Contacts of the helix formed by residues 484 - 498 (chain E) in PDB entry 1IAS
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 THR 484 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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394E GLU* 6.0 2.2 - - - +
401E ILE* 4.1 4.9 - - - -
482E ARG 4.7 4.7 - - - +
483E LEU* 1.3 77.6 - - - +
485E ALA* 1.3 65.5 + - - +
486E LEU* 3.9 6.5 + - - +
487E ARG* 3.0 27.3 + - + +
488E ILE* 3.0 23.8 + - - +
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Residues in contact with ALA 485 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310E ALA* 4.4 5.0 - - - +
313E LEU* 4.0 11.4 - - + +
314E ALA* 3.6 33.0 - - + +
317E HIS* 4.2 11.3 + - + +
401E ILE* 3.6 23.2 - - + +
404E MET* 5.6 2.7 - - - -
484E THR* 1.3 72.3 - - - +
486E LEU* 1.3 57.8 + - - +
488E ILE* 3.3 7.9 + - - +
489E LYS* 2.9 29.3 + - - +
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Residues in contact with LEU 486 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314E ALA* 4.2 8.8 - - + +
318E MET* 3.8 28.9 - - + -
484E THR* 3.2 6.6 + - - +
485E ALA* 1.3 78.4 - - - +
487E ARG* 1.3 58.3 + - - +
489E LYS* 3.3 20.8 + - + +
490E LYS* 2.9 56.2 + - - +
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Residues in contact with ARG 487 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483E LEU* 3.6 28.3 - - + -
484E THR* 3.0 30.5 + - - +
486E LEU* 1.3 78.2 - - - +
488E ILE* 1.3 62.9 + - - +
490E LYS* 3.0 55.5 + - - +
491E THR* 2.9 36.4 + - + +
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Residues in contact with ILE 488 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310E ALA* 4.2 6.1 - - + -
401E ILE* 4.3 10.1 - - + -
404E MET* 4.7 13.9 - - - -
408E PHE* 3.8 28.5 - - + -
470E ILE* 3.7 29.2 - - + -
474E CYS* 3.7 19.3 - - - -
483E LEU* 3.9 22.7 - - + -
484E THR 3.0 15.8 + - - +
485E ALA* 3.7 5.6 - - - +
487E ARG* 1.3 74.6 - - - +
489E LYS* 1.3 57.7 + - - +
491E THR* 3.8 6.4 + - - -
492E LEU* 2.8 40.7 + - + +
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Residues in contact with LYS 489 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256E HIS* 5.8 4.0 - - - -
307E LEU* 4.0 11.0 - - + +
310E ALA* 4.2 15.0 - - + +
311E SER* 3.4 38.2 + - - +
314E ALA* 4.6 10.8 - - + -
485E ALA 2.9 16.8 + - - +
486E LEU* 3.4 22.7 - - + +
488E ILE* 1.3 75.9 - - - +
490E LYS* 1.3 58.3 + - - +
492E LEU 3.8 0.3 - - - -
493E SER* 2.9 35.7 + - - -
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Residues in contact with LYS 490 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486E LEU* 2.9 38.8 + - - +
487E ARG* 3.0 38.9 + - - +
489E LYS* 1.3 78.0 - - - +
491E THR* 1.3 57.6 + - - +
493E SER* 3.1 8.0 + - - -
494E GLN* 3.0 31.0 + - - +
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Residues in contact with THR 491 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466E VAL* 4.3 10.7 - - - +
470E ILE* 4.0 18.1 - - + +
483E LEU* 6.0 3.6 - - + -
487E ARG* 2.9 42.6 + - + +
488E ILE* 3.9 3.6 + - - -
490E LYS* 1.3 74.9 - - - +
492E LEU* 1.3 60.3 + - - +
494E GLN* 3.3 9.7 - - - +
495E LEU* 3.1 25.5 + - - +
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Residues in contact with LEU 492 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303E ILE* 4.2 10.8 - - + +
306E ALA* 3.5 44.4 - - + +
307E LEU* 3.5 14.8 - - + +
310E ALA* 4.6 0.9 - - + -
408E PHE* 3.8 14.8 - - + -
466E VAL* 4.5 10.3 - - + -
467E MET* 4.2 14.1 - - - -
470E ILE* 3.6 22.7 - - + -
488E ILE* 2.8 22.6 + - + +
489E LYS* 4.0 2.5 - - - +
491E THR* 1.3 76.3 + - - +
493E SER* 1.3 65.0 + - - +
494E GLN 3.1 0.4 - - - -
495E LEU* 3.6 12.4 + - + +
496E SER* 3.1 22.9 + - - -
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Residues in contact with SER 493 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307E LEU* 4.3 15.5 - - - +
489E LYS* 2.9 25.8 + - - -
490E LYS* 3.1 8.9 + - - -
492E LEU* 1.3 76.2 - - - +
494E GLN* 1.3 64.1 + - - +
496E SER* 3.5 8.0 - - - -
497E GLN* 3.3 19.1 + - - +
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Residues in contact with GLN 494 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490E LYS* 3.0 15.3 + - - +
491E THR* 3.3 14.1 - - - +
492E LEU 3.1 0.2 - - - -
493E SER* 1.3 75.1 - - - +
495E LEU* 1.3 58.6 + - - +
497E GLN* 2.8 49.9 + - - +
498E GLN* 3.2 21.9 + - + +
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Residues in contact with LEU 495 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303E ILE* 3.8 18.4 - - + -
462E GLU* 3.9 17.7 - - + -
463E ALA* 3.7 29.4 - - + +
466E VAL* 3.7 26.7 - - + -
467E MET* 5.3 3.1 - - + -
491E THR 3.1 12.0 + - - +
492E LEU* 3.9 15.3 - - + +
494E GLN* 1.3 77.6 - - - +
496E SER* 1.3 63.5 + - - +
498E GLN* 2.9 32.3 + - - +
499E GLU* 3.3 28.4 - - - +
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Residues in contact with SER 496 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303E ILE* 3.7 25.3 - - - +
307E LEU* 4.4 12.3 - - - +
492E LEU 3.1 18.4 + - - -
493E SER* 3.5 11.2 - - - -
494E GLN 3.1 0.6 - - - -
495E LEU* 1.3 77.0 - - - +
497E GLN* 1.3 58.0 + - - +
498E GLN 3.4 0.3 + - - -
499E GLU* 3.4 3.5 + - - +
500E GLY* 3.1 28.8 + - - -
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Residues in contact with GLN 497 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493E SER 3.3 9.1 + - - +
494E GLN* 2.8 30.1 + - - +
496E SER* 1.3 75.5 - - - +
498E GLN* 1.3 58.3 + - - +
499E GLU 3.1 9.1 + - - -
500E GLY* 4.3 6.8 + - - +
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Residues in contact with GLN 498 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462E GLU* 3.8 24.3 + - - +
466E VAL* 5.6 0.5 - - - +
494E GLN* 3.2 20.1 + - + +
495E LEU* 2.9 29.7 + - + +
497E GLN* 1.3 79.5 - - - +
499E GLU* 1.3 70.8 + - + +
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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