Contacts of the helix formed by residues 461 - 476 (chain B) in PDB entry 3FAA
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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299B VAL* 4.2 7.9 - - - -
417B ILE* 3.7 28.7 - - + -
457B ARG 4.5 1.0 + - - -
458B TRP 4.3 0.2 - - - +
459B GLN 4.7 0.4 - - - +
460B SER* 1.3 79.9 - - - +
462B GLU* 1.3 66.1 - - - +
463B ALA* 3.7 11.2 - - - -
464B LEU* 3.4 28.6 - - - +
465B ARG* 3.1 30.9 + - - +
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Residues in contact with GLU 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461B CYS* 1.3 70.9 - - - +
463B ALA* 1.3 69.8 + - - +
465B ARG* 2.6 52.9 + - - +
466B VAL* 3.0 31.0 + - + +
495B LEU* 4.7 4.7 - - + -
499B GLU* 4.3 13.9 - - - +
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Residues in contact with ALA 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B VAL* 3.3 35.7 - - + -
302B MET* 4.5 12.6 - - + -
303B ILE* 4.5 9.2 - - + -
461B CYS* 3.4 7.2 - - - -
462B GLU* 1.3 80.9 - - - +
464B LEU* 1.3 65.9 + - + +
465B ARG 3.0 0.3 + - - -
466B VAL* 3.1 10.7 + - - +
467B MET* 3.2 14.9 + - - +
495B LEU* 3.9 17.4 - - + +
499B GLU* 4.6 3.9 + - - +
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Residues in contact with LEU 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B MET* 3.3 34.1 - - + -
412B ALA* 4.6 9.2 - - + +
415B CYS* 4.0 13.5 - - + +
417B ILE* 3.5 32.8 - - + -
457B ARG* 4.1 20.0 - - - +
458B TRP* 3.4 44.4 - - + +
461B CYS* 3.4 11.6 - - - +
462B GLU 3.4 0.2 - - - -
463B ALA* 1.3 79.3 - - + +
465B ARG* 1.3 61.3 + - - +
467B MET* 3.9 3.7 - - + +
468B ALA* 3.1 24.3 + - - +
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Residues in contact with ARG 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458B TRP 3.6 4.3 - - - +
459B GLN* 2.6 68.4 + - - +
460B SER 3.5 17.4 + - - -
461B CYS* 3.1 13.1 + - - +
462B GLU* 2.6 40.9 + - - +
464B LEU* 1.3 74.1 - - - +
466B VAL* 1.3 67.3 + - - +
468B ALA* 3.2 4.8 + - - +
469B LYS* 3.0 22.3 + - - +
472B ARG* 5.1 2.3 + - - +
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Residues in contact with VAL 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462B GLU* 3.0 29.8 + - - +
463B ALA 3.5 5.4 - - - +
465B ARG* 1.3 74.8 - - + +
467B MET* 1.3 64.6 + - - +
469B LYS* 2.9 19.4 + - + +
470B ILE* 2.9 21.8 + - + +
491B THR* 4.2 20.0 - - - +
492B LEU* 4.6 2.2 - - + -
495B LEU* 3.9 35.2 - - + -
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Residues in contact with MET 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B MET* 3.2 51.1 - - + -
303B ILE* 5.9 0.4 - - - -
306B ALA* 3.8 29.2 - - + -
408B PHE* 4.0 43.1 - - + +
411B ILE* 4.9 2.0 - - + -
412B ALA* 4.5 5.8 - - + +
458B TRP* 6.2 0.2 - - + -
463B ALA 3.2 9.3 + - - +
464B LEU* 3.9 5.6 - - - +
466B VAL* 1.3 80.5 - - + +
468B ALA* 1.3 56.6 + - - +
470B ILE* 3.1 9.0 + - - +
471B MET* 2.9 37.2 + - - +
492B LEU* 4.4 15.5 - - + -
495B LEU* 5.2 2.7 - - + -
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Residues in contact with ALA 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454B ILE* 3.5 30.4 - - + +
458B TRP* 4.3 11.4 - - + +
459B GLN* 4.8 2.0 - - - +
464B LEU 3.1 18.1 + - - +
465B ARG* 3.2 6.9 + - - +
467B MET* 1.3 77.1 - - - +
469B LYS* 1.3 58.4 + - - +
471B MET* 3.7 11.8 + - - -
472B ARG* 3.1 39.6 + - - +
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Residues in contact with LYS 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465B ARG 3.0 10.8 + - - +
466B VAL* 2.9 13.7 + - - +
468B ALA* 1.3 76.5 - - - +
470B ILE* 1.3 66.3 - - + +
472B ARG* 2.8 35.2 + - - +
473B GLU* 2.9 47.5 + - + +
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Residues in contact with ILE 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408B PHE* 4.0 17.3 - - + -
466B VAL* 2.9 22.9 + - + +
467B MET* 3.6 9.2 - - - +
469B LYS* 1.3 77.4 - - + +
471B MET* 1.3 62.1 + - - +
473B GLU* 3.4 2.4 + - - -
474B CYS* 3.1 31.7 + - - +
483B LEU* 4.1 14.3 - - + +
488B ILE* 3.6 42.2 - - + -
491B THR* 3.7 18.8 - - + +
492B LEU* 3.6 32.5 - - + -
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Residues in contact with MET 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B GLY* 3.8 20.0 - - - +
408B PHE* 4.1 14.1 - - + +
409B TRP* 3.2 45.1 - - + -
412B ALA* 4.9 0.9 - - - -
454B ILE* 4.3 4.7 - - + -
458B TRP* 3.2 28.3 - - + -
467B MET* 2.9 28.1 + - - +
468B ALA* 3.8 16.2 - - - +
470B ILE* 1.3 77.5 - - - +
472B ARG* 1.3 59.8 + - - +
474B CYS* 3.3 5.5 + - - -
475B TRP* 3.0 51.9 + - + -
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Residues in contact with ARG 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454B ILE* 4.2 18.9 - - + +
459B GLN* 3.2 24.7 + - - -
465B ARG* 5.1 2.0 + - - +
468B ALA* 3.1 28.3 + - - +
469B LYS* 2.8 34.8 + - + +
471B MET* 1.3 74.6 - - - +
473B GLU* 1.3 62.3 + - + +
474B CYS 3.0 9.2 + - - -
475B TRP* 3.3 16.5 + - + +
476B TYR* 3.7 20.6 + - + -
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Residues in contact with GLU 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469B LYS* 2.9 52.4 + - + +
470B ILE* 3.4 2.0 + - - -
472B ARG* 1.3 76.2 - - + +
474B CYS* 1.3 56.8 + - - +
476B TYR* 3.6 35.0 - - + +
481B ALA 5.4 0.2 - - - +
482B ARG* 3.4 3.8 - - - -
483B LEU* 2.9 62.9 + - + +
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Residues in contact with CYS 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401B ILE* 3.7 33.7 - - - +
402B TYR* 3.4 22.2 - - - -
404B MET* 5.3 1.1 - - - -
405B GLY* 4.1 11.9 - - - -
470B ILE* 3.1 23.8 - - - +
471B MET 3.4 6.7 - - - +
472B ARG 3.0 0.4 - - - -
473B GLU* 1.3 80.2 - - - +
475B TRP* 1.3 68.5 + - + +
476B TYR 3.4 2.2 - - - -
482B ARG* 3.5 17.9 + - - +
483B LEU* 4.7 1.3 - - - -
488B ILE* 3.7 23.3 - - - -
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Residues in contact with TRP 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402B TYR* 3.8 22.4 + + - -
405B GLY* 3.4 22.6 - - - -
406B LEU* 3.4 22.2 - - - +
409B TRP* 3.8 20.0 - + + -
451B ARG* 2.4 69.1 + - + +
452B PRO* 3.3 49.1 - - + -
454B ILE* 4.3 11.0 - - + -
471B MET* 3.0 34.6 + - + +
472B ARG* 3.3 9.1 + - + +
474B CYS* 1.3 88.2 - - + +
476B TYR* 1.3 58.5 + - - +
482B ARG* 4.5 0.2 - - - -
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Residues in contact with TYR 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472B ARG* 3.7 15.0 + - + -
473B GLU* 3.6 36.5 - - + +
474B CYS 3.4 1.6 - - - -
475B TRP* 1.3 75.0 - - - +
477B ALA* 1.3 64.0 + - - +
478B ASN* 3.1 15.9 + - + +
481B ALA* 3.0 44.0 - - + -
482B ARG* 2.9 32.1 + - + -
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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