Contacts of the helix formed by residues 418 - 434 (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 ASP 418 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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334B VAL* 6.3 0.4 - - - +
335B ILE 3.3 3.6 + - - -
336B ARG* 3.4 48.4 + - + +
337B PHE 4.5 0.7 + - - -
417B ILE* 1.3 76.4 - - - +
419B ASP* 1.3 65.1 + - - +
420B VAL* 3.7 14.6 - - - +
421B GLY* 2.6 34.8 + - - -
422B ARG* 3.0 23.7 + - - +
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Residues in contact with ASP 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B ASP* 1.3 75.4 - - - +
420B VAL* 1.3 66.7 + - + +
422B ARG* 3.0 27.7 + - - +
423B ARG* 2.9 37.1 + - + +
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Residues in contact with VAL 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B PHE* 4.3 23.8 - - + -
418B ASP* 3.3 15.8 + - - +
419B ASP* 1.3 78.1 - - + +
421B GLY* 1.3 58.3 + - - +
423B ARG* 3.6 24.7 + - - +
424B LEU* 3.0 52.0 + - + +
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Residues in contact with GLY 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B ILE* 4.7 3.6 - - - -
336B ARG 4.7 1.3 - - - -
340B ALA* 3.8 20.9 - - - -
417B ILE* 3.7 12.1 - - - -
418B ASP* 2.6 22.1 + - - -
420B VAL* 1.3 71.5 - - - +
422B ARG* 1.3 65.0 + - - +
424B LEU* 3.9 0.2 - - - +
425B ILE* 3.1 32.1 + - - +
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Residues in contact with ARG 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417B ILE* 2.5 45.4 + - + +
418B ASP* 3.0 16.3 + - - +
419B ASP* 3.0 33.1 + - - +
421B GLY* 1.3 77.1 - - - +
423B ARG* 1.3 57.8 + - + +
425B ILE* 4.1 0.9 - - - +
426B ALA* 2.9 33.2 + - - +
447B ILE* 3.3 27.0 + - - +
448B LEU* 3.8 30.9 - - + +
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Residues in contact with ARG 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B ASP* 2.9 21.7 + - + +
420B VAL* 3.6 35.6 + - - +
422B ARG* 1.3 78.9 - - + +
424B LEU* 1.3 76.7 + - - +
426B ALA* 3.7 5.8 - - - +
427B GLU* 3.0 24.8 + - - +
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Residues in contact with LEU 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B PHE* 4.0 23.3 - - + -
340B ALA* 3.5 26.7 - - + -
341B GLU 4.7 1.6 - - - +
344B LEU* 3.5 35.2 - - + +
420B VAL* 3.0 40.4 + - + +
421B GLY 3.9 3.6 - - - +
422B ARG 3.3 0.2 - - - -
423B ARG* 1.3 90.4 - - - +
425B ILE* 1.3 57.7 + - - +
427B GLU* 3.4 5.9 + - + +
428B GLY 3.0 20.6 + - - -
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Residues in contact with ILE 425 (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 LEU* 4.4 18.4 - - + -
335B ILE* 4.0 26.9 - - + -
340B ALA* 4.3 16.6 - - + +
343B VAL* 4.6 18.4 - - + -
344B LEU* 4.7 4.3 - - + -
347B LEU* 5.3 3.4 - - + +
409B LEU* 4.0 26.0 - - + -
411B LEU* 6.0 0.9 - - + -
417B ILE* 4.9 9.6 - - + -
421B GLY 3.1 18.8 + - - +
422B ARG* 4.2 2.5 - - - +
424B LEU* 1.3 73.6 - - - +
426B ALA* 1.3 61.4 + - - +
428B GLY* 3.0 3.7 + - - +
429B VAL* 2.9 29.3 + - + +
448B LEU* 5.0 13.0 - - + -
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Residues in contact with ALA 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422B ARG 2.9 20.7 + - - +
423B ARG* 3.7 7.2 - - - +
425B ILE* 1.3 77.8 - - - +
427B GLU* 1.3 58.2 + - - +
428B GLY 2.9 0.2 - - - -
429B VAL* 3.0 10.2 + - - +
430B ARG* 2.9 28.3 + - - +
448B LEU* 5.3 7.1 - - + +
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Residues in contact with GLU 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B LEU* 5.4 0.9 - - + -
423B ARG 3.0 16.2 + - - +
424B LEU* 3.6 7.2 - - + +
426B ALA* 1.3 78.3 - - - +
428B GLY* 1.3 60.5 + - - +
430B ARG* 2.6 43.8 + - - +
431B ARG* 2.7 66.0 + - - +
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Residues in contact with GLY 428 (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* 4.0 17.3 - - - -
347B LEU* 4.3 14.4 - - - +
424B LEU 3.0 9.8 + - - -
425B ILE 3.0 8.1 + - - -
426B ALA 2.9 1.0 - - - -
427B GLU* 1.3 77.4 - - - +
429B VAL* 1.3 64.3 + - - +
431B ARG* 3.3 8.6 + - - +
432B LEU* 3.2 22.7 + - - +
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Residues in contact with VAL 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B LEU* 5.5 2.5 - - + -
409B LEU* 4.4 23.1 - - + -
425B ILE* 2.9 23.6 + - + +
426B ALA* 3.0 8.3 + - - +
428B GLY* 1.3 74.3 - - - +
430B ARG* 1.3 65.8 + - - +
432B LEU* 2.9 21.2 + - + +
433B GLN* 3.1 30.9 + - - +
439B VAL* 3.6 32.1 - - + +
441B VAL* 5.0 12.3 - - + -
448B LEU* 6.2 1.8 - - + -
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Residues in contact with ARG 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426B ALA 2.9 14.8 + - - +
427B GLU* 2.6 51.0 + - - +
429B VAL* 1.3 76.6 - - - +
431B ARG* 1.3 60.5 + - - +
433B GLN* 3.7 18.0 + - - +
434B ALA* 3.2 24.3 + - - +
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Residues in contact with ARG 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B GLU* 2.7 51.4 + - - +
428B GLY* 3.3 7.3 + - - +
429B VAL 3.1 0.8 - - - -
430B ARG* 1.3 79.7 - - - +
432B LEU* 1.3 63.3 + - - +
434B ALA* 3.4 18.2 - - + +
435B ASP* 2.9 19.0 - - - +
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Residues in contact with LEU 432 (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 LEU* 3.7 42.2 - - + +
350B LEU* 5.2 1.6 - - + -
352B THR* 3.5 38.4 - - + +
407B VAL* 4.2 19.3 - - + -
428B GLY 3.2 11.1 + - - +
429B VAL* 2.9 12.3 + - + +
431B ARG* 1.3 74.2 - - - +
433B GLN* 1.3 57.8 + - - +
435B ASP* 2.6 36.5 + - - +
437B VAL* 3.6 13.6 + - + +
439B VAL* 3.8 26.5 - - + -
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Residues in contact with GLN 433 (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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429B VAL* 3.2 26.3 - - + +
430B ARG* 3.7 20.0 - - - +
432B LEU* 1.3 75.3 - - - +
434B ALA* 1.3 54.8 + - - +
436B GLY* 2.6 27.7 + - - -
437B VAL 3.5 15.9 + - - +
439B VAL* 4.2 24.2 + - + +
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Residues in contact with ALA 434 (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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430B ARG 3.2 13.1 + - - +
431B ARG* 3.4 17.3 - - + +
432B LEU 3.0 0.4 - - - -
433B GLN* 1.3 77.9 - - - +
435B ASP* 1.3 60.3 + - - +
436B GLY 3.2 2.6 + - - -
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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