Contacts of the helix formed by residues 336 - 349 (chain B) in PDB entry 3IH9
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 ARG 336 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227B SER* 5.9 3.8 + - - -
334B VAL* 3.6 23.9 + - + +
335B ILE* 1.3 77.5 - - - +
337B PHE* 1.3 70.4 + - + +
338B GLY* 3.0 4.8 + - - +
339B GLY 3.1 3.7 + - - +
340B ALA* 2.8 25.6 + - - +
418B ASP* 3.4 35.5 + - + +
421B GLY* 4.7 1.1 - - - -
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Residues in contact with PHE 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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336B ARG* 1.3 75.9 - - + +
338B GLY* 1.3 62.4 + - - +
340B ALA* 3.9 5.3 - - - +
341B GLU* 2.8 59.0 + - + +
418B ASP* 4.5 3.4 + - - -
420B VAL* 4.3 18.9 - - + +
424B LEU* 4.0 21.1 - - + -
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Residues in contact with GLY 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B SER* 5.8 6.1 - - - -
312B LEU* 6.1 0.2 - - - -
313B GLY* 4.1 15.8 - - - +
336B ARG* 3.0 4.4 - - - +
337B PHE* 1.3 88.3 - - - +
339B GLY* 1.3 60.0 + - - +
341B GLU* 3.6 5.1 - - - +
342B ALA* 3.4 17.5 + - - +
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Residues in contact with GLY 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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312B LEU* 4.8 7.4 - - - +
313B GLY 3.7 8.2 + - - +
316B ALA* 3.5 24.9 - - - +
335B ILE* 4.1 8.3 - - - +
336B ARG 3.1 8.9 + - - +
338B GLY* 1.3 71.6 - - - +
340B ALA* 1.3 67.5 + - - +
342B ALA* 2.9 14.4 + - - +
343B VAL* 2.9 18.6 + - - +
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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
----------------------------------------------------------
335B ILE* 3.5 11.8 - - + +
336B ARG 2.8 21.1 + - - +
337B PHE 3.9 0.2 - - - +
339B GLY* 1.3 70.1 - - - -
341B GLU* 1.3 62.5 + - - +
343B VAL* 3.2 4.8 + - - +
344B LEU* 3.0 28.9 + - - +
421B GLY* 3.8 20.6 - - - +
424B LEU* 3.5 30.1 - - + -
425B ILE* 4.3 10.1 - - + +
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Residues in contact with GLU 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B PHE* 2.8 50.4 + - + +
338B GLY* 3.6 5.8 - - - +
340B ALA* 1.3 72.8 - - - +
342B ALA* 1.3 65.1 + - - +
344B LEU* 3.2 23.1 + - + +
345B ASP* 2.6 41.1 + - - +
424B LEU* 4.7 1.7 - - - +
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Residues in contact with ALA 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B GLY* 3.6 22.7 - - - +
314B GLY* 3.8 17.0 - - - +
316B ALA* 5.2 0.2 - - + -
317B VAL* 4.8 2.2 - - + -
338B GLY 3.4 5.6 + - - +
339B GLY 2.9 9.0 + - - +
341B GLU* 1.3 80.5 + - - +
343B VAL* 1.3 63.4 + - - +
345B ASP* 2.6 26.7 - - - +
346B ALA* 3.1 11.1 + - - +
388B VAL* 3.5 11.5 - - + +
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Residues in contact with VAL 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B ALA* 4.6 6.3 - - + -
317B VAL* 4.2 8.5 - - + -
329B LEU* 4.3 17.9 - - + -
331B LEU* 3.9 36.6 - - + -
335B ILE* 4.9 1.3 - - + -
339B GLY 2.9 21.8 + - - +
340B ALA* 3.2 10.7 + - - +
342B ALA* 1.3 73.4 - - - +
344B LEU* 1.3 61.3 + - - +
346B ALA* 2.9 10.6 + - - +
347B LEU* 2.8 43.4 + - + +
409B LEU* 5.5 1.1 - - + -
425B ILE* 4.6 17.3 - - + -
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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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340B ALA 3.0 19.3 + - - +
341B GLU* 3.2 17.7 + - + +
343B VAL* 1.3 77.9 - - + +
345B ASP* 1.3 57.6 + - - +
347B LEU* 3.4 11.5 - - + +
348B THR* 2.9 30.0 + - - -
424B LEU* 3.5 52.5 - - + +
425B ILE* 4.7 3.1 - - + -
427B GLU* 5.4 0.7 - - + -
428B GLY* 4.0 18.2 - - - -
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Residues in contact with ASP 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 GLU* 2.6 37.0 - - - +
342B ALA* 2.6 26.3 - - - +
344B LEU* 1.3 75.1 - - - +
346B ALA* 1.3 60.2 + - - +
347B LEU 3.1 0.4 - - - -
348B THR* 3.6 8.9 - - + -
349B ASP* 2.7 46.1 + - - +
388B VAL* 3.3 13.2 - - - +
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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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317B VAL* 4.3 11.9 - - + -
329B LEU* 4.5 13.5 - - + -
342B ALA 3.5 9.6 - - - +
343B VAL* 2.9 13.3 + - - +
345B ASP* 1.3 81.4 + - - +
347B LEU* 1.3 64.0 + - - +
349B ASP* 3.1 8.6 + - - +
350B LEU* 3.6 4.6 - - - +
388B VAL* 3.6 22.0 - - + +
391B ALA* 3.1 32.2 - - + +
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Residues in contact with LEU 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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329B LEU* 3.8 23.6 - - + -
343B VAL* 2.8 29.9 + - + +
344B LEU* 3.4 14.8 - - + +
346B ALA* 1.3 77.2 - - - +
348B THR* 1.3 57.2 + - - +
350B LEU* 2.8 41.8 + - + +
352B THR* 5.1 0.3 + - - +
407B VAL* 4.9 3.6 - - + -
409B LEU* 5.8 4.9 - - + -
425B ILE* 5.3 5.2 - - + +
428B GLY* 4.3 30.3 - - - +
429B VAL* 4.9 3.1 - - + +
432B LEU* 3.7 35.0 - - + +
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Residues in contact with THR 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 LEU 2.9 20.5 + - - -
345B ASP* 3.4 10.0 + - + +
347B LEU* 1.3 75.1 - - - +
349B ASP* 1.3 60.6 + - - +
350B LEU 3.0 12.7 + - - +
351B ARG* 5.1 4.5 + - - -
357B PRO* 6.0 5.6 - - + -
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Residues in contact with ASP 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B ASP* 2.7 30.6 + - - +
346B ALA 3.3 9.9 - - - +
347B LEU 3.0 1.0 - - - -
348B THR* 1.3 81.8 - - - +
350B LEU* 1.3 58.0 + - - +
351B ARG* 4.0 10.1 + - - +
376B ARG* 5.6 1.4 - - - -
388B VAL* 4.1 17.2 - - - +
389B HIS* 5.2 1.7 - - - -
391B ALA* 3.7 2.5 - - + +
392B ALA* 3.6 41.7 - - + +
395B ALA* 3.7 7.6 - - - +
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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