 1.3 78.6 - - - +
353B GLU* 1.3 60.9 + - + +
354B LEU 3.2 1.8 - - - -
355B GLU* 3.2 24.4 + - - +
360B HIS* 5.7 2.2 - - + -
393B SER 5.1 4.4 + - - -
395B THR* 3.8 28.9 + - + +
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Residues in contact with GLU 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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358A HIS* 4.0 10.0 + - - -
213B ALA* 4.3 10.4 - - - +
216B ARG* 3.3 34.4 + - - +
256B ARG* 4.1 26.1 + - - +
260B LEU* 5.0 6.5 - - + +
349B HIS* 2.9 22.6 + - + +
350B CYS* 3.5 8.7 + - - +
351B LEU 3.4 0.4 - - - -
352B LYS* 1.3 73.7 - - + +
354B LEU* 1.3 65.6 + - + +
355B GLU* 3.2 12.9 - - - +
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Residues in contact with LEU 354 (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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358A HIS* 3.7 12.2 - - - +
359A PHE* 4.0 13.3 - - + -
327B LEU* 5.2 1.3 - - + -
330B GLU* 4.0 40.8 - - + +
331B ILE* 3.8 29.2 - - + -
334B LEU* 4.0 15.3 - - + -
350B CYS 3.1 21.0 + - - +
351B LEU* 3.6 11.2 - - + +
352B LYS 3.2 0.6 - - - -
353B GLU* 1.3 78.8 - - + +
355B GLU* 1.3 70.3 + - - +
356B VAL* 3.6 19.0 + - + +
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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