Contacts of the helix formed by residues 554 - 565 (chain D) in PDB entry 5UHO
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 554 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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388C LEU* 3.4 11.8 - - - +
552D PRO* 3.7 12.8 - - + +
553D VAL* 1.3 75.6 - - - +
555D LEU* 1.3 62.8 + - - +
556D GLU* 3.2 21.5 + - - +
557D ASP* 2.8 37.3 + - - +
558D LEU* 3.4 14.4 + - - +
627D ARG* 4.4 7.2 - - - +
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Residues in contact with LEU 555 (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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381C LYS* 4.6 16.8 - - + +
384C LEU* 4.2 7.8 - - + +
385C THR* 3.4 47.6 - - + +
388C LEU* 3.9 20.5 - - + +
554D THR* 1.3 71.9 - - - +
556D GLU* 1.3 70.3 + - - +
558D LEU* 3.3 6.6 + - - +
559D GLN* 2.8 68.2 + - + +
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Residues in contact with GLU 556 (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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554D THR* 3.4 20.0 + - - +
555D LEU* 1.3 95.1 + - - +
557D ASP* 1.4 54.9 + - - +
559D GLN* 3.1 13.6 + - - +
560D LEU* 2.7 37.4 + - - +
574D LYS* 5.5 1.2 - - - +
620D LEU* 5.6 10.9 - - + +
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Residues in contact with ASP 557 (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 VAL* 3.4 15.1 - - + +
554D THR* 2.8 40.1 + - - +
556D GLU* 1.4 75.9 - - - +
558D LEU* 1.3 57.6 - - + +
560D LEU* 3.2 3.8 + - - +
561D LEU* 3.0 23.4 + - - +
620D LEU* 4.8 6.2 - - - +
624D MET* 3.4 35.1 - - + +
627D ARG* 2.7 49.6 + - - +
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Residues in contact with LEU 558 (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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384C LEU* 3.7 36.7 - - + +
387C TRP* 3.7 21.3 - - + -
388C LEU* 3.8 14.4 - - + +
391C PHE* 3.7 35.9 - - + -
553D VAL* 3.8 21.1 - - + -
554D THR 3.4 4.6 + - - +
555D LEU* 3.3 7.9 + - - +
556D GLU 3.3 0.4 - - - -
557D ASP* 1.3 80.6 - - - +
559D GLN* 1.3 55.7 + - - +
561D LEU* 3.1 23.1 + - + +
562D ALA* 2.9 28.4 + - - +
628D LEU* 4.8 4.3 - - + -
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Residues in contact with GLN 559 (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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381C LYS* 3.8 31.1 - - - +
384C LEU* 3.8 23.3 - - + +
555D LEU* 2.8 46.4 + - + +
556D GLU* 3.1 17.2 + - - +
558D LEU* 1.3 71.2 - - - +
560D LEU* 1.3 61.1 + - - +
562D ALA* 3.6 1.0 + - - +
563D ASP* 3.0 31.7 + - - +
574D LYS* 4.6 11.6 - - + +
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Residues in contact with LEU 560 (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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556D GLU 2.7 20.6 + - - +
557D ASP* 3.4 6.5 - - - +
558D LEU 3.2 0.2 - - - -
559D GLN* 1.3 72.3 - - - +
561D LEU* 1.4 56.3 + - - +
563D ASP* 3.1 4.5 + - - +
564D LEU* 2.9 52.2 + - + +
574D LYS* 4.0 34.0 - - + +
578D MET* 4.9 7.6 - - - -
617D MET* 5.5 4.5 - - + +
620D LEU* 3.6 27.6 - - + +
621D VAL* 3.6 42.0 - - + +
624D MET* 4.5 5.6 - - + -
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Residues in contact with LEU 561 (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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293C LEU* 3.7 22.8 - - + +
387C TRP* 4.5 6.3 - - + -
557D ASP 3.0 12.2 + - - +
558D LEU* 3.3 24.2 - - + +
560D LEU* 1.4 76.1 - - - +
562D ALA* 1.3 55.2 + - - +
564D LEU* 3.1 4.5 + - - -
565D PHE* 3.1 62.4 + - + +
624D MET* 3.7 25.7 - - + -
628D LEU* 4.2 15.5 - - + -
640D MET* 4.4 14.8 - - + -
644D VAL* 3.8 17.9 - - + -
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Residues in contact with ALA 562 (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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293C LEU* 3.5 27.3 - - + +
380C LEU* 4.2 6.5 - - + -
384C LEU* 3.7 28.3 - - + -
387C TRP* 6.5 0.2 - - - -
558D LEU 2.9 15.1 + - - +
559D GLN 3.7 4.7 - - - +
560D LEU 3.3 0.2 - - - -
561D LEU* 1.3 76.0 - - - +
563D ASP* 1.3 63.8 + - - +
565D PHE 3.0 17.2 - - - +
566D TYR* 3.0 17.8 - - - -
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Residues in contact with ASP 563 (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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685B LEU* 5.3 0.5 - - - +
380C LEU* 4.5 6.2 - - - +
384C LEU* 5.8 0.2 - - - +
559D GLN* 3.0 19.1 + - - +
560D LEU 3.1 6.6 + - - +
562D ALA* 1.3 81.6 - - - +
564D LEU* 1.4 63.9 + - - +
565D PHE 3.3 0.6 + - - -
566D TYR* 4.1 7.4 - - - +
571D HIS* 4.8 2.4 + - - +
572D GLY* 3.1 36.1 + - - +
573D PRO* 3.0 20.9 - - - +
574D LYS* 2.8 48.2 + - + +
575D GLY* 4.1 7.0 - - - +
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Residues in contact with LEU 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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685B LEU* 3.9 45.4 + - + +
560D LEU* 2.9 45.3 + - + +
561D LEU* 3.1 11.8 + - - +
563D ASP* 1.4 80.6 - - - +
565D PHE* 1.4 75.4 + - + +
566D TYR 3.8 0.7 + - - -
571D HIS* 5.3 1.9 + - - -
575D GLY* 4.8 8.5 - - - -
578D MET* 4.9 4.0 - - - -
621D VAL* 3.8 31.6 - - + -
624D MET* 4.2 9.0 - - - -
647D ILE* 4.1 20.1 - - + +
651D MET* 4.7 3.8 - - + -
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Residues in contact with PHE 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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686B ALA* 5.9 2.5 - - + -
289C LYS 6.1 0.7 - - - -
291C LEU* 3.6 42.6 - - + +
293C LEU* 2.8 29.8 + - + +
561D LEU* 3.1 48.6 + - + +
562D ALA 3.0 10.1 - - - +
564D LEU* 1.4 88.0 - - + +
566D TYR* 1.3 59.6 + - - +
643D TYR* 3.2 42.8 - + + -
644D VAL* 4.1 5.2 - - + -
647D ILE* 3.5 28.3 - - + -
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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