Contacts of the helix formed by residues 332 - 346 (chain B) in PDB entry 3H1I
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 HIS 332 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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303B THR* 3.5 18.8 + - - +
304B THR* 4.0 13.4 + - + -
305B GLN* 3.3 42.9 - - + +
306B PRO 5.8 1.6 - - - +
328B SER* 4.0 0.7 - - - -
329B GLN* 3.2 25.2 + - + +
331B ALA* 1.3 85.2 + - + +
333B ALA* 1.3 57.2 + - - +
334B GLY 3.2 2.2 - - - -
335B GLU* 3.7 24.3 + - - +
336B VAL* 2.7 39.7 + - + +
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Residues in contact with ALA 333 (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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253B VAL* 3.8 14.4 - - + -
328B SER* 3.1 18.2 - - - +
329B GLN 2.9 12.9 + - - +
330B ALA 3.6 9.9 - - - +
331B ALA 3.2 1.2 - - - -
332B HIS* 1.3 76.2 - - - +
334B GLY* 1.3 71.3 + - - +
336B VAL* 4.3 0.2 - - - -
337B ILE* 2.9 28.9 + - + +
433B THR* 3.6 25.1 - - + +
434B PRO* 4.7 0.4 - - - -
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Residues in contact with GLY 334 (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 ALA 4.0 6.0 + - - -
332B HIS 3.2 1.0 - - - -
333B ALA* 1.3 85.4 - - - +
335B GLU* 1.3 63.4 + - - +
336B VAL 2.9 0.2 + - - -
337B ILE* 3.0 9.2 + - - +
338B ARG* 3.3 26.6 + - - +
432B SER* 3.4 22.7 + - - -
434B PRO* 4.1 9.0 - - - +
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Residues in contact with GLU 335 (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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302B ALA* 3.7 30.5 - - + +
303B THR* 4.2 8.5 - - - -
304B THR* 5.1 1.0 + - - +
331B ALA 5.1 2.7 - - - +
332B HIS* 3.7 37.6 + - + +
334B GLY* 1.3 69.0 - - - -
336B VAL* 1.3 55.6 + - - +
338B ARG* 3.8 24.7 + - - +
339B ALA* 2.7 39.4 + - + +
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Residues in contact with VAL 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B VAL* 4.0 25.2 - - + +
302B ALA* 6.0 0.4 - - - -
303B THR* 4.0 26.2 - - + +
307B PHE* 4.6 8.3 - - + -
308B ASP 5.4 0.2 - - - +
309B ALA* 5.3 0.4 - - + -
326B THR* 3.7 28.3 - - + +
327B ILE 5.2 0.4 - - - +
328B SER* 3.6 23.1 - - - +
332B HIS* 2.7 25.9 + - + +
333B ALA 3.9 4.0 - - - +
334B GLY 2.9 3.8 + - - -
335B GLU* 1.3 74.0 - - - +
337B ILE* 1.3 58.6 + - - +
339B ALA* 3.9 2.5 - - - +
340B ALA* 3.1 24.3 + - - +
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Residues in contact with ILE 337 (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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253B VAL* 5.4 0.7 - - + -
255B ALA* 4.1 17.0 - - + -
257B VAL* 4.4 12.3 - - + -
324B PHE* 3.6 26.4 - - + -
326B THR* 3.7 16.4 - - - +
328B SER* 5.4 0.4 - - - +
333B ALA* 2.9 22.7 - - + +
334B GLY 3.0 1.7 + - - +
336B VAL* 1.3 74.1 - - + +
338B ARG* 1.3 66.4 + - - +
340B ALA* 3.0 20.3 + - - +
341B MET* 3.1 11.7 + - - +
424B MET* 4.3 7.2 - - + -
433B THR* 3.6 16.8 - - + -
434B PRO* 3.5 26.2 - - + -
439B LEU* 5.0 7.6 - - + -
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Residues in contact with ARG 338 (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 GLY* 3.3 16.0 + - - +
335B GLU* 3.3 36.3 + - - +
337B ILE* 1.3 79.0 - - - +
339B ALA* 1.3 58.0 + - - +
341B MET* 3.0 26.7 + - - +
342B ASN* 3.2 15.3 + - - +
432B SER 5.4 1.4 + - - -
434B PRO* 4.6 15.9 - - + +
438B GLU* 4.8 10.2 - - - +
439B LEU* 4.2 21.5 - - + -
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Residues in contact with ALA 339 (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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298B GLY 4.9 5.5 - - - +
299B VAL* 4.8 12.6 - - - +
302B ALA* 3.8 25.4 - - + -
335B GLU* 2.7 22.4 + - + +
336B VAL* 3.9 3.4 - - - +
338B ARG* 1.3 71.7 - - - +
340B ALA* 1.3 58.0 + - - +
341B MET 3.1 3.3 + - - -
342B ASN* 3.3 16.1 + - - +
343B GLN* 3.4 22.9 + - - +
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Residues in contact with ALA 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B LEU* 3.2 31.0 - - + +
299B VAL* 4.5 7.9 - - + -
324B PHE* 3.6 31.0 - - + -
326B THR* 4.1 7.2 - - + -
336B VAL 3.1 16.2 + - - +
337B ILE* 3.0 15.0 + - - +
339B ALA* 1.3 77.5 - - - +
341B MET* 1.3 58.1 + - - +
343B GLN 4.3 0.4 - - - -
344B LEU* 3.7 11.4 + - - +
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Residues in contact with MET 341 (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 VAL* 4.9 1.8 - - + -
324B PHE* 3.9 18.6 - - + -
337B ILE 3.1 11.3 + - - +
338B ARG* 3.0 12.3 + - - +
340B ALA* 1.3 74.8 - - - +
342B ASN* 1.3 58.0 + - - +
343B GLN 2.8 1.3 - - - -
344B LEU* 2.3 32.0 + - - +
345B LYS* 2.6 32.4 + - + +
417B PHE* 3.7 30.7 - - + -
418B VAL* 5.8 2.5 - - + -
422B LYS* 4.0 28.7 - - + +
439B LEU* 4.0 41.1 - - + +
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Residues in contact with ASN 342 (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 ARG* 3.2 21.3 + - - +
339B ALA* 3.3 17.6 - - - +
341B MET* 1.3 74.8 - - - +
343B GLN* 1.3 53.9 + - - +
345B LYS* 3.1 28.4 + - - +
346B ALA* 2.6 38.9 + - + +
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Residues in contact with GLN 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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279B LEU* 4.1 4.9 - - + +
294B LYS* 3.5 36.8 + - + +
295B LEU* 3.6 29.6 - - + +
298B GLY* 3.2 19.7 - - - -
339B ALA 3.4 17.4 + - - +
340B ALA 4.1 6.3 - - - +
341B MET 2.8 0.6 - - - -
342B ASN* 1.3 80.5 - - - +
344B LEU* 1.3 57.8 + - - +
346B ALA* 4.3 5.2 + - - +
347B ALA* 2.9 22.1 + - - +
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Residues in contact with LEU 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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275B LEU* 5.2 4.7 - - + -
279B LEU* 3.3 42.4 - - + -
295B LEU* 5.3 3.8 - - + -
322B PHE* 5.1 5.6 - - + -
323B GLY* 5.1 4.3 - - - -
324B PHE* 4.1 14.6 - - + -
340B ALA 3.7 10.5 + - - +
341B MET* 2.3 30.2 + - - +
343B GLN* 1.3 72.0 - - - +
345B LYS* 1.3 59.0 + - - -
347B ALA* 3.3 12.6 - - + +
348B ALA* 3.4 11.8 + - - +
414B ALA* 4.5 4.7 - - + +
417B PHE* 3.2 56.1 - - + -
418B VAL* 4.1 3.4 - - + +
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Residues in contact with LYS 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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341B MET* 2.6 25.9 + - + +
342B ASN* 3.1 42.5 + - - +
344B LEU* 1.3 75.5 - - + +
346B ALA* 1.3 54.9 + - - +
347B ALA 2.5 5.5 + - - -
348B ALA* 2.5 26.5 + - - +
349B GLN* 3.1 21.3 + - - +
418B VAL* 4.0 34.3 - - + -
439B LEU 6.2 1.6 - - - -
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Residues in contact with ALA 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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342B ASN* 2.6 21.4 + - + +
343B GLN* 4.3 6.5 + - - +
345B LYS* 1.3 68.8 - - - +
347B ALA* 1.3 55.9 + - - +
348B ALA 3.6 0.4 - - - -
349B GLN* 4.1 16.5 - - - +
351B GLY* 3.4 24.0 + - - +
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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