Contacts of the helix formed by residues 484 - 496 (chain A) in PDB entry 1U2Z
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 ASP 484 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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367A PHE* 5.2 7.3 - - - +
368A SER* 5.0 6.0 + - - +
369A ASN* 2.9 33.4 + - - +
482A LEU 3.6 0.8 + - - -
483A PHE* 1.3 73.3 - - - +
485A GLU* 1.3 63.5 + - - +
486A ASP* 3.1 12.8 + - - +
487A LEU* 2.7 24.8 + - - +
488A ASN* 3.0 22.8 + - - -
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Residues in contact with GLU 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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484A ASP* 1.3 74.1 - - - +
486A ASP* 1.3 63.7 + - - +
488A ASN* 3.3 10.6 + - - +
489A LYS* 3.0 24.8 + - + +
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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
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484A ASP* 3.1 13.6 + - - +
485A GLU* 1.3 79.3 - - - +
487A LEU* 1.3 63.4 + - - +
489A LYS* 3.0 18.6 + - - +
490A LYS* 3.1 43.4 + - - +
200C ARG* 5.0 5.9 + - - -
332C GLU* 4.4 8.5 - - - +
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Residues in contact with LEU 487 (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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369A ASN* 3.6 27.6 - - + +
460A PHE* 3.9 25.4 - - + -
461A VAL* 4.6 0.9 - - + -
483A PHE* 3.3 44.0 - - + -
484A ASP* 2.7 22.6 + - - +
486A ASP* 1.3 72.9 - - - +
488A ASN* 1.3 57.8 + - - +
490A LYS* 2.9 23.9 + - + +
491A VAL* 2.8 25.6 + - + +
801A SAH 3.7 23.6 - - - +
197C GLU* 5.6 2.7 - - + -
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Residues in contact with ASN 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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480A ASN* 3.7 21.6 + - - +
483A PHE* 3.3 34.2 + - - +
484A ASP 3.0 22.8 + - - -
485A GLU* 3.7 9.3 - - - +
487A LEU* 1.3 76.2 - - - +
489A LYS* 1.3 57.7 + - - +
491A VAL* 3.3 9.0 + - - +
492A GLU* 2.9 28.3 + - - +
508A LYS* 6.0 2.8 - - - +
509A SER 6.0 1.6 - - - -
510A LEU 5.9 3.4 - - - +
526A PHE* 5.6 0.3 - - - -
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Residues in contact with LYS 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 GLU* 3.0 13.8 + - + +
486A ASP* 3.0 18.7 + - - +
488A ASN* 1.3 76.5 - - - +
490A LYS* 1.3 60.0 + - + +
492A GLU* 3.2 27.6 + - - +
493A LYS* 3.0 21.7 + - - +
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Residues in contact with LYS 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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461A VAL* 4.0 35.7 - - + -
486A ASP* 3.1 41.8 + - - +
487A LEU* 2.9 17.8 + - + +
489A LYS* 1.3 75.2 - - + +
491A VAL* 1.3 65.2 + - - +
493A LYS* 3.2 11.8 + - + +
494A ILE* 3.0 28.3 + - - +
196C ILE* 5.6 0.6 - - - +
197C GLU* 2.9 28.6 + - - +
200C ARG* 5.7 1.4 - - - +
332C GLU* 4.4 10.3 + - - -
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Residues in contact with VAL 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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398A LEU* 4.6 14.1 - - + -
460A PHE* 4.3 16.2 - - + -
478A VAL* 4.7 11.7 - - + -
480A ASN* 5.8 2.2 - - + +
483A PHE* 4.2 28.9 - - + -
487A LEU* 2.8 18.4 + - + +
488A ASN* 3.3 10.7 + - - +
490A LYS* 1.3 75.1 - - - +
492A GLU* 1.3 65.4 + - - +
494A ILE* 3.0 11.3 + - - +
495A LEU* 2.9 42.3 + - + +
510A LEU* 4.8 10.8 - - + -
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Residues in contact with GLU 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 ASN 2.9 12.9 + - - +
489A LYS* 3.2 32.5 + - - +
491A VAL* 1.3 80.1 - - - +
493A LYS* 1.3 62.8 + - - +
495A LEU* 3.3 10.6 + - - +
496A GLN* 2.9 29.9 + - - +
515A TYR* 5.7 0.7 - - - -
524A ASN* 2.7 23.2 + - - +
526A PHE* 3.3 45.9 - - + -
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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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461A VAL* 6.5 0.4 - - + -
462A ASP* 4.7 13.5 + - - -
489A LYS 3.0 11.9 + - - +
490A LYS* 3.4 13.7 - - + +
492A GLU* 1.3 76.7 - - - +
494A ILE* 1.3 65.6 + - + +
496A GLN* 3.2 28.7 + - + +
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Residues in contact with ILE 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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398A LEU* 4.6 13.0 - - + -
460A PHE* 3.3 52.7 - - + +
461A VAL* 4.1 11.2 - - + -
462A ASP 5.5 1.8 - - - +
466A VAL* 4.1 10.5 - - + -
467A ALA* 6.0 1.1 - - - +
470A ILE* 3.8 40.9 - - + +
490A LYS* 3.0 18.2 + - + +
491A VAL* 3.0 10.8 + - - +
493A LYS* 1.3 78.9 - - + +
495A LEU* 1.3 60.8 + - + +
496A GLN 3.4 1.0 + - - -
497A THR* 4.1 5.4 + - - +
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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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398A LEU* 4.6 10.5 - - + -
470A ILE* 4.7 5.4 - - + -
476A ILE* 3.9 37.7 - - + -
478A VAL* 5.8 0.7 - - + -
491A VAL* 2.9 37.9 + - + +
492A GLU* 3.8 5.8 - - - +
493A LYS 3.2 0.2 - - - -
494A ILE* 1.3 73.8 - - - +
496A GLN* 1.3 64.5 + - - +
497A THR 3.0 5.4 + - - -
498A ALA* 3.1 19.2 + - + +
504A ILE* 4.0 19.3 - - + -
510A LEU* 3.8 31.6 - - + -
525A ILE* 3.5 15.7 - - + +
526A PHE* 4.7 8.5 - - + -
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Residues in contact with GLN 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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492A GLU* 2.9 30.0 + - - +
493A LYS* 3.2 25.6 + - + +
495A LEU* 1.3 76.8 - - - +
497A THR* 1.3 63.4 + - + +
498A ALA 3.7 1.0 + - - +
523A GLU 4.3 1.9 - - - +
524A ASN* 3.1 33.0 + - - +
525A ILE* 2.8 46.7 + - - +
528A ARG* 4.9 4.0 + - - -
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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