Contacts of the helix formed by residues 481 - 496 (chain A) in PDB entry 3U44
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 ARG 481 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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480A SER* 1.3 76.8 + - - +
482A ALA* 1.3 79.1 + - + +
483A ASP* 3.5 10.5 - - + +
484A ILE* 3.2 20.8 + - + +
485A LEU* 3.5 6.1 - - - +
513A LEU* 4.2 0.2 - - - -
515A ALA* 4.8 1.3 - - - -
517A TYR* 3.3 38.2 - - + +
518A PRO* 5.0 9.3 + - - +
520A ASN* 5.2 9.0 + - - +
523A THR* 3.0 49.0 - - - +
567A PHE* 5.0 4.8 - - - -
568A LYS 5.7 1.6 + - - -
570A TYR* 5.1 1.4 - - - +
875A LYS 2.7 22.0 + - - +
876A GLU* 3.1 60.0 + - - +
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Residues in contact with ALA 482 (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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481A ARG* 1.3 73.6 - - + +
483A ASP* 1.3 64.8 + - - +
484A ILE 2.9 5.6 + - - -
485A LEU* 3.1 5.8 + - - +
486A ASP* 2.9 38.9 + - - +
513A LEU* 3.8 35.4 - - + +
517A TYR* 5.8 0.4 - - - +
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Residues in contact with ASP 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481A ARG* 3.5 8.2 - - + +
482A ALA* 1.3 78.3 - - - +
484A ILE* 1.3 58.8 + - + +
486A ASP* 4.2 4.7 - - - +
487A SER* 2.8 35.6 + - - +
523A THR* 2.7 44.5 + - - +
524A GLU* 4.3 4.5 + - - +
525A THR* 4.1 3.3 + - - +
946A PRO 4.2 7.4 - - - +
948A ARG* 3.7 35.5 + - - +
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Residues in contact with ILE 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480A SER* 3.3 23.3 - - - +
481A ARG* 3.2 12.6 - - + +
482A ALA 2.9 1.0 + - - -
483A ASP* 1.3 76.2 - - - +
485A LEU* 1.3 71.0 + - + +
486A ASP 3.0 1.1 - - - -
487A SER* 2.8 6.9 + - - -
488A THR* 2.8 28.8 + - - +
523A THR 5.1 2.5 - - - +
525A THR* 5.2 1.8 - - - +
871A LEU 3.6 24.2 - - - +
872A THR* 5.1 2.7 - - - -
874A ALA 3.8 4.9 - - - +
875A LYS 3.5 13.7 - - - +
876A GLU 3.0 27.8 - - - +
877A LYS* 4.3 1.1 - - - -
878A LEU* 3.5 32.8 - - + +
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Residues in contact with LEU 485 (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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477A ASN* 3.8 31.0 - - + +
480A SER* 3.9 15.5 - - - +
481A ARG 3.5 9.9 - - - +
482A ALA* 3.1 3.8 + - - +
484A ILE* 1.3 78.1 - - + +
486A ASP* 1.3 55.8 + - - +
488A THR* 4.5 0.7 - - - -
489A ASN* 2.7 41.5 + - - +
511A LEU* 3.8 38.8 - - + +
512A LYS 3.8 12.3 - - - +
513A LEU* 3.8 42.4 - - + +
872A THR* 6.2 0.7 - - + -
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Residues in contact with ASP 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A ALA* 2.9 32.2 + - - +
483A ASP* 4.2 5.0 + - - +
485A LEU* 1.3 76.4 - - - +
487A SER* 1.3 59.9 + - - +
489A ASN* 4.4 2.5 + - - +
490A PHE* 2.9 31.4 + - - +
945A HIS* 3.4 18.2 + - + -
946A PRO* 3.2 42.0 - - - +
947A ALA* 3.9 4.9 - - + -
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Residues in contact with SER 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A ASP* 2.8 22.7 + - - +
484A ILE* 2.8 5.8 + - - -
486A ASP* 1.3 75.3 - - - +
488A THR* 1.3 62.7 + - - +
490A PHE* 3.3 2.2 + - - +
491A LEU* 3.2 34.1 + - - +
525A THR* 2.9 29.2 + - - -
871A LEU* 5.1 1.3 - - - -
878A LEU* 5.1 5.2 - - - -
947A ALA* 4.1 11.2 - - - +
948A ARG 3.7 11.6 + - - -
949A PHE* 4.1 12.7 - - - -
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Residues in contact with THR 488 (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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484A ILE* 2.8 23.6 + - - +
485A LEU* 4.0 3.6 - - - -
487A SER* 1.3 70.9 - - - +
489A ASN* 1.3 65.5 + - - +
490A PHE 3.2 0.3 + - - -
491A LEU 3.4 0.9 + - - -
492A PHE* 3.1 51.6 + - + +
505A TYR* 4.7 0.2 - - - +
511A LEU* 4.2 11.0 - - + -
868A TYR* 3.7 24.0 - - + -
871A LEU* 3.3 35.3 + - + +
872A THR* 4.2 10.8 - - + +
878A LEU* 4.9 1.0 - - - +
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Residues in contact with ASN 489 (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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485A LEU 2.7 27.2 + - - +
486A ASP* 4.0 6.9 + - - +
488A THR* 1.3 72.0 - - - +
490A PHE* 1.3 61.8 + - - +
493A LYS* 3.2 28.2 + - - +
505A TYR* 2.8 29.9 + - + -
510A GLU* 3.3 20.3 + - + +
511A LEU* 2.9 54.1 + - - +
945A HIS* 4.7 9.6 - - + +
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Residues in contact with PHE 490 (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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486A ASP 2.9 20.3 + - - +
487A SER* 3.4 5.4 - - - +
488A THR 3.1 0.2 - - - -
489A ASN* 1.3 80.4 - - - +
491A LEU* 1.3 76.7 + - + +
493A LYS* 3.8 5.9 + - - +
494A GLN* 3.2 35.1 + - - +
903A TRP* 5.0 6.3 + - - +
923A ALA 3.1 25.4 - - - -
924A LEU* 4.6 1.1 - - - -
926A ARG 5.1 0.4 - - - -
927A HIS* 3.1 42.6 - + + -
942A ILE* 2.9 30.1 - - - -
945A HIS* 3.5 30.3 - + + +
947A ALA* 4.0 8.1 - - + -
949A PHE* 4.2 8.1 - + - -
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Residues in contact with LEU 491 (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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487A SER* 3.2 18.2 + - - +
488A THR 4.1 2.5 - - - +
490A PHE* 1.3 87.9 - - + +
492A PHE* 1.3 63.7 + - + +
493A LYS 3.1 4.7 - - - -
494A GLN* 2.9 22.2 + - - +
495A LEU* 3.1 30.7 + - + +
525A THR* 6.4 0.2 - - + -
871A LEU* 3.9 23.3 - - + -
880A LEU* 4.8 8.3 - - + -
920A ILE* 4.0 26.9 - - + -
923A ALA* 4.2 12.8 - - + -
924A LEU* 3.5 31.0 - - + -
949A PHE* 4.2 4.5 - - + -
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Residues in contact with PHE 492 (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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488A THR* 3.1 45.6 + - + +
491A LEU* 1.3 78.6 - - + +
493A LYS* 1.3 60.7 + - - +
494A GLN 3.2 0.2 - - - -
495A LEU* 3.6 7.6 - - + -
496A MET* 2.9 48.9 + - + +
505A TYR* 3.4 25.6 - - + -
864A LEU* 3.0 43.5 - - + -
867A LEU* 3.6 18.4 - - + -
868A TYR* 3.3 31.6 - + + -
871A LEU* 4.0 17.3 - - + -
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Residues in contact with LYS 493 (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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489A ASN 3.2 20.7 + - - +
490A PHE* 3.9 7.0 - - - +
491A LEU 3.1 0.6 - - - -
492A PHE* 1.3 78.4 - - - +
494A GLN* 1.3 60.3 + - - +
496A MET 4.6 2.1 - - - +
505A TYR* 3.4 31.7 + - + +
506A ASP* 4.6 4.4 - - - +
507A GLU 5.5 0.4 - - - +
510A GLU* 3.3 26.1 + - - +
903A TRP* 3.6 57.5 - - + +
904A LEU* 3.6 22.8 + - - +
945A HIS* 5.9 5.2 - - + +
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Residues in contact with GLN 494 (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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490A PHE* 3.2 32.6 + - - +
491A LEU 2.9 4.9 + - - +
493A LYS* 1.3 76.2 - - - +
495A LEU* 1.3 66.7 + - + +
903A TRP* 3.5 38.1 + - + +
904A LEU* 3.5 12.9 - - - +
905A LEU* 2.8 37.5 + - + +
910A ARG* 3.8 0.3 + - - -
922A PRO 5.1 0.2 - - - +
923A ALA* 2.7 42.2 + - + +
926A ARG* 4.1 28.1 + - - +
942A ILE* 5.0 1.7 - - - +
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Residues in contact with LEU 495 (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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491A LEU* 3.1 23.2 + - + +
492A PHE* 4.0 6.5 - - + +
493A LYS 3.4 0.6 - - - -
494A GLN* 1.3 90.4 - - - +
496A MET* 1.3 67.5 + - - +
497A GLY 3.3 0.7 + - - -
500A ILE* 3.1 21.0 - - - +
864A LEU* 3.6 23.6 - - + -
867A LEU* 5.2 1.8 - - + -
904A LEU* 3.9 0.9 - - - -
905A LEU* 3.6 11.9 - - + -
910A ARG* 3.2 16.8 + - + +
919A PHE* 3.4 45.1 - - + +
920A ILE* 4.4 5.4 - - + +
923A ALA* 3.3 28.0 - - + -
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Residues in contact with MET 496 (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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440A LYS* 3.8 29.2 - - + -
492A PHE* 2.9 45.9 + - + +
493A LYS 4.6 1.0 - - - +
495A LEU* 1.3 73.3 - - - +
497A GLY* 1.3 59.5 + - - +
501A GLY* 3.7 18.2 - - - +
503A VAL* 3.8 16.8 - - - +
505A TYR* 3.4 34.5 + - + +
864A LEU* 3.5 27.8 - - + +
865A ARG* 4.6 12.8 - - + -
868A TYR* 4.4 14.8 - - + -
904A LEU* 4.1 7.6 - - - +
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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