Contacts of the helix formed by residues 553 - 567 (chain J) 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 553 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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551J LEU 2.8 17.7 + - - +
552J SER* 1.3 70.6 - - - +
554J PRO* 1.4 65.3 - - - +
555J ALA 3.4 2.5 - - - +
556J LYS* 3.5 7.1 + - - +
557J LYS* 3.1 12.8 + - - -
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Residues in contact with PRO 554 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552J SER 3.1 6.0 - - - +
553J ASN* 1.4 67.2 - - - +
555J ALA* 1.3 54.0 + - - +
556J LYS 3.0 2.7 - - - -
557J LYS* 2.6 23.1 + - - +
558J PHE* 2.7 17.2 + - - -
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Residues in contact with ALA 555 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553J ASN 3.4 1.0 - - - -
554J PRO* 1.3 74.8 - - - +
556J LYS* 1.3 58.6 + - - +
558J PHE* 3.7 1.8 + - - +
559J LYS* 3.4 18.5 + - - -
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Residues in contact with LYS 556 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551J LEU 5.4 0.7 - - - -
553J ASN* 3.5 7.8 + - - +
554J PRO 3.0 0.4 - - - -
555J ALA* 1.3 75.4 - - - +
557J LYS* 1.3 64.4 + - - +
558J PHE 3.4 0.3 + - - -
559J LYS* 3.7 1.5 + - - +
560J ILE* 3.5 17.3 + - - -
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Residues in contact with LYS 557 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551J LEU 4.7 4.6 + - - -
553J ASN 3.1 10.6 + - - -
554J PRO* 2.6 14.6 + - - -
556J LYS* 1.3 73.9 - - - +
558J PHE* 1.3 58.5 + - - +
560J ILE* 3.8 1.9 + - - -
561J GLU* 3.6 13.7 + - - -
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Residues in contact with PHE 558 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554J PRO 2.7 16.1 + - - -
555J ALA* 4.1 2.2 - - - +
557J LYS* 1.3 68.3 - - - +
559J LYS* 1.3 64.1 + - - +
560J ILE 3.2 1.8 - - - -
561J GLU* 3.1 4.4 + - - +
562J ALA* 3.1 18.4 + - - -
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Residues in contact with LYS 559 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555J ALA 3.4 15.1 + - - -
556J LYS* 3.7 2.2 + - - +
558J PHE* 1.3 73.1 - - - +
560J ILE* 1.3 57.0 - - - +
562J ALA* 3.2 1.9 + - - +
563J ASN* 3.0 29.6 + - - -
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Residues in contact with ILE 560 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556J LYS 3.5 12.1 + - - -
557J LYS 4.2 4.0 - - - -
558J PHE 3.2 1.2 - - - -
559J LYS* 1.3 76.6 - - - +
561J GLU* 1.3 59.3 + - - +
564J ALA* 3.7 16.5 + - - +
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Residues in contact with GLU 561 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557J LYS 3.6 8.8 + - - -
558J PHE* 3.1 7.5 + - - +
560J ILE* 1.3 75.7 - - - +
562J ALA* 1.3 65.8 - - - +
564J ALA* 3.8 0.5 + - - -
565J GLY* 3.3 14.4 + - - -
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Residues in contact with ALA 562 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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558J PHE 3.1 12.7 + - - -
559J LYS* 3.2 2.9 + - - +
561J GLU* 1.3 73.0 - - - +
563J ASN* 1.3 52.0 + - - +
565J GLY* 2.7 8.8 + - - -
566J GLN* 2.5 35.0 + - - -
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Residues in contact with ASN 563 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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559J LYS 3.0 14.3 + - - -
562J ALA* 1.3 73.6 - - - +
564J ALA* 1.3 55.8 + - - +
566J GLN* 4.1 4.0 - - - +
567J LEU* 2.9 27.9 + - - -
569J LEU 5.1 0.2 + - - -
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Residues in contact with ALA 564 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560J ILE 3.7 17.9 + - - -
561J GLU 4.2 0.9 - - - -
562J ALA 3.0 1.4 + - - -
563J ASN* 1.3 77.0 - - - +
565J GLY* 1.3 59.1 + - - +
568J TYR* 3.6 2.3 + - - -
569J LEU* 3.2 40.0 + - - +
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Residues in contact with GLY 565 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561J GLU 3.3 10.1 + - - -
562J ALA* 2.7 12.2 + - - -
564J ALA* 1.3 72.1 - - - +
566J GLN* 1.3 62.0 + - - +
568J TYR* 3.8 7.1 + - - -
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Residues in contact with GLN 566 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533J LEU 4.9 5.9 - - - +
562J ALA 2.5 19.4 + - - -
563J ASN* 3.7 4.0 - - - +
565J GLY* 1.3 75.4 - - - +
567J LEU* 1.3 58.0 + - - +
568J TYR 3.8 0.3 + - - -
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Residues in contact with LEU 567 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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534J LYS* 2.3 33.1 - - - +
563J ASN 2.9 14.0 + - - -
566J GLN* 1.3 76.3 - - - +
568J TYR* 1.3 57.7 + - - +
569J LEU* 3.2 3.6 + - - +
590J ALA* 5.4 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