Contacts of the helix formed by residues 342 - 353 (chain B) in PDB entry 3R29
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 VAL 342 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264B PRO* 5.3 6.7 - - + -
265B VAL* 5.3 11.9 - - + +
337B ALA* 3.2 28.2 + - + +
340B ALA* 4.9 7.4 - - + +
341B GLY* 1.3 80.0 - - - +
343B GLY* 1.3 66.1 + - - +
344B ALA 3.0 4.4 + - - +
345B ILE* 3.1 18.4 + - + -
346B PHE* 2.9 21.3 + - + +
435B HIS* 3.8 14.4 - - + +
439B PHE* 3.8 22.7 - - + -
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Residues in contact with GLY 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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337B ALA 3.6 4.6 + - - -
338B HIS* 3.6 41.9 + - - +
341B GLY* 3.7 1.2 - - - -
342B VAL* 1.3 76.7 - - - +
344B ALA* 1.3 56.1 + - - +
346B PHE* 3.9 4.5 - - - -
347B ASP* 2.8 40.1 + - - +
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Residues in contact with ALA 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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342B VAL* 3.0 0.8 - - - -
343B GLY* 1.3 76.7 - - - +
345B ILE* 1.3 63.3 + - - +
347B ASP* 3.9 4.3 - - - +
348B ARG* 3.2 37.2 + - - +
435B HIS* 4.5 14.6 - - + +
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Residues in contact with ILE 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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342B VAL* 3.3 32.1 - - + +
344B ALA* 1.3 76.0 - - - +
346B PHE* 1.3 63.5 + - - +
348B ARG* 3.2 7.6 + - + +
349B VAL* 2.9 32.9 + - + +
428B ILE* 3.6 24.5 - - + +
431B LYS* 4.2 9.0 - - + -
432B CYS* 3.1 43.3 - - - +
435B HIS* 3.4 32.7 + - + +
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Residues in contact with PHE 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B GLY* 4.1 12.3 - - - -
324B ILE* 4.1 38.8 - - + -
332B VAL* 4.6 3.8 - - + -
333B HIS* 3.6 5.6 - - - -
334B ARG* 2.8 59.7 - - + -
337B ALA* 3.7 20.9 - - + -
338B HIS* 4.3 4.7 - + - -
342B VAL* 2.9 13.8 + - + +
343B GLY* 3.2 10.8 - - - +
345B ILE* 1.3 79.6 - - - +
347B ASP* 1.3 63.2 + - - +
349B VAL* 3.3 8.1 + - + +
350B LEU* 3.2 43.2 + - + +
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Residues in contact with ASP 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 ARG* 1.9 52.1 + - - +
338B HIS* 2.5 37.8 + - - -
343B GLY 2.8 15.2 + - - +
344B ALA* 3.9 4.8 - - - +
346B PHE* 1.3 72.5 - - - +
348B ARG* 1.3 60.1 + - + +
349B VAL 3.3 0.2 + - - -
350B LEU* 3.3 0.8 + - - +
351B THR* 2.7 39.4 + - + +
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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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381A LYS* 5.0 14.9 - - - +
344B ALA* 3.2 29.2 + - - +
345B ILE* 3.2 9.6 + - + +
347B ASP* 1.3 73.6 - - - +
349B VAL* 1.3 55.9 + - - +
351B THR* 3.7 5.6 - - - +
352B GLU* 2.6 60.4 + - - +
428B ILE* 3.4 18.3 - - + +
431B LYS* 3.6 45.2 - - - +
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Residues in contact with VAL 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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310B ILE* 4.7 3.4 - - + -
313B PHE* 4.4 24.0 - - + -
314B SER* 3.8 23.8 - - - +
324B ILE* 5.2 5.4 - - + -
345B ILE* 2.9 25.7 + - + +
346B PHE* 3.6 8.7 - - + +
347B ASP 3.2 0.2 - - - -
348B ARG* 1.3 74.8 - - - +
350B LEU* 1.3 60.8 + - + +
353B LEU* 2.8 19.7 + - + +
354B VAL* 2.7 31.4 + - + -
428B ILE* 3.9 22.9 - - + -
432B CYS* 5.7 0.9 - - - -
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Residues in contact with LEU 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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322B ASP* 5.1 3.8 - - - +
323B GLY* 3.8 31.9 - - - +
324B ILE* 4.1 16.6 - - + -
334B ARG* 3.8 25.8 - - - +
346B PHE* 3.2 39.3 + - + +
347B ASP* 4.0 2.9 - - - +
349B VAL* 1.3 76.3 - - + +
351B THR* 1.3 67.7 + - + +
354B VAL* 4.0 18.8 - - + -
355B SER* 3.0 31.9 + - - +
358B ARG* 6.2 0.2 - - - +
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Residues in contact with THR 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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379A ASP* 4.9 0.7 - - - -
381A LYS* 4.4 24.8 + - - +
334B ARG* 5.1 10.5 - - - +
347B ASP* 2.7 35.4 + - + +
348B ARG* 3.7 5.2 + - - +
350B LEU* 1.3 79.7 - - + +
352B GLU* 1.3 64.9 + - - +
353B LEU 3.7 0.2 + - - -
355B SER* 4.0 9.2 - - - +
356B LYS* 3.7 23.3 + - - +
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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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379A ASP* 4.0 38.3 - - + +
381A LYS* 5.9 1.7 - - - +
426A ARG* 4.7 4.0 + - - -
348B ARG* 2.6 54.8 + - - +
351B THR* 1.3 80.8 + - - +
353B LEU* 1.3 66.2 + - - +
356B LYS* 4.0 2.8 - - - +
421B ARG* 3.0 24.9 + - - +
424B ALA* 4.0 11.6 - - + +
427B SER* 4.2 9.5 + - - -
428B ILE* 3.9 18.6 - - + +
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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
----------------------------------------------------------
310B ILE* 4.2 7.9 - - + -
314B SER* 4.0 22.9 - - - +
349B VAL* 2.8 21.1 + - + +
351B THR 3.5 0.8 - - - -
352B GLU* 1.3 81.4 - - - +
354B VAL* 1.3 64.7 + - - +
355B SER 3.6 0.4 - - - -
356B LYS* 4.0 2.9 - - - +
357B MET* 3.1 44.8 + - + +
421B ARG* 4.2 20.4 - - + +
424B ALA* 4.1 15.5 - - + -
425B LEU* 4.0 28.9 - - + +
428B ILE* 3.8 28.0 - - + -
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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