Contacts of the helix formed by residues 563 - 575 (chain D) 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 GLU 563 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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519D THR* 5.8 1.1 + - - -
562D PHE* 1.3 81.2 - - - +
564D ILE* 1.3 65.3 + - - +
565D THR* 3.4 23.9 - - + +
566D ASN* 3.0 35.5 + - - +
567D LEU 3.4 7.4 + - - -
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Residues in contact with ILE 564 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562D PHE* 3.5 16.1 + - + -
563D GLU* 1.3 71.7 - - - +
565D THR* 1.3 66.9 + - - +
567D LEU* 3.2 34.2 + - + -
568D LYS* 3.3 10.7 + - + +
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Residues in contact with THR 565 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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563D GLU* 3.4 23.1 - - + -
564D ILE* 1.3 85.3 - - - +
566D ASN* 1.3 78.0 + - - +
568D LYS* 3.1 23.5 + - - +
569D ILE* 3.2 16.9 + - - +
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Residues in contact with ASN 566 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516D PHE* 3.7 21.3 - - + +
519D THR* 3.9 30.6 + - + +
563D GLU* 3.0 36.0 + - - +
565D THR* 1.3 85.6 - - - +
567D LEU* 1.3 58.8 + - - +
569D ILE* 3.3 22.8 + - - +
570D LEU* 2.9 27.9 + - - +
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Residues in contact with LEU 567 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516D PHE* 3.9 8.2 - - + -
562D PHE* 3.8 26.5 - - + -
563D GLU 3.4 2.2 + - - -
564D ILE* 3.2 29.0 + - + +
566D ASN* 1.3 78.3 - - - +
568D LYS* 1.3 53.2 + - - +
570D LEU* 3.3 3.5 + - + +
571D PHE* 2.6 35.1 + - + +
639D LEU* 3.9 29.4 - - + +
640D PHE* 3.4 36.1 - - + -
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Residues in contact with LYS 568 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564D ILE* 3.3 9.2 + - + +
565D THR* 3.1 13.9 + - - +
567D LEU* 1.3 77.2 - - - +
569D ILE* 1.3 62.2 + - + +
571D PHE* 3.2 14.0 + - + -
572D ASP* 2.8 70.4 + - - +
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Residues in contact with ILE 569 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565D THR* 3.2 17.9 + - - +
566D ASN* 3.5 28.3 - - - +
568D LYS* 1.3 78.5 - - + +
570D LEU* 1.3 64.1 + - - +
572D ASP* 3.4 6.5 + - - +
573D GLU* 3.1 49.5 + - + +
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Residues in contact with LEU 570 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512D THR* 3.9 23.1 - - - +
513D LEU* 4.4 8.5 - - + +
516D PHE* 3.3 44.0 - - + -
566D ASN 2.9 14.5 + - - +
567D LEU* 3.5 7.0 - - + +
569D ILE* 1.3 77.6 - - - +
571D PHE* 1.3 64.5 + - - +
572D ASP 3.2 0.2 + - - -
573D GLU* 3.4 6.1 + - - -
574D LEU* 2.9 49.0 + - + +
636D THR* 4.6 9.6 - - + -
639D LEU* 4.7 2.5 - - + -
640D PHE* 3.7 26.5 - - + -
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Residues in contact with PHE 571 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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567D LEU* 2.6 22.1 + - + +
568D LYS* 3.6 15.9 - - + +
570D LEU* 1.3 73.9 - - - +
572D ASP* 1.3 69.1 + - - +
574D LEU* 3.5 7.9 + - + +
575D ASN* 2.4 56.2 + - - +
640D PHE* 3.9 35.0 - + + -
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Residues in contact with ASP 572 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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568D LYS* 2.8 65.6 + - - +
569D ILE* 3.7 7.1 + - - +
571D PHE* 1.3 75.3 - - - +
573D GLU* 1.3 69.7 + - + +
575D ASN* 2.9 24.0 + - - +
576D SER* 3.9 2.9 + - - -
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Residues in contact with GLU 573 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512D THR* 3.3 46.6 - - + +
515D GLY* 6.0 0.5 - - - -
569D ILE* 3.1 36.9 + - + +
570D LEU* 4.0 4.0 - - - +
572D ASP* 1.3 75.7 - - + +
574D LEU* 1.3 62.6 + - - +
576D SER* 2.7 28.6 + - - +
577D PHE* 3.2 9.9 - - + -
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Residues in contact with LEU 574 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509D TYR* 3.9 16.6 - - + -
512D THR* 4.3 6.3 - - - +
513D LEU* 3.7 27.1 - - + -
570D LEU* 2.9 25.6 + - + +
571D PHE* 3.5 7.9 - - + +
573D GLU* 1.3 77.1 - - - +
575D ASN* 1.3 63.8 + - - +
576D SER 3.0 1.4 + - - -
577D PHE* 3.0 24.2 + - - +
579D ILE* 4.4 24.0 - - + +
636D THR* 4.6 10.5 - - - -
640D PHE* 3.6 37.9 - - + -
642D LEU* 6.2 1.8 - - + -
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Residues in contact with ASN 575 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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571D PHE* 2.4 58.0 - - - +
572D ASP* 2.9 12.7 + - - +
574D LEU* 1.3 77.4 - - - +
576D SER* 1.3 55.7 + - - +
577D PHE 3.1 8.5 + - - +
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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