Contacts of the helix formed by residues 564 - 578 (chain N) 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 ALA 564 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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560N ARG* 2.0 46.8 + - - +
561N ALA* 4.3 0.3 - - - -
563N TYR* 1.3 67.0 - - - +
565N TYR* 1.3 58.2 + - - +
566N ALA 3.4 2.5 - - - +
567N LEU* 4.1 3.1 - - - +
568N GLN* 2.8 29.0 + - - +
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Residues in contact with TYR 565 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560N ARG 2.8 4.0 + - - -
561N ALA* 4.1 10.5 + - - +
563N TYR 3.0 9.5 + - - -
564N ALA* 1.3 76.0 - - - +
566N ALA* 1.3 61.0 + - - +
569N VAL* 4.0 12.3 + - - -
640N ASN* 4.7 15.5 - - - +
643N GLU* 5.8 4.5 - - - +
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Residues in contact with ALA 566 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564N ALA* 3.4 0.4 - - - +
565N TYR* 1.3 76.4 - - - +
567N LEU* 1.3 61.9 + - - +
570N PHE* 3.7 15.8 + - - -
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Residues in contact with LEU 567 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525N VAL* 6.0 4.8 - - - -
564N ALA* 3.8 5.6 + - - +
566N ALA* 1.3 75.1 - - - +
568N GLN* 1.3 56.8 + - - +
570N PHE* 3.7 1.2 - - - +
571N PRO* 2.8 31.9 - - - +
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Residues in contact with GLN 568 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525N VAL* 6.5 0.9 - - - +
557N GLU* 5.0 17.4 - - - +
560N ARG* 5.0 3.6 - - - +
561N ALA* 5.4 0.7 - - - +
564N ALA* 2.8 25.8 + - - +
566N ALA 3.5 0.4 - - - -
567N LEU* 1.3 70.4 - - - +
569N VAL* 1.3 57.5 + - - +
571N PRO* 3.1 4.7 - - - +
572N SER* 2.8 23.7 + - - -
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Residues in contact with VAL 569 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565N TYR 4.0 11.0 + - - -
568N GLN* 1.3 74.3 - - - +
570N PHE* 1.3 52.4 + - - +
572N SER* 3.3 3.7 - - - +
573N LYS* 2.5 34.7 + - - -
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Residues in contact with PHE 570 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566N ALA 3.7 13.5 + - - -
567N LEU* 3.4 5.4 + - - +
568N GLN 3.2 1.0 - - - -
569N VAL* 1.3 78.4 - - - +
571N PRO* 1.3 58.3 - - - +
573N LYS* 3.7 6.8 + - - +
574N LYS 3.9 7.4 + - - -
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Residues in contact with PRO 571 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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567N LEU 2.8 18.5 - - - +
568N GLN 3.5 4.0 - - - +
570N PHE* 1.3 73.0 - - - +
572N SER* 1.3 60.9 + - - +
574N LYS* 3.9 2.3 + - - -
575N SER* 3.4 15.9 + - - -
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Residues in contact with SER 572 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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568N GLN 2.8 13.2 + - - -
569N VAL* 3.1 6.5 + - - +
571N PRO* 1.3 77.1 - - - +
573N LYS* 1.3 64.6 + - - +
574N LYS 3.3 0.4 - - - -
575N SER* 3.0 11.4 + - - +
576N VAL* 3.0 13.3 + - - -
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Residues in contact with LYS 573 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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569N VAL 2.5 20.1 + - - -
570N PHE* 3.7 4.6 + - - +
571N PRO 3.4 0.6 - - - -
572N SER* 1.3 75.6 - - - +
574N LYS* 1.3 57.5 + - - +
576N VAL* 4.0 0.7 + - - -
577N TRP* 3.8 12.5 + - - -
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Residues in contact with LYS 574 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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570N PHE 3.9 7.7 + - - -
571N PRO 3.9 5.2 + - - -
572N SER 3.3 0.2 - - - -
573N LYS* 1.3 74.2 - - - +
575N SER* 1.3 58.8 + - - +
577N TRP* 3.9 3.7 - - - +
578N LEU* 3.0 23.6 + - - -
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Residues in contact with SER 575 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571N PRO 3.4 12.4 + - - -
572N SER* 3.0 8.9 + - - +
574N LYS* 1.3 76.3 - - - +
576N VAL* 1.3 63.7 + - - +
578N LEU* 3.2 11.6 + - - +
579N ARG* 3.3 10.2 + - - -
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Residues in contact with VAL 576 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572N SER 3.0 12.8 + - - -
573N LYS 4.0 1.1 + - - -
575N SER* 1.3 75.2 - - - +
577N TRP* 1.3 58.7 + - - +
579N ARG* 3.6 10.9 + - - +
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Residues in contact with TRP 577 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573N LYS 3.8 11.3 + - - -
574N LYS* 3.7 6.0 + - - +
575N SER 3.2 0.6 - - - -
576N VAL* 1.3 72.3 - - - +
578N LEU* 1.3 59.2 + - - +
579N ARG 3.2 11.3 + - - +
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Residues in contact with LEU 578 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574N LYS 3.0 18.1 + - - -
575N SER* 3.2 5.7 + - - +
577N TRP* 1.3 72.3 - - - +
579N ARG* 1.3 65.7 + - - +
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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