Contacts of the helix formed by residues 453 - 463 (chain w) 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 GLU 453 (chain w).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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451w GLN* 3.3 1.8 - - - +
452w ILE* 1.3 76.8 - - - +
454w ASP* 1.3 57.8 + - - +
456w VAL* 2.8 23.7 + - - -
457w SER 3.6 3.6 + - - -
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Residues in contact with ASP 454 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4632 ALA* 5.3 16.4 - - - +
4642 GLU* 5.4 5.5 - - - +
4672 GLN* 6.1 0.5 - - - -
451w GLN* 4.1 4.4 + - - +
452w ILE 3.6 0.4 - - - -
453w GLU* 1.3 74.8 - - - +
455w ALA* 1.3 58.5 + - - +
456w VAL 3.1 0.5 + - - -
457w SER* 3.2 4.6 + - - +
458w LEU* 3.0 22.0 + - - -
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Residues in contact with ALA 455 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451w GLN 4.4 7.1 + - - -
452w ILE 3.9 4.8 + - - -
453w GLU 3.3 1.0 - - - -
454w ASP* 1.3 75.9 - - - +
456w VAL* 1.3 58.1 + - - +
457w SER 3.5 0.2 - - - -
458w LEU* 3.6 4.9 - - - +
459w TRP* 2.9 22.9 + - - -
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Residues in contact with VAL 456 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452w ILE 3.8 6.9 + - - -
453w GLU 2.8 12.1 + - - -
455w ALA* 1.3 75.8 - - - +
457w SER* 1.3 58.4 + - - +
459w TRP* 3.2 2.1 + - - +
460w ALA* 2.9 23.2 + - - -
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Residues in contact with SER 457 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4672 GLN* 5.9 0.7 - - - -
453w GLU 3.6 4.4 + - - -
454w ASP* 3.2 6.6 + - - +
456w VAL* 1.3 73.5 - - - +
458w LEU* 1.3 60.5 + - - +
460w ALA* 3.3 3.0 + - - +
461w LYS* 2.9 23.7 + - - -
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Residues in contact with LEU 458 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4662 LYS 5.6 1.1 - - - -
4672 GLN* 4.7 19.0 - - - +
454w ASP 3.0 14.6 + - - -
455w ALA* 3.8 6.3 - - - +
456w VAL 3.2 0.2 - - - -
457w SER* 1.3 77.4 - - - +
459w TRP* 1.3 55.6 + - - +
461w LYS* 3.1 4.5 + - - +
462w LEU* 2.9 21.5 + - - -
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Residues in contact with TRP 459 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440w ILE* 6.0 5.6 - - - +
455w ALA 2.9 18.8 + - - -
456w VAL* 3.2 3.1 + - - +
458w LEU* 1.3 71.8 - - - +
460w ALA* 1.3 60.5 + - - +
462w LEU* 3.1 3.9 + - - +
463w LYS* 2.9 25.1 + - - +
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Residues in contact with ALA 460 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456w VAL 2.9 15.2 + - - -
457w SER* 3.3 4.9 + - - +
458w LEU 3.3 0.2 - - - -
459w TRP* 1.3 75.0 - - - +
461w LYS* 1.3 62.4 + - - +
463w LYS 3.3 21.8 - - - +
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Residues in contact with LYS 461 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4672 GLN 6.1 1.1 - - - -
457w SER 2.9 14.0 + - - -
458w LEU* 3.1 6.4 + - - +
460w ALA* 1.3 76.6 - - - +
462w LEU* 1.3 61.4 + - - +
463w LYS 5.1 0.2 - - - -
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Residues in contact with LEU 462 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458w LEU 2.9 13.1 + - - -
459w TRP* 3.1 5.7 + - - +
461w LYS* 1.3 79.9 - - - +
463w LYS* 1.3 56.2 + - - +
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Residues in contact with LYS 463 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459w TRP 2.9 11.9 + - - +
460w ALA* 3.3 21.7 - - - -
461w LYS 5.1 0.2 - - - -
462w LEU* 1.3 78.3 - - - +
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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