Contacts of the helix formed by residues 417 - 428 (chain A) in PDB entry 4IYM
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 417 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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257A ASP* 3.1 9.9 + - - +
415A THR* 3.0 19.7 + - - +
416A ARG* 1.3 75.7 - - - +
418A GLY* 1.3 66.2 + - - +
419A ASP* 3.2 16.1 + - - +
420A ALA* 2.8 32.9 + - + +
421A ALA* 3.1 19.8 + - - +
480B TRP* 4.2 1.6 - - - -
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Residues in contact with GLY 418 (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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416A ARG 3.5 5.5 + - - -
417A ASP* 1.3 73.1 - - - +
419A ASP* 1.3 62.0 + - - +
421A ALA* 3.5 1.0 + - - +
422A ARG* 3.0 27.4 + - - +
480B TRP* 4.0 16.4 - - - -
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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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417A ASP* 3.2 13.0 + - - +
418A GLY* 1.3 76.9 - - - +
420A ALA* 1.3 58.9 + - - +
422A ARG* 3.9 4.5 - - - +
423A ASP* 2.9 40.1 + - - +
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Residues in contact with ALA 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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255A MSE 4.7 12.8 - - + -
395A TYR* 3.6 19.4 + - + -
413A ILE* 4.4 5.4 - - + -
415A THR* 4.2 12.1 - - + +
417A ASP* 2.8 29.7 + - + +
419A ASP* 1.3 74.8 - - - +
421A ALA* 1.3 57.2 + - - +
423A ASP* 4.7 2.5 - - - -
424A PHE* 2.9 34.2 + - - +
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Residues in contact with ALA 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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413A ILE* 4.4 8.4 - - + +
415A THR* 4.0 10.4 - - + +
417A ASP 3.1 8.3 + - - +
418A GLY 3.9 0.9 - - - +
420A ALA* 1.3 77.5 - - - +
422A ARG* 1.3 61.6 - - - +
424A PHE* 3.9 0.7 - - - +
425A ALA* 2.9 29.4 + - - +
435A VAL* 3.7 23.6 - - + +
480B TRP* 3.5 33.4 - - + -
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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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418A GLY 3.0 18.2 + - - +
419A ASP* 3.9 5.2 - - - +
421A ALA* 1.3 76.3 - - - +
423A ASP* 1.3 66.6 + - - +
425A ALA* 3.7 2.8 - - - +
426A SER* 2.8 52.6 + - - -
123C GLU* 3.8 15.7 - - - +
124C GLY* 4.1 5.5 - - - +
128C GLY* 4.0 36.5 + - - +
130C ASP* 2.8 43.8 + - - +
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Residues in contact with ASP 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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395A TYR* 2.8 25.7 + - + +
419A ASP* 2.9 25.4 + - - +
420A ALA* 4.0 0.7 - - - +
422A ARG* 1.3 89.8 + - - +
424A PHE* 1.3 61.5 + - - +
426A SER* 3.3 3.3 + - - -
427A ARG* 2.8 66.1 + - - +
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Residues in contact with PHE 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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253A ILE* 3.9 32.1 - - + -
395A TYR* 2.9 25.1 + + - +
398A ALA* 5.8 0.2 - - + -
399A LEU* 3.5 37.1 - - + +
402A PRO* 4.4 3.4 - - + -
411A VAL* 3.7 40.8 - - + -
412A ALA 4.3 4.5 - - - -
413A ILE* 3.8 37.7 - - + -
420A ALA 2.9 16.8 + - - +
421A ALA 3.9 2.0 - - - +
423A ASP* 1.3 75.2 - - - +
425A ALA* 1.3 65.3 + - - +
427A ARG* 3.4 0.5 + - - +
428A ILE* 3.1 28.2 + - + +
433A VAL* 4.8 3.1 - - + -
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Residues in contact with ALA 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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421A ALA 2.9 18.8 + - - +
422A ARG* 4.0 3.1 - - - +
424A PHE* 1.3 75.6 - - + +
426A SER* 1.3 61.3 + - - +
428A ILE* 4.0 1.5 - - - +
433A VAL* 3.8 29.6 - - + -
435A VAL* 4.6 8.7 - - + -
132B TYR* 5.7 0.7 - - - +
474B LYS* 2.8 35.0 + - - +
476B ILE* 3.8 22.9 - - + -
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Residues in contact with SER 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* 2.8 40.3 + - - -
423A ASP* 3.8 4.0 - - - -
424A PHE 3.2 0.2 - - - -
425A ALA* 1.3 79.3 - - - +
427A ARG* 1.3 63.1 + - - +
134B ILE* 5.4 2.0 - - - -
136B GLN* 2.9 25.1 + - - +
474B LYS* 3.1 6.9 + - - +
123C GLU* 2.5 31.6 + - - -
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Residues in contact with ARG 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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395A TYR* 4.0 0.4 - - - -
396A GLU* 2.9 39.6 + - - -
399A LEU* 3.5 22.6 - - + +
403A MSE 3.6 24.5 - - + +
423A ASP* 2.8 58.4 + - - +
424A PHE 4.3 0.9 - - - +
426A SER* 1.3 82.5 - - - +
428A ILE* 1.3 65.7 + - - +
429A ASN* 3.6 2.8 + - - +
474B LYS* 4.2 0.2 - - - -
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Residues in contact with ILE 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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399A LEU* 3.7 22.9 - - + +
402A PRO* 3.8 13.0 - - + -
403A MSE 3.5 36.8 - - + +
411A VAL* 4.1 13.0 - - + -
424A PHE* 3.1 23.2 + - + +
425A ALA* 4.0 6.1 - - - +
427A ARG* 1.3 76.9 - - - +
429A ASN* 1.3 63.6 + - - +
430A ILE* 3.1 23.3 + - + +
433A VAL* 3.8 28.9 - - + -
451A TRP* 3.9 1.9 - - - -
474B LYS* 2.7 29.3 + - - +
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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