Contacts of the helix formed by residues 567 - 580 (chain 2) 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 ASP 567 (chain 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5652 ASP 3.9 0.4 + - - -
5662 ILE* 1.3 70.2 - - - +
5682 TYR* 1.3 57.5 + - - +
5692 GLN* 3.2 3.8 - - - +
5702 LYS* 2.6 32.2 + - - +
5712 LEU 3.3 3.5 + - - -
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Residues in contact with TYR 568 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5662 ILE 3.5 6.4 + - - -
5672 ASP* 1.3 68.7 - - - +
5692 GLN* 1.3 66.0 + - - +
5712 LEU* 3.1 12.2 + - - +
5722 HIS* 3.4 7.4 + - - -
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Residues in contact with GLN 569 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5672 ASP 3.2 0.8 - - - -
5682 TYR* 1.3 76.5 - - - +
5702 LYS* 1.3 61.6 + - - +
5722 HIS* 2.9 15.5 + - - +
5732 ASP* 3.1 9.2 + - - -
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Residues in contact with LYS 570 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5672 ASP* 2.6 21.7 + - - +
5692 GLN* 1.3 69.5 - - - +
5712 LEU* 1.3 54.8 + - - +
5732 ASP* 3.2 3.3 + - - +
5742 ALA* 2.9 25.8 + - - -
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Residues in contact with LEU 571 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11261 PHE 4.0 22.6 - - - +
11271 THR* 4.9 8.3 - - - +
5672 ASP 3.3 5.9 + - - -
5682 TYR* 3.1 10.3 + - - +
5702 LYS* 1.3 74.5 - - - +
5722 HIS* 1.3 58.0 + - - +
5742 ALA* 3.2 2.6 + - - +
5752 PHE* 2.9 25.6 + - - -
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Residues in contact with HIS 572 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5682 TYR 3.4 6.4 + - - -
5692 GLN* 2.9 8.8 + - - +
5712 LEU* 1.3 75.3 - - - +
5732 ASP* 1.3 56.0 + - - +
5752 PHE* 3.2 3.1 + - - +
5762 PHE* 2.9 25.6 + - - -
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Residues in contact with ASP 573 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5692 GLN 3.1 11.0 + - - -
5702 LYS* 3.2 4.7 + - - +
5722 HIS* 1.3 76.7 - - - +
5742 ALA* 1.3 55.8 + - - +
5762 PHE* 3.2 3.1 + - - +
5772 LYS* 2.9 25.1 + - - -
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Residues in contact with ALA 574 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11261 PHE 5.9 0.4 - - - -
5272 PHE 5.6 5.8 - - - -
5702 LYS 2.9 14.5 + - - -
5712 LEU* 3.2 4.4 + - - +
5732 ASP* 1.3 75.4 - - - +
5752 PHE* 1.3 57.4 + - - +
5772 LYS* 3.2 2.6 + - - +
5782 TRP* 2.9 25.5 + - - -
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Residues in contact with PHE 575 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11261 PHE* 5.4 4.8 + - - +
5712 LEU 2.9 14.3 + - - -
5722 HIS* 3.2 4.9 + - - +
5742 ALA* 1.3 76.6 - - - +
5762 PHE* 1.3 55.4 + - - +
5782 TRP* 3.2 2.8 + - - +
5792 GLN* 2.9 25.5 + - - -
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Residues in contact with PHE 576 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5722 HIS 2.9 13.4 + - - -
5732 ASP* 3.2 4.4 + - - +
5752 PHE* 1.3 77.4 - - - +
5772 LYS* 1.3 55.4 + - - +
5792 GLN* 3.2 3.0 + - - +
5802 THR* 2.9 25.5 + - - -
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Residues in contact with LYS 577 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5732 ASP 2.9 14.2 + - - -
5742 ALA* 3.6 3.6 - - - +
5762 PHE* 1.3 75.0 - - - +
5782 TRP* 1.3 62.7 + - - +
5802 THR* 3.2 16.5 + - - +
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Residues in contact with TRP 578 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11641 ASP* 5.1 14.8 - - - +
5742 ALA 2.9 14.0 + - - -
5752 PHE* 3.2 4.0 + - - +
5772 LYS* 1.3 77.6 - - - +
5792 GLN* 1.3 60.6 + - - +
5802 THR 3.4 3.6 + - - -
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Residues in contact with GLN 579 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11641 ASP* 5.9 2.9 - - - +
5752 PHE 2.9 14.0 + - - -
5762 PHE* 3.2 4.2 + - - +
5782 TRP* 1.3 75.2 - - - +
5802 THR* 1.3 67.1 + - - +
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Residues in contact with THR 580 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5762 PHE 2.9 13.7 + - - -
5772 LYS* 3.2 14.1 + - - +
5782 TRP 4.2 3.4 - - - -
5792 GLN* 1.3 81.4 - - - +
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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