Contacts of the helix formed by residues 545 - 558 (chain B) in PDB entry 3F7F
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 545 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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543B SER 5.0 2.5 - - - +
544B MET* 1.3 75.9 - - - +
546B THR* 1.3 67.9 + - - +
547B VAL* 3.5 10.6 + - - +
548B GLU* 2.7 62.1 + - + +
549B LYS* 3.1 11.7 + - - +
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Residues in contact with THR 546 (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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544B MET 4.1 0.8 + - - -
545B THR* 1.3 73.3 - - - +
547B VAL* 1.3 63.1 + - - +
549B LYS* 3.1 17.4 + - - +
550B PHE* 3.0 48.8 + - + -
644B THR* 2.9 37.8 + - + +
651B ILE* 4.4 13.1 - - + +
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Residues in contact with VAL 547 (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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545B THR* 3.1 8.7 - - - +
546B THR* 1.3 76.6 - - - +
548B GLU* 1.3 52.1 + - + +
550B PHE* 3.7 4.5 + - - +
551B THR* 2.4 44.0 + - - +
644B THR* 4.0 18.4 - - + -
210C ARG* 3.7 37.7 - - + +
211C PHE* 4.7 1.0 - - + -
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Residues in contact with GLU 548 (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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543B SER 4.7 0.5 - - - +
544B MET* 3.6 21.4 - - + +
545B THR* 2.7 67.0 + - + +
547B VAL* 1.3 71.2 - - + +
549B LYS* 1.3 54.1 + - - +
551B THR* 3.1 8.2 + - - -
552B ASP* 2.8 34.2 + - - +
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Residues in contact with LYS 549 (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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535B ILE* 4.0 49.1 + - + +
540B LEU* 4.5 8.1 + - + +
541B PRO 3.7 17.1 + - - -
542B ASP* 4.6 13.7 + - - +
544B MET* 3.4 46.7 + - + -
545B THR 3.1 9.4 + - - +
546B THR* 3.7 14.8 + - + +
548B GLU* 1.3 72.1 - - - +
550B PHE* 1.3 64.9 + - + +
552B ASP* 3.1 8.4 + - - +
553B ILE* 2.8 33.9 + - - +
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Residues in contact with PHE 550 (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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532B PHE* 4.8 4.3 - + - -
535B ILE* 4.2 18.6 - - + -
546B THR* 3.0 29.8 + - + +
547B VAL* 4.0 6.1 - - - +
549B LYS* 1.3 80.9 - - + +
551B THR* 1.3 57.1 + - - +
553B ILE* 3.6 7.6 + - + +
554B PHE* 3.0 23.0 + - - +
634B LEU* 5.1 4.9 - - + -
637B PHE* 3.0 45.3 - - + -
638B VAL* 3.5 33.9 - - + +
644B THR* 4.9 0.2 - - - -
651B ILE* 3.7 36.8 - - + -
655B LEU* 4.7 4.9 - - + -
210C ARG* 3.7 13.0 - - - -
211C PHE* 3.3 13.2 - - + -
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Residues in contact with THR 551 (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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547B VAL* 2.4 26.5 + - - +
548B GLU* 3.2 12.0 - - - +
549B LYS 3.1 0.2 - - - -
550B PHE* 1.3 75.9 - - - +
552B ASP* 1.3 65.8 + - - +
554B PHE* 3.3 2.8 + - - +
555B LYS* 3.1 49.5 + - + +
211C PHE* 3.2 30.1 - - + -
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Residues in contact with ASP 552 (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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531B LYS* 3.3 18.5 + - - +
540B LEU* 3.8 22.1 - - + +
544B MET* 5.2 6.0 - - - +
548B GLU 2.8 13.4 + - - +
549B LYS* 3.4 12.1 - - - +
551B THR* 1.3 78.5 - - - +
553B ILE* 1.3 63.7 + - - +
555B LYS* 3.9 3.3 - - - +
556B ASN* 2.7 57.4 + - - +
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Residues in contact with ILE 553 (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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528B ILE* 4.5 11.7 - - + -
531B LYS* 3.3 37.5 - - + +
532B PHE* 3.4 38.4 - - + -
535B ILE* 4.2 16.2 - - + -
540B LEU* 4.5 3.1 - - + -
549B LYS 2.8 22.0 + - - +
550B PHE* 3.8 11.7 - - + +
552B ASP* 1.3 74.0 - - - +
554B PHE* 1.3 55.2 + - - +
557B CYS* 2.7 49.7 + - + +
558B LEU* 5.2 1.1 - - + -
638B VAL* 4.4 15.5 - - + -
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Residues in contact with PHE 554 (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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550B PHE 3.0 12.7 + - - +
551B THR 3.5 2.0 - - - +
552B ASP 3.3 0.2 - - - -
553B ILE* 1.3 76.9 - - - +
555B LYS* 1.3 73.7 + - + +
558B LEU* 2.8 44.4 + - + +
559B GLU* 2.9 37.1 + - + -
562B PHE* 4.2 17.7 - + - -
638B VAL* 4.6 2.0 - - + +
639B LEU* 3.8 24.7 - - + -
209C THR* 4.1 6.1 - - + -
211C PHE* 3.1 49.6 - + + -
212C PHE* 3.9 24.2 - + - -
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Residues in contact with LYS 555 (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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551B THR* 3.1 36.7 + - + +
552B ASP* 4.1 4.0 - - - +
554B PHE* 1.3 89.6 - - + +
556B ASN* 1.3 64.3 + - - +
559B GLU* 3.5 35.6 + - - +
211C PHE* 5.7 5.4 - - - -
212C PHE* 6.0 4.9 - - - -
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Residues in contact with ASN 556 (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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527B SER* 5.7 0.3 - - - -
531B LYS* 4.0 12.6 - - - +
552B ASP* 2.7 49.1 + - - +
553B ILE 4.2 1.1 - - - +
555B LYS* 1.3 80.1 - - - +
557B CYS* 1.3 68.8 + - - +
265C SER* 5.6 1.7 + - - -
267C PRO* 4.0 23.3 - - - +
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Residues in contact with CYS 557 (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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524B VAL* 3.7 10.4 - - - +
527B SER* 3.4 46.3 + - - +
528B ILE* 3.6 17.0 - - + -
531B LYS* 3.8 19.3 - - - -
553B ILE* 2.7 24.4 + - - +
554B PHE 3.2 0.4 + - - -
555B LYS 5.1 0.2 - - - -
556B ASN* 1.3 83.6 - - - +
558B LEU* 1.3 59.3 + - - +
559B GLU 3.8 0.7 - - - -
561B GLN* 3.3 22.7 - - - +
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Residues in contact with LEU 558 (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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516B PHE* 5.6 2.0 - - + -
520B LEU* 4.0 27.4 - - + -
524B VAL* 4.1 6.3 - - + -
528B ILE* 3.3 28.9 - - + -
553B ILE* 3.7 1.5 + - + +
554B PHE* 2.8 27.8 + - + +
557B CYS* 1.3 74.0 - - + +
559B GLU* 1.3 67.2 + - - +
560B ASN 3.2 0.3 + - - -
561B GLN* 2.8 17.9 + - - +
562B PHE* 3.4 19.1 - - + -
635B LEU* 3.4 25.1 - - + -
638B VAL* 3.7 23.1 - - + -
639B LEU* 4.1 14.1 - - + -
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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