Contacts of the helix formed by residues 565 - 576 (chain D) in PDB entry 3UEO
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 ASN 565 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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564D SER* 1.3 77.1 - - - +
566D GLU* 1.3 61.3 + - - +
568D GLU* 4.1 7.0 - - - +
569D SER* 3.8 11.8 + - - -
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Residues in contact with GLU 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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564D SER* 3.3 5.8 + - - +
565D ASN* 1.3 76.9 - - - +
567D ASN* 1.3 57.4 - - - +
568D GLU 3.2 1.8 - - - -
569D SER* 2.7 33.0 + - - -
570D ASN* 2.9 31.9 + - - +
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Residues in contact with ASN 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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563D PHE* 3.7 17.9 - - + -
564D SER* 3.0 33.0 + - - +
566D GLU* 1.3 78.5 - - - +
568D GLU* 1.3 63.0 + - - +
570D ASN* 3.4 16.2 + - - +
571D ILE* 3.3 26.6 + - + +
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Residues in contact with GLU 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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560D VAL* 3.7 37.5 + - + +
561D LEU* 6.1 0.2 - - - -
563D PHE* 3.6 13.9 - - + +
564D SER 3.2 18.4 + - - +
565D ASN 4.1 5.1 - - - +
566D GLU 3.2 0.2 - - - -
567D ASN* 1.3 77.0 - - - +
569D SER* 1.3 69.2 + - - +
571D ILE* 3.3 2.9 + - - +
572D ALA* 3.0 35.3 + - - +
582D ILE* 5.1 6.8 - - - +
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Residues in contact with SER 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 ASN 3.8 10.9 + - - -
566D GLU* 2.7 20.5 + - - -
568D GLU* 1.3 81.2 + - - +
570D ASN* 1.3 60.5 + - - -
572D ALA* 3.3 5.0 + - - +
573D ASN* 2.8 41.9 + - - -
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Residues in contact with ASN 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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566D GLU* 2.9 54.0 + - - +
567D ASN* 3.4 17.9 + - - +
568D GLU 3.4 0.2 - - - -
569D SER* 1.3 75.8 - - - +
571D ILE* 1.3 64.7 + - + +
573D ASN* 3.4 8.8 + - - +
574D ILE* 3.1 24.1 + - - +
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Residues in contact with ILE 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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560D VAL* 3.8 20.0 - - + -
563D PHE* 3.3 48.9 - - + -
567D ASN 3.3 9.7 + - - +
568D GLU 3.7 6.5 - - - +
569D SER 3.2 0.4 - - - -
570D ASN* 1.3 76.9 - - + +
572D ALA* 1.3 67.1 + - - +
574D ILE* 3.1 8.2 + - + +
575D ILE* 3.0 31.4 + - + +
595D VAL* 4.1 6.5 - - + -
613D ASN* 3.7 18.2 - - + -
616D LEU* 3.7 21.8 - - + -
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Residues in contact with ALA 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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560D VAL* 4.5 5.6 - - + -
568D GLU* 3.0 28.7 + - - +
569D SER* 3.7 8.3 - - - +
571D ILE* 1.3 76.3 - - - +
573D ASN* 1.3 61.9 + - - +
575D ILE* 3.4 6.0 + - - +
576D LYS* 3.3 32.6 + - + +
582D ILE* 4.0 25.8 - - + +
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Residues in contact with ASN 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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569D SER* 2.8 28.2 + - - +
570D ASN* 3.5 9.1 + - - +
572D ALA* 1.3 77.7 - - - +
574D ILE* 1.3 58.0 + - - +
575D ILE 3.1 0.5 + - - -
576D LYS* 3.2 26.1 + - - +
577D GLU* 2.8 48.1 + - - +
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Residues in contact with ILE 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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570D ASN 3.1 12.4 + - - +
571D ILE* 3.1 17.2 + - + +
573D ASN* 1.3 78.3 - - - +
575D ILE* 1.3 59.2 + - - +
577D GLU* 3.3 18.4 - - - +
578D ASN* 2.6 35.4 + - - +
616D LEU* 3.8 22.4 - - + -
617D VAL* 5.1 15.9 - - + -
620D ILE* 3.7 28.4 - - + +
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Residues in contact with ILE 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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553D PHE* 3.9 8.0 - - + -
558D PHE* 3.4 58.8 - - + -
560D VAL* 4.1 12.3 - - + -
571D ILE* 3.0 31.1 + - + +
572D ALA 3.6 6.5 - - - +
573D ASN 3.1 0.2 - - - -
574D ILE* 1.3 76.0 - - - +
576D LYS* 1.3 64.6 + - - +
578D ASN* 3.1 10.4 + - - -
579D ALA 3.1 0.9 + - - -
580D GLY* 2.9 25.5 + - - -
582D ILE* 3.9 13.5 - - + -
595D VAL* 4.5 3.1 - - + -
616D LEU* 3.9 22.2 - - + -
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Residues in contact with LYS 576 (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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572D ALA* 3.3 18.3 + - + +
573D ASN* 3.2 27.7 + - - +
575D ILE* 1.3 70.9 - - - +
577D GLU* 1.3 58.6 + - + +
578D ASN 2.9 4.7 - - - -
579D ALA* 2.6 24.8 + - - -
580D GLY 3.7 19.5 - - - +
581D LYS* 5.6 0.2 - - - -
582D ILE* 4.1 18.8 - - + -
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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