Contacts of the helix formed by residues 465 - 482 (chain A) in PDB entry 2ADS
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 465 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A GLU* 1.3 76.2 - - - +
466A LEU* 1.3 59.3 + - - +
467A LYS* 2.8 56.4 + - - +
468A PHE* 3.0 34.0 + - + +
469A VAL 3.4 6.9 + - - -
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Residues in contact with LEU 466 (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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368A ARG 6.2 0.2 - - - +
371A GLU* 6.5 0.9 - - + -
372A PHE* 4.1 8.7 - - + -
375A GLU* 4.6 22.2 - - - +
461A LEU* 3.6 46.9 - - + +
464A GLU 3.4 1.8 + - - -
465A ASN* 1.3 75.9 - - - +
467A LYS* 1.3 64.2 + - + +
469A VAL* 3.4 6.8 + - - +
470A LEU* 3.0 25.9 + - - +
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Residues in contact with LYS 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A GLU* 5.4 2.2 - - - +
465A ASN* 2.8 26.0 + - - +
466A LEU* 1.3 75.4 - - + +
468A PHE* 1.3 68.9 + - + +
470A LEU* 3.5 9.3 - - + +
471A LEU* 3.1 37.5 + - + +
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Residues in contact with PHE 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A GLU* 2.8 48.3 - - + +
465A ASN* 3.0 15.0 + - + -
467A LYS* 1.3 82.7 - - + +
469A VAL* 1.3 59.7 + - - +
471A LEU* 4.8 5.8 - - + -
472A ASN* 2.9 36.1 + - - +
670A PHE* 6.4 2.7 - + - -
2G C 4.4 0.3 - - - +
21M G 4.1 59.9 - + - +
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Residues in contact with VAL 469 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A PHE* 3.6 22.7 - - + -
456A ILE* 5.6 1.1 - - + -
460A THR* 3.6 34.3 - - + +
461A LEU* 3.9 12.1 - - + -
464A GLU* 3.1 31.9 - - + +
465A ASN 3.6 13.7 - - - +
466A LEU* 3.4 7.2 + - - +
467A LYS 3.2 1.2 - - - -
468A PHE* 1.3 72.6 - - - +
470A LEU* 1.3 56.6 + - - +
473A VAL* 3.0 46.9 + - + +
2G C 4.2 5.4 - - + +
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Residues in contact with LEU 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A PHE* 3.6 14.3 - - + -
375A GLU* 3.5 56.1 - - + +
376A LEU* 3.6 15.8 - - + +
379A PHE* 4.0 20.6 - - + -
466A LEU 3.0 17.6 + - - +
467A LYS* 3.5 8.5 - - + +
469A VAL* 1.3 74.1 - - - +
471A LEU* 1.3 70.8 + - + +
473A VAL* 3.9 0.5 - - - +
474A ALA* 2.9 36.6 + - + +
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Residues in contact with LEU 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A PHE* 3.4 40.6 - - + -
383A LYS* 5.2 2.1 + - - -
467A LYS* 3.1 28.8 + - + +
468A PHE* 4.8 6.1 - - + +
470A LEU* 1.3 88.0 - - + +
472A ASN* 1.3 67.6 + - - +
474A ALA* 3.8 3.2 - - - +
475A GLU* 3.5 17.7 + - - +
670A PHE* 3.7 42.2 - - + -
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Residues in contact with ASN 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A PHE* 2.9 30.2 + - - +
470A LEU 3.1 0.6 - - - -
471A LEU* 1.3 88.8 - - - +
473A VAL* 1.3 64.6 + - - +
474A ALA 3.1 1.1 - - - -
475A GLU* 3.2 20.4 - - - +
476A GLN* 2.9 16.9 + - - -
669A SER* 4.1 1.8 + - - -
670A PHE* 4.1 18.4 - - - +
671A GLN* 3.0 38.9 + - - +
2G C 3.5 30.3 + - - +
21M G 4.4 4.6 + - - +
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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
----------------------------------------------------------
372A PHE* 4.7 5.6 - - + -
376A LEU* 4.4 15.5 - - + -
454A GLN* 3.6 15.4 - - + +
456A ILE* 3.9 27.1 - - + -
469A VAL* 3.0 32.0 + - + +
470A LEU 4.1 0.9 - - - +
472A ASN* 1.3 73.9 - - - +
474A ALA* 1.3 63.0 + - - +
476A GLN* 3.1 18.7 + - - +
477A VAL* 3.1 11.9 + - + +
2G C 3.5 42.2 - - - +
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Residues in contact with ALA 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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376A LEU* 5.2 4.6 - - + +
379A PHE* 3.5 36.1 - - + -
380A LEU* 3.9 16.3 - - + +
470A LEU* 2.9 21.7 + - + +
471A LEU 3.8 0.9 - - - +
473A VAL* 1.3 74.6 - - - +
475A GLU* 1.3 62.4 + - - +
477A VAL* 3.2 8.8 + - - +
478A LEU* 3.0 30.0 + - - +
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Residues in contact with GLU 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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340A LEU* 5.0 2.6 - - + +
383A LYS* 5.6 0.9 - - - +
471A LEU 3.5 9.3 + - - +
472A ASN* 3.2 15.7 + - - +
474A ALA* 1.3 78.7 - - - +
476A GLN* 1.3 60.1 + - - +
478A LEU* 3.4 11.4 + - + +
479A ALA* 2.9 30.4 + - + +
485A PRO* 4.8 9.8 - - + +
666A ASN 4.9 0.8 - - - +
667A TYR* 2.6 36.0 - - + +
668A SER 3.0 5.4 - - - +
669A SER* 2.7 38.4 + - - +
671A GLN* 3.2 23.6 + - - +
673A ILE* 4.6 0.7 - - - +
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Residues in contact with GLN 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A GLN* 3.2 19.4 - - - +
472A ASN 2.9 21.1 + - - +
473A VAL* 3.1 10.5 + - - +
475A GLU* 1.3 78.3 - - + +
477A VAL* 1.3 58.1 + - - +
479A ALA* 4.1 5.6 - - + -
480A LYS* 2.9 51.3 + - - +
671A GLN* 4.8 5.4 - - - +
706A LEU* 4.4 13.0 - - + +
1G A 2.8 25.0 + - - -
2G C 3.2 39.0 - - - +
3G C 4.2 4.3 + - - +
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Residues in contact with VAL 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A LEU* 4.7 8.3 - - + -
376A LEU* 4.9 11.4 - - + -
380A LEU* 3.9 25.1 - - + -
385A ILE* 5.1 1.6 - - + -
387A LEU* 4.3 7.2 - - + -
419A LEU* 3.6 35.4 - - + -
421A ILE* 5.3 1.1 - - + -
454A GLN* 3.5 25.8 - - + +
473A VAL 3.1 11.7 + - - +
474A ALA* 3.2 9.2 + - - +
476A GLN* 1.3 74.9 - - - +
478A LEU* 1.3 63.1 + - - +
479A ALA 3.2 0.9 + - - -
480A LYS* 4.3 0.8 - - - +
481A THR* 2.9 28.4 + - - +
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Residues in contact with LEU 478 (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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345A PRO* 4.0 21.8 - - + -
352A LEU* 6.3 0.2 - - - -
380A LEU* 3.5 22.7 - - + -
383A LYS* 3.4 35.0 - - + +
385A ILE* 3.9 28.0 - - + -
474A ALA 3.0 19.8 + - - +
475A GLU* 3.6 12.1 - - + +
477A VAL* 1.3 73.8 - - - +
479A ALA* 1.3 59.1 + - - +
481A THR* 3.3 5.4 + - - -
483A ASN* 3.0 39.7 + - - +
485A PRO* 4.6 18.6 - - + -
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Residues in contact with ALA 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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475A GLU* 2.9 18.8 + - + +
476A GLN* 3.8 6.5 - - + +
478A LEU* 1.3 75.4 - - - +
480A LYS* 1.3 60.8 + - - +
482A GLY* 3.1 19.1 + - - -
485A PRO* 4.6 2.2 - - + -
666A ASN 4.4 3.1 - - - +
667A TYR* 3.3 38.0 - - + -
703A MSE 3.9 14.6 - - - +
706A LEU* 3.7 16.6 - - + -
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Residues in contact with LYS 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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419A LEU* 5.7 0.7 - - + -
452A PRO* 3.8 17.4 - - + +
453A SER 3.8 30.3 - - - +
454A GLN* 3.8 13.2 - - + +
476A GLN* 2.9 43.7 + - - +
477A VAL* 4.4 2.2 - - - +
479A ALA* 1.3 75.1 - - - +
481A THR* 1.3 62.2 + - - +
482A GLY* 3.5 0.7 + - - -
702A ILE* 4.0 8.3 - - - +
703A MSE 3.3 41.8 + - - +
704A TYR* 3.3 20.6 - - - +
706A LEU* 2.9 32.7 + - + +
1G A 3.7 12.7 + - - -
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Residues in contact with THR 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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348A LYS* 4.7 8.3 + - - +
352A LEU* 3.9 30.1 - - + +
418A ASP 4.2 8.1 - - - +
419A LEU* 4.3 12.3 - - + -
452A PRO* 4.1 19.1 - - + -
477A VAL 2.9 19.3 + - - +
478A LEU* 3.3 5.2 + - - -
480A LYS* 1.3 73.5 - - - +
482A GLY* 1.3 60.4 + - - +
483A ASN* 3.0 29.1 + - - +
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Residues in contact with GLY 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A PHE* 4.3 2.1 - - - +
348A LYS* 3.2 28.6 + - - +
478A LEU 3.4 0.4 + - - -
479A ALA 3.1 17.6 + - - -
480A LYS 4.4 1.1 - - - -
481A THR* 1.3 80.2 + - - +
483A ASN* 1.3 54.5 + - - +
484A ILE* 2.7 33.7 + - - +
703A MSE 4.7 7.9 - - - -
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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