Contacts of the helix formed by residues 342 - 356 (chain B) in PDB entry 4OL0
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 SER 342 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A ARG* 4.5 4.5 - - - +
296B CYS* 5.0 3.4 - - - -
300B THR* 3.3 34.2 - - - +
327B LEU* 3.7 20.4 + - - +
339B VAL* 3.9 9.4 + - - +
341B ILE* 1.3 90.4 + - - +
343B PHE* 1.3 64.3 + - - +
344B ASN* 3.1 3.7 - - - +
345B PHE* 3.2 5.1 + - - +
346B TRP* 2.9 41.7 + - - -
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Residues in contact with PHE 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B VAL* 3.0 24.7 - - + -
340B GLU* 3.5 22.4 + - + +
341B ILE 3.1 5.0 + - - -
342B SER* 1.3 80.3 - - - +
344B ASN* 1.3 56.3 + - - +
346B TRP* 3.2 8.2 + + - +
347B TYR* 2.8 45.0 + + + -
372B LEU* 5.6 0.4 - - + -
376B LEU* 3.6 24.5 - - + -
399B PHE* 3.9 11.0 - + - -
402B ARG* 4.2 21.8 - - + -
403B VAL* 3.7 40.2 - - + -
406B LEU* 3.4 27.2 - - + +
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Residues in contact with ASN 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A LYS 3.3 21.2 + - - +
135A SER* 4.1 12.9 + - - +
136A ILE 5.8 0.7 - - - +
137A VAL* 4.2 23.4 - - + +
140A ARG* 4.5 6.7 - - - +
304B GLU* 2.8 33.3 - - - +
342B SER* 3.1 1.2 - - - +
343B PHE* 1.3 76.0 - - - +
345B PHE* 1.3 59.3 + - - +
347B TYR* 3.2 12.0 + - - +
348B ARG* 2.8 38.9 + - - +
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Residues in contact with PHE 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ARG* 5.2 0.2 - - - +
300B THR* 4.5 10.1 - - + -
303B CYS* 3.4 25.1 - - + -
304B GLU* 3.7 27.9 + - + +
307B LEU* 3.7 28.5 - - + -
310B ILE* 4.7 7.2 - - + -
324B LEU* 3.4 35.0 - - + -
327B LEU* 3.4 22.9 - - + -
342B SER* 3.2 15.8 + - - +
344B ASN* 1.3 80.5 + - - +
346B TRP* 1.3 70.3 + + - +
348B ARG* 3.1 12.0 + - - +
349B LEU* 2.8 42.8 + - + +
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Residues in contact with TRP 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B LEU* 4.0 16.8 - - + -
327B LEU* 4.3 22.7 + - + +
328B LEU* 3.9 32.3 - - + -
339B VAL* 6.2 0.6 - - + +
342B SER* 2.9 41.4 + - - -
343B PHE* 3.6 12.3 - + - +
345B PHE* 1.3 83.3 - + - +
347B TYR* 1.3 57.3 + - - +
349B LEU* 3.6 30.1 - - + +
350B GLY* 2.8 27.0 + - - -
368B TYR* 4.6 17.5 - - + -
369B ILE* 4.8 9.6 - - + -
372B LEU* 3.5 43.0 - - + +
406B LEU* 4.1 13.2 - - + -
410B LEU* 3.7 10.9 - - + +
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Residues in contact with TYR 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A LYS* 3.6 50.3 - - + +
343B PHE* 2.8 37.1 + + + -
344B ASN* 3.3 15.7 - - - +
346B TRP* 1.3 75.5 - - - +
348B ARG* 1.3 56.8 + - + +
350B GLY* 3.2 2.5 + - - -
351B GLU* 2.8 30.7 + - - +
402B ARG* 4.0 2.4 + - - +
405B ASP* 3.3 15.4 - - - +
406B LEU* 3.0 46.7 + - + +
409B ASP* 3.5 32.1 - - + -
410B LEU* 5.2 1.6 - - + -
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Residues in contact with ARG 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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257B GLU* 5.6 3.2 + - - -
304B GLU* 3.4 39.3 + - - +
307B LEU* 3.5 32.3 - - + +
344B ASN* 2.8 45.5 + - - +
345B PHE* 3.4 6.9 - - - +
347B TYR* 1.3 73.0 - - + +
349B LEU* 1.3 57.6 + - - +
351B GLU* 3.3 16.8 + - - +
352B HIS* 2.9 30.3 + - - +
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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
----------------------------------------------------------
307B LEU* 4.1 14.3 - - + +
310B ILE* 5.5 0.4 - - + -
311B VAL* 3.4 32.3 - - + -
324B LEU* 4.5 2.7 - - + -
345B PHE* 2.8 31.6 + - + +
346B TRP* 3.6 37.7 - - + +
348B ARG* 1.3 72.7 - - - +
350B GLY* 1.3 57.9 + - - +
352B HIS* 3.3 2.3 + - - +
353B LEU* 2.8 53.1 + - + +
365B PHE* 4.1 25.4 - - + -
369B ILE* 5.2 4.5 - - + -
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Residues in contact with GLY 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B TRP 2.8 14.8 + - - -
347B TYR 3.6 3.1 - - - -
349B LEU* 1.3 75.4 - - - +
351B GLU* 1.3 52.0 + - - +
353B LEU* 3.3 1.6 + - - +
354B TYR* 2.8 30.1 + - - +
410B LEU* 3.9 18.8 - - - +
412B PHE* 3.4 16.5 - - - -
413B LEU* 4.0 13.5 - - - -
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Residues in contact with GLU 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 TYR 2.8 12.3 + - - +
348B ARG* 3.3 20.7 - - - +
350B GLY* 1.3 74.2 - - - +
352B HIS* 1.3 65.2 + - - +
354B TYR* 2.9 18.6 + - - +
355B LYS* 2.9 41.9 + - - +
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Residues in contact with HIS 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B LEU* 5.4 6.7 - - + -
308B GLU* 5.8 1.3 - - + -
311B VAL* 3.1 49.4 + - + +
312B CYS* 4.6 11.7 - - - -
348B ARG 2.9 19.0 + - - +
349B LEU* 3.7 5.4 - - - +
351B GLU* 1.3 74.4 - - - +
353B LEU* 1.3 65.0 + - + +
355B LYS* 3.2 13.9 + - + +
356B THR* 3.0 45.9 + - - -
361B ILE* 6.2 2.1 - - + +
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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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349B LEU* 2.8 39.8 + - + +
350B GLY 3.6 4.3 - - - +
352B HIS* 1.3 81.7 - - + +
354B TYR* 1.3 62.0 + - - +
356B THR* 2.9 26.0 + - - +
361B ILE* 3.8 29.8 - - + +
362B HIS* 3.2 21.8 + - + +
365B PHE* 3.8 32.3 - - + -
369B ILE* 4.0 4.0 - - + -
412B PHE* 4.7 1.1 - - - -
413B LEU* 3.7 36.8 - - + -
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Residues in contact with TYR 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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350B GLY 2.8 15.8 + - - +
351B GLU* 2.9 11.4 + - - +
353B LEU* 1.3 73.4 - - - +
355B LYS* 1.3 66.7 + - + +
356B THR 3.4 5.5 + - - +
362B HIS* 5.4 0.2 - - - -
412B PHE* 3.2 51.9 - + + +
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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 GLU* 2.9 47.6 + - - +
352B HIS* 3.2 14.6 + - + +
354B TYR* 1.3 82.1 - - + +
356B THR* 1.3 60.8 + - - +
357B ASN* 3.8 2.6 + - - +
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Residues in contact with THR 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 HIS* 3.0 36.7 + - - -
353B LEU* 2.9 23.3 - - - +
354B TYR 3.2 5.4 - - - +
355B LYS* 1.3 78.7 - - - +
357B ASN* 1.3 62.2 + - - +
358B ASP* 3.6 26.9 - - + +
361B ILE* 4.2 15.7 - - + +
362B HIS* 3.3 14.5 + - + +
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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