Contacts of the helix formed by residues 445 - 457 (chain X) in PDB entry 4B3F
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 HIS 445 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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444X MET* 1.3 71.1 - - - +
446X GLN* 1.3 77.0 + - + +
447X ALA* 3.1 32.4 + - + +
448X ILE* 2.8 29.9 + - + +
449X MET 3.0 10.4 + - - -
467X VAL 3.8 9.0 - - - -
469X ARG* 3.5 29.2 + - - -
470X HIS* 3.5 25.2 - - - +
471X LEU* 4.0 8.4 - - + +
487X PRO* 3.7 36.7 - - + +
605X ARG 3.1 17.5 + - - +
606X ARG 4.9 0.4 - - - +
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Residues in contact with GLN 446 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444X MET 3.5 3.3 + - - -
445X HIS* 1.3 85.8 + - + +
447X ALA* 1.3 59.4 + - + +
449X MET* 3.6 14.8 - - + +
450X ARG* 2.8 68.0 + - - +
463X ALA* 4.4 13.5 - - + -
468X ALA* 4.0 16.5 - - + +
469X ARG* 3.6 37.0 + - - +
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Residues in contact with ALA 447 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445X HIS* 3.1 23.3 + - + +
446X GLN* 1.3 81.1 - - + +
448X ILE* 1.3 60.7 + - - +
450X ARG* 4.4 7.2 - - - +
487X PRO* 4.1 8.5 - - + -
488X LEU* 3.8 19.8 - - + +
629X TYR* 2.7 37.4 + - - +
633X HIS* 5.2 6.3 - - + -
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Residues in contact with ILE 448 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444X MET* 4.0 17.0 - - + +
445X HIS* 2.8 22.0 + - + +
447X ALA* 1.3 69.6 - - - +
449X MET* 1.3 65.5 + - - +
450X ARG 3.2 0.7 + - - -
451X TRP* 3.3 17.5 + - - +
452X ALA* 3.7 7.8 + - - +
487X PRO* 3.8 24.9 - - + +
488X LEU* 4.0 11.9 - - + -
601X VAL* 4.0 33.5 - - + +
604X ALA* 4.3 10.5 - - + +
605X ARG 3.8 22.0 - - - +
606X ARG 4.4 2.2 - - - -
607X HIS 4.1 10.8 - - - +
608X VAL* 3.8 12.6 - - + +
629X TYR* 5.4 0.4 - - - -
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Residues in contact with MET 449 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441X GLN* 3.4 33.7 - - + +
444X MET* 4.0 16.2 - - + +
445X HIS 3.0 7.9 + - - +
446X GLN* 3.6 20.2 - - + +
448X ILE* 1.3 77.9 - - - +
450X ARG* 1.3 71.4 + - + +
452X ALA* 3.0 5.0 + - - +
453X SER* 2.7 34.3 + - - -
461X LEU* 3.7 29.1 - - + +
462X THR* 3.3 35.7 - - - +
463X ALA* 3.4 12.8 - - + +
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Residues in contact with ARG 450 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446X GLN* 2.8 65.7 + - - +
447X ALA* 4.2 6.1 - - - +
448X ILE 3.2 0.4 - - - -
449X MET* 1.3 85.7 - - + +
451X TRP* 1.3 61.2 + - - +
453X SER* 3.5 6.0 - - - -
454X ASP* 3.1 42.7 + - - +
629X TYR* 3.0 22.4 - - + +
633X HIS* 5.8 7.2 - - - -
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Residues in contact with TRP 451 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448X ILE* 3.3 7.6 + - - +
449X MET 3.2 0.6 - - - -
450X ARG* 1.3 80.0 - - - +
452X ALA* 1.3 88.0 + - + +
454X ASP* 5.2 0.7 - - - -
455X THR* 2.9 56.9 + - + +
456X MET* 5.9 0.2 - - - -
597X ILE 4.2 0.7 - - - -
598X ASN* 3.9 23.8 - - + -
601X VAL* 3.5 42.6 - - + -
622X PHE* 3.2 39.3 + + - -
625X THR* 4.6 2.6 + - - -
626X LEU* 3.8 34.7 - - + +
629X TYR* 3.3 55.0 + + + -
630X PHE* 5.9 2.9 - + + -
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Residues in contact with ALA 452 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216X PRO* 5.7 0.2 - - + -
444X MET* 5.4 0.9 - - + -
448X ILE 3.7 4.1 + - - +
449X MET* 3.0 8.3 + - - +
451X TRP* 1.3 95.2 - - + +
453X SER* 1.3 69.1 + - - +
455X THR* 4.3 2.7 - - - -
456X MET* 2.8 25.3 + - - +
457X TYR* 3.3 15.1 + - + -
461X LEU* 5.4 3.6 - - + -
598X ASN* 3.9 9.4 - - - +
602X THR* 3.9 25.6 - - + -
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Residues in contact with SER 453 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449X MET* 2.7 23.5 + - - -
450X ARG* 3.5 11.4 - - - -
452X ALA* 1.3 72.6 - - - +
454X ASP* 1.3 57.6 + - - +
457X TYR* 2.9 28.4 + - - -
459X GLY* 2.7 48.2 + - - -
461X LEU* 3.2 29.3 + - - +
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Residues in contact with ASP 454 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450X ARG* 3.1 28.7 + - - +
451X TRP* 4.4 1.8 - - - +
453X SER* 1.3 80.2 + - - +
455X THR* 1.3 69.5 + - + +
458X LEU* 4.3 8.5 + - - -
459X GLY* 3.1 25.1 - - - +
629X TYR* 5.8 2.3 - - - -
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Residues in contact with THR 455 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451X TRP* 2.9 46.3 + - + +
452X ALA* 4.2 1.0 + - - -
454X ASP* 1.3 83.1 - - + +
456X MET* 1.3 71.0 + - - +
622X PHE* 3.2 33.0 - - - -
625X THR* 4.3 12.8 - - - +
629X TYR* 6.2 0.2 - - + -
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Residues in contact with MET 456 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402X LYS* 4.0 36.7 - - + +
452X ALA* 2.8 13.4 + - - +
455X THR* 1.3 89.9 - - - +
457X TYR* 1.3 75.4 + - + +
458X LEU* 3.6 5.0 + - - +
594X ASP* 4.6 13.0 - - + +
595X ARG* 4.3 23.1 - - + -
598X ASN* 3.7 30.3 - - - +
622X PHE* 4.0 23.8 - - + -
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Residues in contact with TYR 457 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213X HIS* 3.8 13.9 - + - -
215X PRO* 3.8 16.8 - - + -
216X PRO* 3.2 23.2 - - + +
400X ASP* 2.4 35.7 + - - -
402X LYS* 3.4 23.1 - - + +
403X GLN* 3.8 0.3 - - - +
452X ALA* 3.3 19.7 + - + -
453X SER 2.9 12.9 + - - +
456X MET* 1.3 92.2 - - + +
458X LEU* 1.3 69.7 + - - +
459X GLY 3.0 1.4 + - - -
460X GLN* 3.0 18.1 + - + +
461X LEU* 4.1 26.7 - - + -
598X ASN* 3.2 24.4 + - - -
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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