Contacts of the helix formed by residues 347 - 358 (chain B) in PDB entry 4I6J
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 LEU 347 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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321B LYS* 3.8 24.0 - - + -
324B LEU* 4.4 14.6 - - + -
339B VAL* 6.0 0.4 - - + -
342B ASN* 3.4 30.3 - - + +
345B ARG 3.6 14.6 - - - +
346B PRO* 1.3 70.3 - - - +
348B ASP* 1.3 64.7 + - - +
349B GLU 3.1 2.9 - - - -
350B GLU* 2.7 30.6 + - + +
351B LEU* 3.2 12.3 + - + +
366B LEU* 5.9 5.4 - - + -
369B CYS* 3.8 35.7 - - + -
370B GLU 2.9 14.5 + - - +
371B VAL* 4.4 11.2 - - + -
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Residues in contact with ASP 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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346B PRO* 3.3 19.1 + - - +
347B LEU* 1.3 75.2 - - - +
349B GLU* 1.3 65.1 + - + +
351B LEU* 3.9 3.0 + - - +
352B ILE* 2.8 32.6 + - + +
370B GLU 4.6 0.4 + - - -
371B VAL* 3.6 5.8 - - - +
372B SER* 2.7 45.3 + - - -
375B ALA* 3.3 22.0 - - + +
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Residues in contact with GLU 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 LYS* 3.2 26.6 + - - -
346B PRO 4.7 1.7 - - - +
347B LEU 2.8 2.4 + - - -
348B ASP* 1.3 80.2 - - + +
350B GLU* 1.3 70.1 + - - +
352B ILE* 3.8 8.9 - - - +
353B ARG* 3.0 37.9 + - - +
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Residues in contact with GLU 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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321B LYS* 2.6 52.0 + - + +
324B LEU* 4.0 13.5 - - + -
325B GLY* 3.5 34.9 - - - +
347B LEU* 2.7 22.7 + - + +
349B GLU* 1.3 87.5 + - - +
351B LEU* 1.3 58.3 + - + +
353B ARG* 3.5 11.5 + - - +
354B ILE* 2.8 40.5 + - + +
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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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337B LEU* 5.4 3.1 - - + -
347B LEU* 3.2 13.1 + - + +
348B ASP* 4.3 4.9 - - - +
350B GLU* 1.3 78.9 - - + +
352B ILE* 1.3 64.2 + - + +
354B ILE* 3.4 11.6 + - + +
355B ALA 3.1 8.5 + - - -
364B ILE* 4.4 10.3 - - + -
366B LEU* 3.7 34.5 - - + -
371B VAL* 3.8 24.9 - - + -
375B ALA 5.8 1.1 - - - +
376B PHE* 4.2 18.4 - - + -
379B PHE* 2.9 59.2 - - + -
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Residues in contact with ILE 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 ASP* 2.8 27.8 + - + +
349B GLU* 3.8 7.9 - - - +
350B GLU 3.3 0.4 - - - -
351B LEU* 1.3 75.4 - - + +
353B ARG* 1.3 65.4 + - - +
355B ALA* 3.4 7.9 + - - +
356B GLU* 3.0 23.6 + - + +
375B ALA* 4.5 16.8 - - + +
378B GLU* 3.4 41.3 - - + +
379B PHE* 4.6 4.5 - - - +
382B MET* 3.9 17.8 - - + +
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Residues in contact with ARG 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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325B GLY* 3.7 20.3 + - - -
328B GLY* 3.9 7.9 - - - -
329B MET* 3.1 56.2 - - - +
349B GLU* 3.0 27.2 + - - +
350B GLU* 3.9 11.9 + - - +
352B ILE* 1.3 78.4 - - - +
354B ILE* 1.3 58.3 + - - +
356B GLU* 3.0 9.2 - - + +
357B ARG* 2.8 40.5 + - - +
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Residues in contact with ILE 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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324B LEU* 4.3 13.7 - - + +
327B VAL* 4.2 19.7 - - + -
328B GLY* 3.9 13.7 - - - -
334B LEU* 4.1 10.8 - - + -
337B LEU* 3.9 25.6 - - + -
350B GLU* 2.8 28.2 + - + +
351B LEU* 3.8 10.8 - - + +
352B ILE 3.2 0.2 - - - -
353B ARG* 1.3 72.9 - - - +
355B ALA* 1.3 61.5 + - - +
356B GLU 3.0 1.8 - - - -
358B CYS* 2.9 60.0 + - + +
361B LEU* 4.5 13.8 - - + +
364B ILE* 6.4 0.2 - - + -
379B PHE* 5.0 2.7 - - + -
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Residues in contact with ALA 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 LEU 3.1 5.1 + - - -
352B ILE 3.5 9.0 - - - +
354B ILE* 1.3 76.5 - - - +
356B GLU* 1.3 62.4 + - - +
358B CYS 4.4 9.2 - - - +
359B LYS* 5.0 4.9 + - - +
361B LEU* 5.5 2.7 - - - -
379B PHE* 3.6 31.0 - - + -
382B MET* 3.9 32.3 - - + +
383B CYS* 4.1 11.4 - - - -
386B ARG* 4.8 10.6 + - - -
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Residues in contact with GLU 356 (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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352B ILE* 3.0 14.8 + - + +
353B ARG* 3.0 18.2 - - + +
355B ALA* 1.3 80.4 - - - +
357B ARG* 1.3 66.9 + - + +
359B LYS* 3.9 20.3 - - - +
382B MET* 3.9 19.3 - - + +
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Residues in contact with ARG 357 (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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307B GLU* 6.0 0.2 + - - -
328B GLY 3.3 27.4 + - - +
329B MET* 3.2 44.7 + - - +
330B THR 4.2 0.4 - - - +
331B CYS 5.2 2.2 - - - +
332B PRO* 3.7 27.8 - - + +
353B ARG* 2.8 38.2 + - + +
356B GLU* 1.3 85.3 - - + +
358B CYS* 1.3 62.6 + - - +
359B LYS* 3.5 8.2 + - - +
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Residues in contact with CYS 358 (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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327B VAL 5.1 0.2 - - - -
328B GLY* 4.6 9.6 - - - -
331B CYS* 3.4 24.2 - - - +
332B PRO 4.4 6.3 - - - -
334B LEU* 3.8 25.8 - - + +
354B ILE* 2.9 45.9 + - + +
355B ALA 4.4 2.7 - - - +
357B ARG* 1.3 79.2 - - - +
359B LYS* 1.3 58.5 + - - +
360B ASN 2.8 11.3 + - - -
361B LEU* 3.0 20.2 + - + +
386B ARG* 4.0 4.2 + - - -
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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