Contacts of the helix formed by residues 484 - 496 (chain A) in PDB entry 3I5Y
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 GLU 484 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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352A PHE* 3.7 12.1 - - - -
452A GLY* 3.6 10.6 - - - -
453A VAL* 3.6 8.6 - - + +
479A PHE 4.7 0.2 - - - +
480A ILE* 3.3 23.8 - - + +
481A CYS* 2.8 47.2 + - - +
483A ASP* 1.3 75.8 - - - +
485A LEU* 1.3 65.2 + - - +
486A PRO* 3.2 3.8 - - - -
487A PHE* 3.1 22.2 + - - +
488A VAL 3.9 1.0 + - - -
537A TYR* 2.5 37.4 + - + -
546A PHE* 3.7 11.4 - - + -
551A ILE* 3.9 12.8 - - + -
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Residues in contact with LEU 485 (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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346A VAL* 5.6 0.2 - - + -
348A ILE* 3.8 33.9 - - + -
480A ILE* 3.9 18.6 - - + -
481A CYS 3.7 1.2 + - - +
482A LYS* 3.1 31.1 + - + +
484A GLU* 1.3 78.3 - - - +
486A PRO* 1.3 68.2 - - + +
488A VAL* 2.9 27.7 + - + +
489A ARG* 3.0 31.9 + - - +
502A GLN* 5.3 2.2 - - - +
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Residues in contact with PRO 486 (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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482A LYS 4.3 0.9 - - - +
483A ASP* 3.5 13.7 - - - +
484A GLU* 3.2 5.4 - - - -
485A LEU* 1.3 93.2 - - + +
487A PHE* 1.3 55.0 - - - +
489A ARG* 3.3 30.6 + - + +
490A GLU* 2.9 29.8 + - - +
544A TYR 3.3 10.2 - - - +
545A ARG* 3.3 29.9 - - + +
546A PHE* 3.9 11.7 - - + -
547A SER 5.3 2.0 - - - +
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Residues in contact with PHE 487 (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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453A VAL* 3.7 23.1 - - + -
454A PRO* 3.4 38.1 - - + -
457A LEU* 3.9 12.7 - - + +
460A TYR* 4.1 11.4 - + + -
478A LEU* 3.6 26.9 - - + -
480A ILE* 5.3 1.8 - - + -
484A GLU 3.1 13.5 + - - +
485A LEU 3.1 0.2 - - - -
486A PRO* 1.3 75.2 - - - +
488A VAL* 1.3 70.6 + - + +
490A GLU* 3.2 6.4 + - - +
491A LEU* 3.0 46.5 + - + +
544A TYR* 3.6 40.6 + + + -
546A PHE* 3.9 7.9 - - + -
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Residues in contact with VAL 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A VAL* 4.6 5.4 - - + -
478A LEU* 4.2 9.6 - - + -
480A ILE* 3.4 33.2 - - + -
485A LEU* 2.9 19.5 + - + +
487A PHE* 1.3 86.6 - - + +
489A ARG* 1.3 63.7 + - + +
491A LEU* 3.3 21.2 + - + +
492A GLU* 3.5 16.3 + - + +
497A ILE 4.7 0.5 - - - +
499A ILE* 4.6 15.7 - - + +
502A GLN* 4.0 24.2 - - - +
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Residues in contact with ARG 489 (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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485A LEU* 3.0 31.8 + - - +
486A PRO* 3.4 42.8 - - - +
488A VAL* 1.3 78.8 - - + +
490A GLU* 1.3 61.7 + - - +
492A GLU* 3.0 29.0 + - - +
493A ASP* 3.0 21.5 + - - +
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Residues in contact with GLU 490 (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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457A LEU* 4.0 21.1 - - + +
486A PRO 2.9 18.2 + - - +
487A PHE* 3.2 9.4 + - - +
489A ARG* 1.3 75.6 - - - +
491A LEU* 1.3 56.1 + - - +
493A ASP* 3.8 16.1 - - - +
494A ALA* 2.7 46.4 + - - +
543A GLU 3.8 22.7 - - - +
544A TYR* 4.9 6.5 - - - +
545A ARG* 4.0 28.5 + - + +
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Residues in contact with LEU 491 (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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457A LEU* 4.0 24.3 - - + +
460A TYR* 3.7 44.9 - - + -
461A ILE* 5.4 0.4 - - + -
487A PHE* 3.0 41.5 + - + +
488A VAL* 3.3 13.7 - - - +
489A ARG 3.2 0.2 - - - -
490A GLU* 1.3 76.6 - - - +
492A GLU* 1.3 55.7 + - - +
495A LYS* 3.2 14.8 + - + +
496A ASN 3.0 10.4 + - - -
497A ILE* 2.9 47.5 + - + +
499A ILE* 4.5 10.5 - - + -
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Residues in contact with GLU 492 (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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488A VAL* 3.5 20.7 + - + +
489A ARG* 3.0 19.4 + - - +
491A LEU* 1.3 76.2 - - - +
493A ASP* 1.3 68.0 + - - +
496A ASN* 3.0 25.0 + - - +
497A ILE 3.5 20.4 - - - +
498A VAL* 4.0 26.6 - - + +
499A ILE 5.4 1.3 + - - +
502A GLN* 5.3 4.3 + - - -
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Residues in contact with ASP 493 (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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489A ARG* 3.0 22.8 + - - +
490A GLU* 3.8 16.6 - - - +
492A GLU* 1.3 86.5 - - - +
494A ALA* 1.3 60.1 + - - +
496A ASN 4.7 0.5 + - - -
545A ARG* 5.9 1.6 + - - -
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Residues in contact with ALA 494 (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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457A LEU* 3.7 21.3 - - + -
490A GLU* 2.7 34.9 + - - +
493A ASP* 1.3 73.4 - - - +
495A LYS* 1.3 65.6 + - + +
496A ASN 3.9 0.2 - - - -
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Residues in contact with LYS 495 (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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307A THR* 4.2 14.5 - - - -
308A LEU* 5.4 0.6 - - - +
309A ASP* 6.4 0.4 - - - -
336A PRO* 4.1 9.9 - - - +
337A GLU* 2.9 35.5 + - + +
457A LEU* 4.0 25.8 - - + -
458A ALA* 4.8 12.9 - - - +
461A ILE* 3.9 16.2 - - + -
491A LEU* 3.2 16.0 + - + +
494A ALA* 1.3 83.3 - - - +
496A ASN* 1.3 73.2 + - - +
497A ILE* 3.3 20.1 + - + +
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Residues in contact with ASN 496 (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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334A ASN* 3.1 32.3 + - - +
336A PRO* 3.5 23.1 - - + +
491A LEU 3.0 3.0 + - - -
492A GLU* 3.0 18.7 + - - +
493A ASP 4.7 0.6 + - - -
494A ALA 3.9 0.4 - - - -
495A LYS* 1.3 81.0 - - - +
497A ILE* 1.3 59.7 + - - +
498A VAL* 3.8 12.1 + - - +
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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