Contacts of the helix formed by residues 418 - 434 (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 ASP 418 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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334A VAL* 6.1 0.6 - - - +
335A ILE 3.0 15.0 + - - +
336A ARG* 3.1 37.2 + - + +
337A PHE 4.6 0.2 + - - -
417A ILE* 1.3 74.8 - - - +
419A ASP* 1.3 58.8 + - - +
420A VAL* 3.5 21.8 + - - +
421A GLY 3.0 19.1 + - - -
422A ARG* 2.9 28.8 + - - +
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Residues in contact with ASP 419 (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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418A ASP* 1.3 73.5 - - - +
420A VAL* 1.3 56.7 + - + +
422A ARG* 2.9 23.1 + - - +
423A ARG* 2.8 65.8 + - - +
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Residues in contact with VAL 420 (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* 4.2 25.4 - - + +
418A ASP* 3.4 16.5 + - - +
419A ASP* 1.3 75.9 - - + +
421A GLY* 1.3 63.1 + - - +
423A ARG* 3.4 9.3 + - - +
424A LEU* 3.0 48.4 + - + +
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Residues in contact with GLY 421 (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 4.4 1.6 - - - -
336A ARG 4.5 1.8 - - - -
340A ALA* 3.8 20.4 - - - -
417A ILE* 3.3 13.2 - - - -
418A ASP* 3.0 21.0 + - - -
420A VAL* 1.3 76.9 - - - +
422A ARG* 1.3 57.2 + - - +
425A ILE* 2.9 36.6 + - - +
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Residues in contact with ARG 422 (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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417A ILE* 2.9 35.1 + - + +
418A ASP 2.9 8.4 + - - +
419A ASP* 2.9 42.0 + - - +
421A GLY* 1.3 77.2 - - - +
423A ARG* 1.3 58.5 + - + +
425A ILE* 4.4 1.9 - - - +
426A ALA* 3.0 33.3 + - + +
447A ILE* 3.6 13.9 + - - +
448A LEU* 2.5 38.5 + - + +
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Residues in contact with ARG 423 (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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419A ASP* 2.8 49.8 + - - +
420A VAL* 3.9 7.0 - - - +
422A ARG* 1.3 71.9 - - + +
424A LEU* 1.3 68.5 + - + +
426A ALA* 3.6 3.9 + - - +
427A GLU* 3.1 24.1 + - - +
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Residues in contact with LEU 424 (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* 3.8 32.8 - - + -
340A ALA* 3.7 23.6 - - + -
341A GLU* 4.7 2.7 - - - +
344A LEU* 3.5 34.2 - - + +
420A VAL* 3.0 27.8 + - + +
421A GLY 3.9 2.2 - - - +
423A ARG* 1.3 76.6 - - + +
425A ILE* 1.3 65.6 + - - +
427A GLU* 3.3 7.3 + - + +
428A GLY 3.0 17.8 + - - -
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Residues in contact with ILE 425 (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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331A LEU* 4.2 21.8 - - + -
335A ILE* 3.7 18.2 - - + -
340A ALA* 4.4 7.4 - - + +
343A VAL* 4.1 26.0 - - + -
344A LEU* 4.8 4.3 - - - -
347A LEU* 5.3 2.4 - - + +
409A LEU* 4.4 21.8 - - + -
411A LEU* 6.0 1.6 - - + -
417A ILE* 3.5 27.8 - - + -
421A GLY 2.9 13.8 + - - +
422A ARG* 4.4 1.6 - - - +
424A LEU* 1.3 77.2 - - - +
426A ALA* 1.3 64.4 + - - +
428A GLY* 3.1 10.8 + - - +
429A VAL* 3.1 14.2 + - + +
448A LEU* 4.5 18.2 - - + -
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Residues in contact with ALA 426 (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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422A ARG* 3.0 24.0 + - + +
423A ARG* 3.8 6.3 - - - +
425A ILE* 1.3 79.0 - - - +
427A GLU* 1.3 58.2 + - - +
429A VAL* 3.2 9.6 + - - +
430A ARG* 2.9 26.8 + - - +
448A LEU* 5.6 13.0 - - + +
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Residues in contact with GLU 427 (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* 5.8 0.7 - - + -
423A ARG 3.1 18.8 + - - +
424A LEU* 3.5 7.6 - - + +
425A ILE 3.2 0.2 - - - -
426A ALA* 1.3 73.1 - - - +
428A GLY* 1.3 67.2 + - - +
430A ARG* 2.9 41.6 + - - +
431A ARG* 2.9 62.4 + - - +
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Residues in contact with GLY 428 (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* 3.7 22.6 - - - +
347A LEU* 4.1 14.1 - - - +
424A LEU 3.0 11.1 + - - -
425A ILE 3.1 4.2 + - - -
427A GLU* 1.3 77.8 - - - +
429A VAL* 1.3 60.6 + - - +
431A ARG* 3.3 8.3 + - - +
432A LEU* 3.0 24.9 + - - +
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Residues in contact with VAL 429 (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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347A LEU* 4.6 3.1 - - + +
409A LEU* 3.6 31.4 - - + -
425A ILE* 3.1 16.6 + - + +
426A ALA* 3.5 9.2 - - - +
428A GLY* 1.3 76.6 - - - +
430A ARG* 1.3 63.9 + - - +
432A LEU* 3.0 20.3 + - + +
433A GLN* 3.1 30.8 + - - +
439A VAL* 3.6 27.8 - - + +
441A VAL* 4.7 9.6 - - + -
448A LEU* 5.9 2.7 - - + -
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Residues in contact with ARG 430 (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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426A ALA 2.9 13.4 + - - +
427A GLU* 2.9 44.5 + - - +
429A VAL* 1.3 77.6 - - - +
431A ARG* 1.3 64.1 + - - +
433A GLN* 3.7 16.1 + - - +
434A ALA* 3.3 20.3 + - - +
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Residues in contact with ARG 431 (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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427A GLU* 2.9 54.8 + - - +
428A GLY* 3.7 6.7 - - - +
430A ARG* 1.3 78.8 - - - +
432A LEU* 1.3 66.2 + - - +
434A ALA* 3.5 16.7 + - - +
435A ASP* 3.3 15.2 - - - +
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Residues in contact with LEU 432 (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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347A LEU* 3.6 40.6 - - + +
350A LEU* 4.7 6.3 - - + -
352A THR* 3.8 34.8 - - + +
407A VAL* 4.1 20.6 - - + -
409A LEU* 6.3 1.1 - - + -
428A GLY 3.0 11.3 + - - +
429A VAL* 3.0 14.8 + - + +
431A ARG* 1.3 73.8 - - - +
433A GLN* 1.3 57.4 + - - +
435A ASP* 2.6 38.2 + - - +
437A VAL* 3.8 14.2 - - + +
439A VAL* 3.9 22.2 - - + -
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Residues in contact with GLN 433 (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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429A VAL* 3.1 20.4 + - - +
430A ARG* 3.8 20.0 - - - +
432A LEU* 1.3 79.0 - - - +
434A ALA* 1.3 52.9 + - - +
436A GLY* 2.7 28.9 + - - -
437A VAL 3.4 14.9 + - - +
439A VAL* 3.8 30.8 + - + +
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Residues in contact with ALA 434 (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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430A ARG* 3.3 13.1 + - - +
431A ARG* 3.6 15.3 - - - +
432A LEU 3.1 0.8 + - - -
433A GLN* 1.3 76.4 - - - +
435A ASP* 1.3 58.5 + - - +
436A GLY 3.2 2.1 + - - -
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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