Contacts of the helix formed by residues 438 - 452 (chain B) in PDB entry 4YHF
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 SER 438 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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437B MET* 1.3 67.1 - - - +
439B GLU* 1.3 66.3 + - - +
440B ASP 3.5 1.6 - - - -
441B GLU* 3.2 30.8 + - - -
442B PHE* 2.9 22.2 + - - +
545B TYR* 3.1 17.3 + - - +
547B LEU* 3.8 13.4 - - - +
712B NA 4.1 18.6 - - - -
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Residues in contact with GLU 439 (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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437B MET* 2.9 11.2 + - - +
438B SER* 1.3 70.0 - - - +
440B ASP* 1.3 64.5 + - - +
441B GLU* 4.1 0.2 + - - -
442B PHE* 3.1 5.3 + - - +
443B ILE* 2.9 35.6 + - - +
468B ARG* 4.2 23.6 - - - +
470B ILE* 5.9 1.8 - - + -
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Residues in contact with ASP 440 (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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439B GLU* 1.3 85.8 - - - +
441B GLU* 1.3 69.5 + - + +
443B ILE* 3.8 14.3 - - - +
444B GLU* 3.1 23.6 + - - +
468B ARG* 5.4 1.0 + - - -
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Residues in contact with GLU 441 (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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438B SER* 3.2 25.6 - - - +
439B GLU 4.1 0.3 + - - -
440B ASP* 1.3 89.4 + - + +
442B PHE* 1.3 57.3 + - - +
444B GLU* 3.4 8.0 + - - +
445B GLU* 2.9 27.7 + - - +
545B TYR* 3.4 39.9 + - + +
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Residues in contact with PHE 442 (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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432B ILE* 3.7 37.9 - - + -
437B MET* 3.7 37.5 - - + -
438B SER 2.9 17.5 + - - +
439B GLU* 3.5 4.7 - - - +
441B GLU* 1.3 74.8 - - - +
443B ILE* 1.3 61.2 + - - +
445B GLU* 3.1 16.9 + - - +
446B ALA* 2.8 35.0 + - + +
449B MET* 4.9 4.7 - - + -
470B ILE* 4.1 30.7 - - + -
472B ILE* 4.0 14.4 - - + -
542B LEU* 3.8 22.2 - - + -
545B TYR* 4.0 12.3 - - + -
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Residues in contact with ILE 443 (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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439B GLU 2.9 25.5 + - - +
440B ASP* 3.8 14.6 - - - +
442B PHE* 1.3 75.9 - - - +
444B GLU* 1.3 63.7 + - - +
446B ALA* 3.3 7.9 + - - +
447B LYS* 3.2 39.3 + - - +
465B THR* 3.8 28.5 - - + +
468B ARG* 3.8 27.1 - - - +
470B ILE* 3.7 23.6 - - + -
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Residues in contact with GLU 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440B ASP 3.1 14.3 + - - +
441B GLU* 3.5 11.0 - - - +
443B ILE* 1.3 78.9 - - - +
445B GLU* 1.3 61.8 + - - +
447B LYS* 3.3 21.2 + - - +
448B VAL* 3.2 27.9 + - + +
714B NA 4.5 9.2 - - - -
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Residues in contact with GLU 445 (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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441B GLU 2.9 15.1 + - - +
442B PHE* 3.1 16.0 + - - +
444B GLU* 1.3 73.8 - - - +
446B ALA* 1.3 59.8 + - - +
448B VAL* 3.1 5.8 + - + +
449B MET* 2.8 44.9 + - + +
517B PHE* 4.2 9.1 - - + -
541B GLY* 2.7 37.0 - - - +
542B LEU* 4.8 0.7 - - - +
544B ARG* 3.4 8.8 - - - +
545B TYR* 3.3 25.6 + - + -
714B NA 3.8 18.6 - - - -
722B EDO 3.7 11.5 - - - -
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Residues in contact with ALA 446 (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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442B PHE* 2.8 33.6 + - + +
443B ILE* 3.6 9.2 - - - +
444B GLU 3.3 0.2 - - - -
445B GLU* 1.3 73.2 - - - +
447B LYS* 1.3 63.8 + - + +
449B MET* 3.3 19.8 + - - +
450B MET* 3.3 24.3 + - - +
460B LEU* 4.9 0.7 - - - +
463B VAL* 4.5 21.7 - - + +
465B THR* 5.6 4.0 - - + -
470B ILE* 5.9 1.8 - - + -
472B ILE* 5.0 6.7 - - + -
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Residues in contact with LYS 447 (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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395B TRP* 3.3 66.4 + - + +
396B GLU* 4.7 12.3 - - - -
443B ILE* 3.2 32.5 + - + +
444B GLU* 3.5 21.6 + - - +
446B ALA* 1.3 78.3 - - + +
448B VAL* 1.3 61.5 - - + +
450B MET* 3.1 3.6 + - - +
451B ASN* 3.1 26.1 + - - +
463B VAL* 5.5 4.9 - - + -
465B THR* 5.5 0.4 - - - -
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Residues in contact with VAL 448 (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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444B GLU* 3.2 24.7 + - + +
445B GLU* 3.1 11.8 + - + +
447B LYS* 1.3 75.8 - - + +
449B MET* 1.3 65.2 + - - +
451B ASN* 3.0 27.5 + - + +
452B LEU* 3.3 15.7 + - + +
517B PHE* 4.0 25.8 - - + -
714B NA 4.6 7.4 - - - -
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Residues in contact with MET 449 (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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442B PHE* 4.9 3.8 - - + -
445B GLU* 2.8 45.6 + - + +
446B ALA* 3.4 20.2 - - - +
448B VAL* 1.3 77.6 - - - +
450B MET* 1.3 60.6 + - - +
452B LEU* 3.4 28.0 + - - +
460B LEU* 3.9 19.9 - - + +
472B ILE* 5.0 4.0 - - - -
517B PHE* 4.2 9.2 - - + -
540B PHE* 3.4 34.7 - - + +
542B LEU* 3.9 23.6 - - + +
703B 4C9 3.5 25.6 - - + -
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Residues in contact with MET 450 (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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390B LEU* 4.1 15.8 - - - +
391B GLY* 3.6 14.1 + - - -
394B SER 4.1 13.9 - - - +
395B TRP* 3.5 38.1 - - + +
446B ALA 3.3 11.0 + - - +
447B LYS 3.1 10.6 + - - +
449B MET* 1.3 77.5 - - - +
451B ASN* 1.3 65.8 + - - +
452B LEU 3.3 7.7 - - - +
460B LEU* 3.8 28.3 - - + +
461B TYR* 3.6 30.1 - - - +
462B GLY* 3.6 17.0 - - - -
463B VAL* 3.9 9.6 - - + -
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Residues in contact with ASN 451 (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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390B LEU* 5.7 1.6 - - - -
391B GLY* 3.9 2.0 + - - +
392B TYR* 3.2 76.1 + - + +
395B TRP* 3.3 8.9 + - - +
447B LYS* 3.1 16.1 + - - +
448B VAL* 3.0 23.8 + - + +
450B MET* 1.3 76.2 - - - +
452B LEU* 1.3 65.5 + - + +
453B SER* 3.6 6.1 + - - -
511B TYR* 4.7 0.5 + - - -
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Residues in contact with LEU 452 (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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448B VAL* 3.5 17.5 - - + +
449B MET* 3.6 16.8 - - - +
450B MET 3.3 9.1 - - - +
451B ASN* 1.3 80.9 - - + +
453B SER* 1.3 60.1 + - - +
457B LEU* 4.2 8.7 - - + +
459B GLN* 5.8 2.3 + - - -
511B TYR* 3.5 25.6 - - + +
512B LEU* 3.9 22.7 - - + -
515B LYS* 4.0 24.5 - - + -
517B PHE* 4.1 24.2 - - + -
540B PHE* 4.0 15.3 - - + -
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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