Contacts of the helix formed by residues 466 - 484 (chain A) in PDB entry 5XA0
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 466 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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464A THR* 3.3 28.6 + - + +
465A ILE* 1.3 97.7 + - - +
467A GLN* 1.3 53.8 - - - +
468A ASN* 3.5 0.9 - - - -
469A GLU* 2.6 26.9 + - - +
470A ARG* 2.1 42.7 + - - +
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Residues in contact with GLN 467 (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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466A THR* 1.3 69.4 - - - +
468A ASN* 1.3 61.8 + - - +
470A ARG* 2.9 10.5 - - - +
471A ARG* 2.8 28.1 + - - +
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Residues in contact with ASN 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A LEU* 6.3 3.4 - - + -
466A THR* 4.9 0.8 - - - -
467A GLN* 1.3 76.8 - - - +
469A GLU* 1.3 61.3 + - - +
471A ARG* 3.4 15.5 + - - +
472A SER* 3.5 11.3 + - - -
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Residues in contact with GLU 469 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455A SER* 4.3 18.2 + - - +
456A ILE* 5.0 11.9 - - + +
459A LYS* 4.8 7.9 - - - +
464A THR 4.6 1.2 - - - +
465A ILE* 2.3 31.1 - - - +
466A THR* 2.6 28.6 + - - +
467A GLN 3.3 0.4 - - - -
468A ASN* 1.3 75.0 - - - +
470A ARG* 1.3 64.6 + - - +
472A SER* 2.7 24.5 + - - +
473A VAL* 2.9 18.8 + - + +
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Residues in contact with ARG 470 (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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465A ILE* 3.4 21.7 + - + -
466A THR 2.1 31.2 + - - +
467A GLN* 2.9 19.7 - - - +
469A GLU* 1.3 68.5 - - - +
471A ARG* 1.3 59.7 + - - +
473A VAL* 3.1 10.8 - - - +
474A THR* 3.0 30.8 + - + +
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Residues in contact with ARG 471 (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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467A GLN 2.8 13.8 + - - +
468A ASN* 3.6 11.2 - - - +
469A GLU 3.2 0.4 - - - -
470A ARG* 1.3 73.4 - - - +
472A SER* 1.3 58.1 + - - +
474A THR* 3.0 7.0 + - - -
475A LYS* 2.9 32.8 + - - +
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Residues in contact with SER 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A VAL 5.9 2.7 - - - -
452A VAL* 5.2 5.4 - - - +
456A ILE* 5.7 0.9 - - - -
468A ASN 3.5 4.4 + - - -
469A GLU* 2.7 34.8 + - - +
471A ARG* 1.3 76.7 - - - +
473A VAL* 1.3 58.1 + - - +
475A LYS* 3.8 5.3 - - - +
476A LEU* 2.9 26.9 + - - +
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Residues in contact with VAL 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A ILE* 3.4 50.0 - - + +
465A ILE* 4.6 14.6 - - + -
469A GLU* 2.9 21.9 + - + +
470A ARG* 3.1 19.7 - - - +
472A SER* 1.3 71.8 + - - +
474A THR* 1.3 68.1 + - + +
476A LEU* 3.0 14.0 + - - +
477A LEU* 2.9 35.7 - - + +
552A ILE* 4.5 12.1 - - + -
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Residues in contact with THR 474 (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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465A ILE* 6.0 2.2 - - + -
470A ARG* 3.0 17.0 + - + +
471A ARG* 3.0 14.6 + - - -
473A VAL* 1.3 76.3 - - + +
475A LYS* 1.3 74.5 + - - +
477A LEU 3.1 2.3 + - - -
478A GLU* 3.1 19.2 + - - +
551A HIS* 4.9 7.9 - - + -
552A ILE* 2.9 36.8 - - + -
555A LEU* 3.4 8.6 - - - +
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Residues in contact with LYS 475 (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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471A ARG 2.9 16.7 + - - +
472A SER* 3.8 7.4 - - - +
474A THR* 1.3 81.3 + - - +
476A LEU* 1.3 58.8 + - - +
478A GLU* 2.9 21.1 + - + -
479A ASP* 2.3 45.5 + - - +
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Residues in contact with LEU 476 (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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445A PHE* 4.8 7.3 - - + -
449A ALA* 4.1 9.0 - - + -
452A VAL* 2.9 49.6 - - + -
453A LEU* 3.4 19.1 - - + +
456A ILE* 4.1 8.3 - - + -
472A SER 2.9 19.6 + - - +
473A VAL 3.1 7.2 - - - +
475A LYS* 1.3 70.3 - - - +
477A LEU* 1.3 71.2 + - + +
479A ASP* 2.7 17.1 + - - +
480A LEU* 2.8 44.5 + - + +
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Residues in contact with LEU 477 (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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453A LEU* 5.5 2.5 - - + -
456A ILE* 5.7 0.9 - - + -
473A VAL* 2.9 37.5 - - + +
474A THR 3.5 0.2 - - - +
475A LYS 3.1 0.2 - - - -
476A LEU* 1.3 86.1 - - + +
478A GLU* 1.3 59.5 + - - +
480A LEU* 2.5 33.3 - - + +
481A VAL* 3.1 4.3 - - - +
519A ILE* 6.2 2.5 - - + -
552A ILE* 3.0 64.4 - - + +
555A LEU* 2.7 38.8 - - + +
556A CYS 5.0 0.7 - - - +
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Residues in contact with GLU 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A THR* 3.8 6.7 - - - +
475A LYS* 2.9 15.3 + - + +
477A LEU* 1.3 73.2 - - - +
479A ASP* 1.3 68.4 + - - +
481A VAL* 3.1 8.9 + - - +
482A TYR* 3.0 17.2 + - - +
551A HIS 5.3 1.8 - - - -
554A ARG* 4.8 5.7 - - - +
555A LEU* 2.3 60.6 + - + +
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Residues in contact with ASP 479 (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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445A PHE* 4.8 12.5 - - + -
475A LYS* 2.3 45.8 + - - +
476A LEU* 2.7 22.5 + - - +
478A GLU* 1.3 75.6 - - - +
480A LEU* 1.3 48.2 + - - +
482A TYR* 2.6 14.3 + - + +
483A PHE* 2.5 36.1 + - - +
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Residues in contact with LEU 480 (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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445A PHE* 4.6 8.9 - - + -
449A ALA* 4.7 3.6 - - + -
453A LEU* 4.0 17.5 - - + -
476A LEU* 2.8 33.5 + - + +
477A LEU* 2.5 52.5 - - + +
479A ASP* 1.3 70.5 - - - +
481A VAL* 1.3 68.3 + - - +
483A PHE* 3.6 11.4 - - + +
484A VAL* 2.9 25.3 + - - +
515A ILE* 4.7 17.9 - - + -
519A ILE* 5.0 8.7 - - + -
555A LEU 6.2 0.2 - - - -
559A VAL* 3.8 24.4 - - + +
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Residues in contact with VAL 481 (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 LEU 3.1 3.8 + - - +
478A GLU* 3.4 7.2 - - - +
480A LEU* 1.3 73.1 - - - +
482A TYR* 1.3 60.3 + - - +
484A VAL* 2.5 34.0 - - + +
485A THR* 5.2 1.0 - - - +
555A LEU* 2.8 43.3 - - + +
558A ARG* 2.9 39.3 - - + +
559A VAL* 3.6 4.1 - - - +
562A HIS* 5.9 0.4 - - + -
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Residues in contact with TYR 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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478A GLU 3.0 9.1 + - - +
479A ASP* 2.6 24.4 + - + +
481A VAL* 1.3 74.6 - - - +
483A PHE* 1.3 55.3 + - - +
484A VAL 2.7 11.1 + - - -
485A THR* 3.1 26.1 + - - +
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Residues in contact with PHE 483 (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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441A ARG 4.8 1.6 - - - -
442A ASP* 3.5 45.5 - - + -
445A PHE* 3.1 50.3 - + + -
446A ALA* 4.8 3.8 - - - -
479A ASP* 2.5 15.2 + - + +
480A LEU* 3.0 6.5 + - + +
482A TYR* 1.3 75.5 - - - +
484A VAL* 1.3 63.2 + - - +
485A THR 3.3 3.9 + - - -
506A ARG* 4.4 24.2 - - + +
509A LEU* 5.1 7.4 - - + -
515A ILE* 6.1 4.5 - - + -
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Residues in contact with VAL 484 (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 LEU 2.9 11.3 + - - +
481A VAL* 2.5 33.0 - - + +
482A TYR 2.7 4.0 + - - -
483A PHE* 1.3 83.3 - - - +
485A THR* 1.4 52.6 + - + +
502A PRO* 2.9 9.0 - - - +
506A ARG* 4.4 7.7 - - - +
507A GLN* 3.8 1.4 + - - -
558A ARG 4.8 0.4 - - - +
559A VAL* 3.8 12.6 - - + +
562A HIS* 2.2 71.6 + - + +
563A SER* 2.7 34.3 - - - +
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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