Contacts of the helix formed by residues 545 - 558 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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543A SER 5.0 2.5 - - - +
544A MET* 1.3 76.9 - - - +
546A THR* 1.3 67.5 + - - +
547A VAL* 3.4 10.8 + - - +
548A GLU* 2.6 62.3 + - + +
549A LYS* 3.1 11.9 + - - +
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Residues in contact with THR 546 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544A MET 4.1 0.8 + - - -
545A THR* 1.3 73.7 - - - +
547A VAL* 1.3 63.5 + - - +
549A LYS* 3.1 18.3 + - - +
550A PHE* 3.0 48.8 + - + -
644A THR* 2.9 38.7 + - + +
651A ILE* 4.4 12.6 - - + +
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Residues in contact with VAL 547 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545A THR* 3.1 8.6 - - - +
546A THR* 1.3 76.6 - - - +
548A GLU* 1.3 52.6 + - + +
550A PHE* 3.7 6.9 + - + +
551A THR* 2.4 44.0 + - - +
644A THR* 4.0 25.6 - - + +
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Residues in contact with GLU 548 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543A SER 4.7 0.5 - - - +
544A MET* 3.6 21.1 - - + +
545A THR* 2.6 62.1 + - + +
547A VAL* 1.3 76.1 - - + +
549A LYS* 1.3 54.0 + - - +
551A THR* 3.1 8.2 + - - -
552A ASP* 2.8 34.4 + - - +
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Residues in contact with LYS 549 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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535A ILE* 4.0 47.7 + - + +
540A LEU* 4.5 8.4 + - + +
541A PRO 3.7 16.8 + - - -
542A ASP* 4.6 13.5 + - - +
544A MET* 3.4 47.3 + - + -
545A THR 3.1 9.1 + - - +
546A THR* 3.7 15.4 + - + +
548A GLU* 1.3 72.3 - - - +
550A PHE* 1.3 64.5 + - + +
552A ASP* 3.1 8.2 + - - +
553A ILE* 2.8 34.3 + - - +
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Residues in contact with PHE 550 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532A PHE* 4.9 4.0 - + - -
535A ILE* 4.2 18.4 - - + -
546A THR* 3.0 27.6 + - + +
547A VAL* 4.0 7.0 - - - +
549A LYS* 1.3 80.6 - - + +
551A THR* 1.3 56.9 + - - +
553A ILE* 3.5 7.3 + - + +
554A PHE* 3.0 28.6 + - - +
634A LEU* 5.2 4.9 - - + -
637A PHE* 3.0 44.6 - - + -
638A VAL* 3.5 38.7 - - + +
644A THR* 4.9 2.9 - - - -
651A ILE* 3.7 36.8 - - + -
655A LEU* 4.7 5.2 - - + -
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Residues in contact with THR 551 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547A VAL* 2.4 27.7 + - - +
548A GLU* 3.1 12.5 - - - +
549A LYS 3.1 0.2 - - - -
550A PHE* 1.3 75.5 - - - +
552A ASP* 1.3 65.9 + - - +
554A PHE* 3.3 7.8 + - + +
555A LYS* 3.1 51.6 + - + +
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Residues in contact with ASP 552 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531A LYS* 3.2 18.5 + - - +
540A LEU* 3.8 22.2 - - + +
544A MET* 5.2 5.6 - - - +
548A GLU 2.8 13.4 + - - +
549A LYS* 3.4 11.7 - - - +
551A THR* 1.3 78.1 - - - +
553A ILE* 1.3 63.7 + - - +
555A LYS* 3.5 3.7 + - - +
556A ASN* 2.7 57.2 + - - +
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Residues in contact with ILE 553 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528A ILE* 4.5 11.2 - - + -
531A LYS* 3.3 37.9 - - + +
532A PHE* 3.4 38.1 - - + -
535A ILE* 4.2 15.9 - - + -
540A LEU* 4.5 3.1 - - + -
549A LYS 2.8 22.6 + - - +
550A PHE* 3.8 11.2 - - + +
552A ASP* 1.3 74.8 - - - +
554A PHE* 1.3 55.1 + - - +
557A CYS* 2.7 50.0 + - + +
558A LEU* 5.2 1.1 - - + -
638A VAL* 4.4 15.7 - - + -
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Residues in contact with PHE 554 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550A PHE 3.0 18.5 + - - +
551A THR* 3.5 7.2 - - + +
552A ASP 3.3 0.2 - - - -
553A ILE* 1.3 77.3 - - - +
555A LYS* 1.3 76.6 + - + +
558A LEU* 2.8 44.0 + - + +
559A GLU* 2.9 40.4 + - + -
562A PHE* 4.2 17.9 - + - -
638A VAL* 4.6 11.7 - - + +
639A LEU* 3.8 27.8 - - + -
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Residues in contact with LYS 555 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551A THR* 3.1 36.3 + - + +
552A ASP* 4.1 4.0 - - - +
554A PHE* 1.3 89.2 - - + +
556A ASN* 1.3 64.5 + - - +
559A GLU* 3.5 36.3 + - - +
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Residues in contact with ASN 556 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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527A SER* 5.7 0.3 - - - -
531A LYS* 4.0 12.4 - - - +
552A ASP* 2.7 49.7 + - - +
553A ILE 4.2 1.3 - - - +
555A LYS* 1.3 80.3 - - - +
557A CYS* 1.3 69.7 + - - +
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Residues in contact with CYS 557 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524A VAL* 3.7 12.2 - - - +
527A SER* 3.4 46.5 + - - +
528A ILE* 3.6 17.3 - - + -
531A LYS* 3.8 18.6 - - - -
553A ILE* 2.7 24.6 + - - +
554A PHE 3.2 0.4 + - - -
556A ASN* 1.3 84.0 - - - +
558A LEU* 1.3 58.6 + - - +
559A GLU 3.8 0.7 - - - -
561A GLN* 3.3 21.9 - - - +
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Residues in contact with LEU 558 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516A PHE* 5.6 1.8 - - + -
520A LEU* 3.9 26.7 - - + -
524A VAL* 4.0 6.7 - - + -
528A ILE* 3.3 29.2 - - + -
553A ILE* 3.7 1.5 + - + +
554A PHE* 2.8 27.6 + - + +
557A CYS* 1.3 73.7 - - + +
559A GLU* 1.3 67.4 + - - +
560A ASN 3.2 0.3 + - - -
561A GLN* 2.8 18.2 + - - +
562A PHE* 3.4 19.1 - - + -
635A LEU* 3.4 25.1 - - + -
638A VAL* 3.7 23.3 - - + -
639A LEU* 4.1 13.9 - - + -
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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