Contacts of the helix formed by residues 482 - 495 (chain D) in PDB entry 6AH0
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 482 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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461D LEU* 6.3 0.2 - - - -
480D THR 4.0 1.4 + - - -
481D LEU* 1.3 72.9 - - - +
483D ARG* 1.3 56.5 + - - +
484D ILE 3.2 2.5 - - - -
485D GLN* 3.1 8.0 + - - +
486D SER* 2.6 34.1 + - - -
507D ALA 5.7 4.5 - - - -
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Residues in contact with ARG 483 (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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461D LEU* 6.1 4.9 - - - +
481D LEU 3.7 1.2 + - - -
482D ASN* 1.3 71.1 - - - +
484D ILE* 1.3 56.1 + - - +
486D SER* 3.5 2.4 + - - +
487D LYS* 2.9 22.5 + - - -
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Residues in contact with ILE 484 (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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482D ASN 3.2 0.2 - - - -
483D ARG* 1.3 72.6 - - - +
485D GLN* 1.3 60.7 + - - +
486D SER 3.1 0.9 - - - -
487D LYS* 2.8 18.8 + - - +
488D LEU* 3.0 12.5 + - - -
507D ALA 5.9 2.1 + - - -
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Residues in contact with GLN 485 (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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481D LEU* 5.9 0.7 - - - -
482D ASN* 3.1 11.5 + - - +
484D ILE* 1.3 73.6 - - - +
486D SER* 1.3 57.4 + - - +
488D LEU 3.8 0.5 - - - -
489D TYR* 3.0 30.5 + - - -
507D ALA 5.7 3.2 + - - -
511D ASN 6.2 0.7 - - - -
512D VAL* 5.5 12.1 - - - +
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Residues in contact with SER 486 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461D LEU* 5.9 2.5 - - - +
462D LEU* 5.1 13.7 - - - +
481D LEU* 4.9 5.1 - - - +
482D ASN 2.6 20.7 + - - +
483D ARG* 3.6 4.3 - - - +
485D GLN* 1.3 69.1 - - - +
487D LYS* 1.3 65.5 + - - +
489D TYR* 4.2 4.2 + - - +
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Residues in contact with LYS 487 (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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483D ARG 2.9 12.1 + - - -
484D ILE* 2.8 11.5 + - - +
486D SER* 1.3 80.5 - - - +
488D LEU* 1.3 57.4 + - - +
489D TYR 3.8 0.3 + - - -
490D ARG* 4.7 2.8 + - - -
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Residues in contact with LEU 488 (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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484D ILE 3.0 11.6 + - - -
485D GLN 3.8 1.3 - - - -
487D LYS* 1.3 76.2 - - - +
489D TYR* 1.3 64.5 + - - +
490D ARG 3.1 4.2 + - - -
491D ALA* 3.2 6.3 + - - +
492D ALA* 3.0 19.1 + - - -
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Residues in contact with TYR 489 (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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485D GLN 3.0 16.5 + - - -
486D SER* 4.2 3.6 + - - +
487D LYS 3.6 2.2 - - - -
488D LEU* 1.3 75.7 - - - +
490D ARG* 1.3 60.5 + - - +
492D ALA* 3.1 2.8 + - - +
493D LEU* 2.9 22.9 + - - -
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Residues in contact with ARG 490 (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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486D SER 5.5 0.6 + - - -
487D LYS 4.7 2.6 + - - -
488D LEU 3.1 1.6 + - - -
489D TYR* 1.3 75.1 - - - +
491D ALA* 1.3 56.8 + - - +
494D GLU* 2.9 30.1 + - - -
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Residues in contact with ALA 491 (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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488D LEU* 3.2 8.0 + - - +
490D ARG* 1.3 72.9 - - - +
492D ALA* 1.3 65.7 + - - +
494D GLU 5.3 0.4 - - - -
495D THR* 3.6 22.4 + - - +
497D GLU 5.2 3.1 - - - +
671D LYS 6.0 2.2 - - - -
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Residues in contact with ALA 492 (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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488D LEU 3.0 14.2 + - - -
489D TYR* 3.1 6.4 + - - +
491D ALA* 1.3 81.1 - - - +
493D LEU* 1.3 58.0 + - - +
495D THR 3.9 8.1 - - - +
515D MET 4.9 1.7 - - - +
516D CYS* 4.4 24.2 - - - +
519D ARG* 5.7 1.4 - - - -
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Residues in contact with LEU 493 (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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489D TYR 2.9 13.9 + - - -
490D ARG 4.2 0.2 - - - -
492D ALA* 1.3 73.8 - - - +
494D GLU* 1.3 60.8 + - - +
495D THR 3.6 0.6 + - - -
515D MET 5.3 6.5 - - - -
519D ARG* 5.3 11.5 - - - +
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Residues in contact with GLU 494 (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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490D ARG 2.9 17.9 + - - -
491D ALA* 5.3 0.7 - - - -
493D LEU* 1.3 79.4 - - - +
495D THR* 1.3 55.7 + - - +
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Residues in contact with THR 495 (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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491D ALA* 3.6 20.6 + - - +
492D ALA 3.9 7.3 - - - +
493D LEU 3.6 1.6 - - - -
494D GLU* 1.3 80.0 - - - +
496D ASP* 1.3 60.0 + - - +
497D GLU 3.1 11.7 + - - +
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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