Contacts of the helix formed by residues 336 - 349 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227A SER* 6.0 3.6 - - - -
334A VAL* 3.4 27.2 + - + +
335A ILE* 1.3 78.4 - - - +
337A PHE* 1.3 69.2 + - - +
338A GLY 3.2 3.9 + - - +
339A GLY 3.2 3.7 + - - +
340A ALA* 2.7 25.5 + - - +
418A ASP* 3.1 35.0 + - + +
421A GLY* 4.5 1.6 - - - -
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Residues in contact with PHE 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336A ARG* 1.3 76.6 - - - +
338A GLY* 1.3 58.7 + - - +
340A ALA* 4.3 4.7 - - - -
341A GLU* 2.7 59.9 + - + +
418A ASP* 4.5 1.0 + - - -
420A VAL* 4.2 20.7 - - + +
424A LEU* 3.8 23.1 - - + -
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Residues in contact with GLY 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311A SER* 6.0 4.5 - - - -
313A GLY* 4.1 15.5 - - - +
336A ARG* 3.3 3.2 - - - +
337A PHE* 1.3 88.5 - - - +
339A GLY* 1.3 59.9 + - - +
341A GLU* 3.6 7.7 + - - +
342A ALA* 3.3 18.5 + - - +
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Residues in contact with GLY 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312A LEU* 4.5 9.3 - - - +
313A GLY 3.7 7.8 - - - +
316A ALA* 3.5 23.9 - - - +
335A ILE* 4.1 6.3 - - - -
336A ARG* 3.2 7.9 + - - +
338A GLY* 1.3 73.0 - - - +
340A ALA* 1.3 65.7 + - - +
342A ALA* 3.1 4.3 + - - +
343A VAL* 2.9 29.2 + - - +
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Residues in contact with ALA 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335A ILE* 3.6 10.5 - - + +
336A ARG 2.7 22.9 + - - +
337A PHE 3.7 2.5 - - - +
339A GLY* 1.3 70.5 - - - -
341A GLU* 1.3 57.9 + - - +
343A VAL* 3.1 9.7 + - - +
344A LEU* 2.9 33.8 + - - +
421A GLY* 3.8 21.1 - - - +
424A LEU* 3.7 26.7 - - + -
425A ILE* 4.4 4.2 - - + +
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Residues in contact with GLU 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337A PHE* 2.7 47.6 + - + +
338A GLY* 3.6 7.1 - - - +
340A ALA* 1.3 72.0 - - - +
342A ALA* 1.3 66.7 + - - +
344A LEU* 3.3 14.9 + - + +
345A ASP* 2.6 48.9 + - - +
424A LEU* 4.7 2.4 - - - +
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Residues in contact with ALA 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313A GLY 3.6 21.8 - - - +
314A GLY* 3.7 16.6 - - - -
316A ALA* 5.0 0.2 - - + -
317A VAL* 4.5 2.9 - - + -
338A GLY 3.3 5.8 + - - +
339A GLY 3.1 9.3 + - - +
341A GLU* 1.3 82.0 + - - +
343A VAL* 1.3 66.0 + - - +
345A ASP* 3.1 11.2 + - - +
346A ALA* 3.0 17.5 + - - +
388A VAL* 3.7 17.7 - - + +
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Residues in contact with VAL 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A ALA* 4.4 11.0 - - + -
317A VAL* 4.5 5.2 - - + -
329A LEU* 5.3 4.0 - - + -
331A LEU* 4.2 37.0 - - + -
335A ILE* 5.1 1.1 - - + -
339A GLY 2.9 22.2 + - - +
340A ALA* 3.1 12.1 + - - +
342A ALA* 1.3 76.5 - - - +
344A LEU* 1.3 59.4 + - + +
346A ALA* 2.9 25.7 + - - +
347A LEU* 3.0 29.1 + - + +
409A LEU* 5.4 3.8 - - + -
425A ILE* 4.1 23.6 - - + -
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Residues in contact with LEU 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340A ALA 2.9 16.5 + - - +
341A GLU* 3.5 10.3 - - - +
343A VAL* 1.3 77.5 - - + +
345A ASP* 1.3 59.4 + - - +
347A LEU* 3.7 10.5 + - + +
348A THR* 2.8 33.7 + - - +
424A LEU* 3.5 56.5 - - + +
425A ILE* 4.8 2.7 - - - +
427A GLU* 5.8 0.7 - - + -
428A GLY* 3.7 21.8 - - - +
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Residues in contact with ASP 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341A GLU* 2.6 41.4 + - - +
342A ALA* 3.2 12.3 - - - +
343A VAL 3.0 0.4 - - - -
344A LEU* 1.3 77.7 - - - +
346A ALA* 1.3 60.0 + - - +
348A THR* 3.3 4.8 + - - -
349A ASP* 2.9 40.8 + - - +
388A VAL* 4.0 11.0 - - + -
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Residues in contact with ALA 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317A VAL* 4.6 10.1 - - + -
320A VAL* 5.3 0.4 - - + -
329A LEU* 4.4 17.3 - - + -
342A ALA 3.0 11.2 + - - +
343A VAL* 2.9 11.8 + - - +
345A ASP* 1.3 76.1 - - - +
347A LEU* 1.3 64.0 + - - +
349A ASP* 3.0 11.0 + - - +
350A LEU* 3.6 5.5 + - - +
388A VAL* 3.7 19.9 - - + +
391A ALA* 3.2 32.1 - - + +
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Residues in contact with LEU 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329A LEU* 3.5 27.4 - - + -
343A VAL* 3.0 29.2 + - + +
344A LEU* 3.9 11.0 - - + +
346A ALA* 1.3 76.3 - - - +
348A THR* 1.3 61.5 + - - +
350A LEU* 3.2 32.1 + - + +
352A THR* 5.0 1.6 + - - -
407A VAL* 4.7 4.0 - - + -
409A LEU* 5.5 7.2 - - + -
425A ILE* 5.3 3.1 - - + +
428A GLY* 4.1 33.2 - - - +
429A VAL* 4.6 4.3 - - + +
432A LEU* 3.6 36.1 - - + +
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Residues in contact with THR 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344A LEU* 2.8 22.0 + - - +
345A ASP* 3.8 6.7 + - - -
346A ALA 3.3 0.4 - - - -
347A LEU* 1.3 73.1 - - - +
349A ASP* 1.3 60.3 + - - +
350A LEU 3.0 17.1 + - - +
351A ARG* 5.0 2.9 + - - -
357A PRO* 6.2 4.5 - - + -
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Residues in contact with ASP 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A ASP* 2.9 30.8 + - - +
346A ALA 3.0 10.0 + - - +
348A THR* 1.3 80.7 - - - +
350A LEU* 1.3 57.7 + - - +
351A ARG* 3.8 11.1 + - - +
388A VAL* 4.1 16.8 - - - +
389A HIS* 5.3 1.7 - - - -
391A ALA* 3.5 12.6 - - + +
392A ALA* 3.4 25.7 - - + +
395A ALA* 3.4 15.6 - - - +
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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