Contacts of the helix formed by residues 555 - 565 (chain B) in PDB entry 6AHU
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 555 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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326B GLN* 5.6 1.6 + - - -
551B SER 5.6 0.4 + - - -
552B PHE* 3.7 28.7 + - - +
553B ILE 3.3 2.1 - - - +
554B TRP* 1.3 83.8 - - - +
556B GLN* 1.3 64.5 + - - +
557B ASP 4.8 0.2 - - - +
558B ILE* 3.4 40.3 - - + +
559B CYS* 3.3 23.4 + - - +
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Residues in contact with GLN 556 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254B GLU* 4.5 21.4 + - - +
256B LYS* 5.5 6.1 - - - +
326B GLN* 6.0 1.1 - - - +
423B SER* 5.2 6.9 + - - -
554B TRP 5.0 4.0 - - - +
555B ASN* 1.3 74.4 - - - +
557B ASP* 1.3 64.8 + - - +
559B CYS* 4.1 2.5 - - - +
560B LYS* 3.3 35.7 + - - +
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Residues in contact with ASP 557 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555B ASN* 4.8 0.6 - - - +
556B GLN* 1.3 77.6 - - - +
558B ILE* 1.3 69.5 + - + +
560B LYS* 3.5 15.0 + - - +
561B SER* 3.4 19.8 + - - -
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Residues in contact with ILE 558 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466B TRP* 3.7 47.6 - - + -
552B PHE* 3.7 29.2 - - + +
555B ASN* 3.4 38.1 + - + +
556B GLN 3.3 0.4 - - - -
557B ASP* 1.3 81.4 - - + +
559B CYS* 1.3 62.7 + - - +
561B SER* 2.5 24.5 + - - -
562B VAL* 3.2 10.9 + - + +
596B PRO* 6.3 0.4 - - + -
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Residues in contact with CYS 559 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428B GLU* 5.0 15.7 - - - -
429B MET* 5.2 11.2 - - - -
553B ILE* 4.6 15.9 - - + +
555B ASN 3.3 20.9 + - - +
556B GLN* 4.1 3.1 - - - +
557B ASP 3.4 0.4 - - - -
558B ILE* 1.3 76.7 - - - +
560B LYS* 1.3 63.4 + - - +
562B VAL* 3.4 20.3 + - - +
563B THR* 3.5 10.3 + - - -
623B PRO* 4.0 30.7 - - - -
624B LYS* 4.7 6.0 + - - -
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Residues in contact with LYS 560 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397B LYS* 6.1 2.7 - - - +
428B GLU* 5.7 4.5 - - - +
556B GLN* 3.3 24.4 + - - +
557B ASP* 3.7 18.4 - - - +
558B ILE 3.2 0.4 - - - -
559B CYS* 1.3 78.1 - - - +
561B SER* 1.3 56.8 + - - +
563B THR* 3.1 7.8 + - - -
564B GLU* 2.8 31.3 + - - +
624B LYS* 5.2 6.7 - - - +
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Residues in contact with SER 561 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464B HIS* 4.9 0.2 - - - -
466B TRP* 3.5 31.6 + - - -
557B ASP* 3.4 8.9 + - - -
558B ILE* 2.5 23.9 + - - -
560B LYS* 1.3 75.5 - - - +
562B VAL* 1.3 64.0 + - - +
564B GLU* 3.6 25.4 + - - +
565B ASN* 3.5 20.6 + - - +
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Residues in contact with VAL 562 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464B HIS* 5.6 1.2 - - - -
466B TRP* 4.4 11.7 - - + -
553B ILE* 6.2 2.0 - - + -
558B ILE* 3.2 18.1 + - + +
559B CYS* 3.5 15.5 - - - +
560B LYS 3.2 0.8 - - - -
561B SER* 1.3 79.4 - - - +
563B THR* 1.3 58.9 + - - +
564B GLU 3.7 0.3 + - - -
565B ASN* 4.3 11.4 + - - +
566B LYS 5.2 0.7 + - - -
567B ILE* 6.1 0.5 - - - +
595B ILE* 3.8 29.2 - - + -
596B PRO* 5.6 2.9 - - + -
623B PRO* 4.2 21.3 - - + -
625B GLY* 6.0 0.6 - - - +
626B TRP* 3.4 39.7 + - + +
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Residues in contact with THR 563 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396B ILE* 3.8 29.2 - - + +
559B CYS* 3.5 7.9 + - - -
560B LYS* 3.1 7.6 + - - -
562B VAL* 1.3 76.8 - - - +
564B GLU* 1.3 63.3 + - - +
565B ASN 3.2 4.0 + - - -
566B LYS* 3.5 21.3 + - - +
623B PRO* 4.8 1.4 - - - +
624B LYS* 3.5 42.3 + - - +
625B GLY* 4.0 17.8 + - - -
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Residues in contact with GLU 564 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560B LYS* 2.8 15.7 + - + +
561B SER* 3.8 23.2 + - - +
562B VAL 3.4 0.8 - - - -
563B THR* 1.3 79.3 - - - +
565B ASN* 1.3 64.7 + - - +
566B LYS* 3.4 13.3 + - - +
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Residues in contact with ASN 565 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463B PRO* 5.7 4.5 - - - +
464B HIS* 3.1 42.5 + - - +
561B SER 3.5 16.6 + - - +
562B VAL 4.4 7.2 + - - +
563B THR 3.2 0.8 - - - -
564B GLU* 1.3 80.7 - - - +
566B LYS* 1.3 69.0 + - - +
567B ILE* 4.4 17.4 - - + +
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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