Contacts of the helix formed by residues 461 - 476 (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 CYS 461 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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299E VAL* 4.3 7.6 - - + -
417E ILE* 3.5 18.8 - - + -
460E SER* 1.3 78.3 - - - +
462E GLU* 1.3 66.9 + - - +
463E ALA* 4.1 8.7 - - - +
464E LEU* 3.3 41.6 + - - +
465E ARG* 3.2 30.8 + - - +
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Residues in contact with GLU 462 (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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461E CYS* 1.3 73.0 - - - +
463E ALA* 1.3 66.3 + - - +
465E ARG* 2.9 37.1 + - - +
466E VAL* 2.8 34.8 + - + +
495E LEU* 3.9 19.5 - - + -
498E GLN* 3.8 22.8 + - - +
499E GLU* 4.9 6.3 - - - +
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Residues in contact with ALA 463 (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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299E VAL* 3.4 32.5 - - + -
302E MET* 3.9 15.3 - - + -
303E ILE* 4.6 1.6 - - + -
461E CYS* 3.3 5.9 - - - +
462E GLU* 1.3 81.1 - - - +
464E LEU* 1.3 63.9 + - - +
466E VAL* 3.1 2.6 + - - +
467E MET* 3.0 24.9 + - - +
495E LEU* 3.7 26.8 - - + +
499E GLU* 4.9 3.0 + - - +
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Residues in contact with LEU 464 (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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299E VAL* 4.5 1.1 - - + -
302E MET* 4.3 7.9 - - + -
412E ALA* 4.1 21.5 - - + +
415E CYS* 3.9 19.3 - - + +
417E ILE* 3.5 17.7 - - + -
457E ARG* 5.2 4.3 - - - +
458E TRP* 3.1 65.6 - - + +
460E SER* 5.5 0.2 - - - -
461E CYS* 3.3 29.7 + - - +
462E GLU 3.4 0.4 - - - -
463E ALA* 1.3 78.5 - - - +
465E ARG* 1.3 56.4 + - - +
467E MET* 3.7 5.9 + - - +
468E ALA* 3.0 27.9 + - - +
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Residues in contact with ARG 465 (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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458E TRP 3.8 3.1 - - - +
459E GLN* 2.8 49.8 + - - +
460E SER 3.3 21.4 + - - -
461E CYS* 3.2 16.4 + - - +
462E GLU* 2.9 40.8 + - - +
464E LEU* 1.3 75.2 - - - +
466E VAL* 1.3 67.7 + - + +
468E ALA* 3.0 6.4 + - - +
469E LYS* 2.7 24.9 + - - +
472E ARG* 5.2 0.5 + - - -
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Residues in contact with VAL 466 (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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462E GLU* 2.8 44.3 + - + +
463E ALA 3.5 4.5 - - - +
465E ARG* 1.3 70.8 - - - +
467E MET* 1.3 63.4 + - - +
469E LYS* 3.0 10.8 - - + +
470E ILE* 3.0 34.1 + - + +
491E THR* 4.3 20.2 - - - +
492E LEU* 4.5 4.0 - - + -
495E LEU* 3.7 34.8 - - + -
498E GLN* 5.6 0.4 - - - +
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Residues in contact with MET 467 (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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302E MET* 3.9 38.1 - - + +
303E ILE* 6.0 1.6 - - - -
306E ALA* 4.0 25.4 - - + -
408E PHE* 3.6 52.0 - - + +
411E ILE* 4.8 1.8 - - + -
412E ALA* 4.4 8.1 - - + +
458E TRP* 6.1 0.4 - - + -
463E ALA 3.0 18.2 + - - +
464E LEU* 3.7 6.5 - - - +
466E VAL* 1.3 77.9 - - + +
468E ALA* 1.3 63.0 + - - +
470E ILE* 3.2 7.3 + - - +
471E MET* 3.0 32.6 + - - +
492E LEU* 4.2 15.9 - - + -
495E LEU* 5.3 2.2 - - + -
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Residues in contact with ALA 468 (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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454E ILE* 3.8 26.8 - - + +
458E TRP* 4.4 8.5 - - + +
459E GLN* 5.2 2.5 - - - +
464E LEU 3.0 17.7 + - - +
465E ARG* 3.0 8.6 + - - +
467E MET* 1.3 74.8 - - - +
469E LYS* 1.3 63.2 + - - +
471E MET* 3.5 14.2 + - - +
472E ARG* 3.1 42.5 + - - +
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Residues in contact with LYS 469 (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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465E ARG 2.7 13.0 + - - +
466E VAL* 3.0 15.9 - - + +
468E ALA* 1.3 76.8 - - - +
470E ILE* 1.3 65.7 + - + +
472E ARG* 3.1 22.4 + - + +
473E GLU* 3.1 57.8 + - + +
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Residues in contact with ILE 470 (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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408E PHE* 4.2 15.3 - - + -
466E VAL* 3.0 19.0 + - + +
467E MET* 3.4 9.0 - - - +
469E LYS* 1.3 77.4 - - + +
471E MET* 1.3 63.9 + - - +
473E GLU* 2.8 17.2 + - - +
474E CYS* 2.9 19.8 + - - -
483E LEU* 3.9 16.8 - - + -
488E ILE* 3.7 45.5 - - + -
491E THR* 4.0 15.5 - - - +
492E LEU* 3.6 30.7 - - + -
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Residues in contact with MET 471 (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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405E GLY* 4.2 4.7 - - - +
408E PHE* 4.2 20.6 - - + +
409E TRP* 3.1 59.0 - - + -
412E ALA* 4.9 0.9 - - - -
454E ILE* 4.6 2.9 - - + -
458E TRP* 3.7 21.3 - - + -
467E MET* 3.0 21.7 + - - +
468E ALA* 3.6 13.9 - - - +
470E ILE* 1.3 75.5 - - + +
472E ARG* 1.3 57.4 + - - +
474E CYS* 3.2 7.8 + - - +
475E TRP* 3.0 56.9 + - + -
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Residues in contact with ARG 472 (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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454E ILE* 3.6 28.0 - - + +
459E GLN* 3.6 21.8 + - - -
465E ARG 5.2 0.4 + - - -
468E ALA* 3.1 28.5 - - - +
469E LYS* 3.1 34.9 + - - +
471E MET* 1.3 70.8 - - - +
473E GLU* 1.3 62.2 + - + +
474E CYS 2.9 9.3 + - - -
475E TRP* 3.1 19.0 + - + +
476E TYR* 3.4 22.5 + - + +
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Residues in contact with GLU 473 (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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469E LYS* 3.1 55.5 + - + +
470E ILE* 2.8 5.1 + - - +
472E ARG* 1.3 76.1 - - + +
474E CYS* 1.3 56.4 + - - +
476E TYR* 3.7 31.3 + - + +
482E ARG* 3.2 7.4 - - - -
483E LEU* 3.0 62.6 + - + +
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Residues in contact with CYS 474 (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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401E ILE* 3.5 36.8 - - - +
402E TYR* 3.5 12.0 - - - -
404E MET 5.4 0.7 - - - -
405E GLY* 4.0 17.5 - - - -
408E PHE* 5.9 0.4 - - - -
470E ILE* 2.9 21.9 + - - +
471E MET 3.4 10.5 - - - +
472E ARG 2.9 0.2 - - - -
473E GLU* 1.3 80.4 - - - +
475E TRP* 1.3 62.9 + - + +
476E TYR 3.4 2.9 - - - -
482E ARG* 3.2 27.4 + - - -
483E LEU* 4.7 1.3 - - - -
488E ILE* 3.7 21.8 - - - -
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Residues in contact with TRP 475 (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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402E TYR* 3.9 25.1 - + - -
405E GLY 3.5 12.2 - - - -
406E LEU* 3.3 30.5 - - + +
409E TRP* 3.8 7.6 - + + -
451E ARG* 2.8 54.1 + - + +
452E PRO* 3.5 43.1 - - + -
454E ILE* 3.8 19.5 - - + -
471E MET* 3.0 52.9 + - + +
472E ARG* 3.1 9.1 + - + +
474E CYS* 1.3 82.6 - - + +
476E TYR* 1.3 67.0 + - - +
477E ALA 3.4 0.3 + - - -
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Residues in contact with TYR 476 (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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451E ARG* 4.0 0.3 + - - -
472E ARG* 3.4 18.8 - - + +
473E GLU* 3.7 34.6 + - + +
474E CYS 3.4 1.6 - - - -
475E TRP* 1.3 78.9 - - - +
477E ALA* 1.3 59.7 + - - +
478E ASN* 3.6 15.0 - - + +
481E ALA* 3.2 44.4 - - + -
482E ARG* 3.0 36.8 + - + -
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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