Contacts of the helix formed by residues 567 - 581 (chain B) in PDB entry 1SY7
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566B TYR* 1.3 72.1 - - - +
568B ASN* 1.3 66.1 + - - +
569B VAL* 3.0 25.6 + - - +
570B ALA* 3.1 27.0 + - - +
571B TYR* 3.2 21.3 + - - +
598B ALA* 5.0 4.9 - - - -
623B PRO* 3.9 2.8 - - - +
624B GLY* 2.9 34.2 + - - +
625B GLY* 4.1 3.6 - - - +
655B THR* 5.0 0.5 + - - -
691B VAL* 5.1 9.9 - - - +
696B PHE* 5.2 0.5 - - - -
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Residues in contact with ASN 568 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566B TYR* 3.3 12.5 + - + -
567B ASP* 1.3 73.3 - - - +
569B VAL* 1.3 75.0 + - - +
571B TYR* 3.9 7.2 - - + -
572B ASP* 2.9 48.8 + - - +
597B ALA* 3.9 4.7 - - + -
598B ALA* 5.6 1.1 - - - +
599B ASN* 3.0 48.5 + - - +
601B SER* 3.9 8.8 + - - +
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Residues in contact with VAL 569 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567B ASP* 3.0 15.8 + - - +
568B ASN* 1.3 88.5 - - - +
570B ALA* 1.3 66.8 + - - +
572B ASP* 3.3 5.6 + - - +
573B ALA* 3.0 23.1 + - + +
691B VAL* 5.4 5.8 - - + -
696B PHE* 4.4 17.3 - - + -
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Residues in contact with ALA 570 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567B ASP* 3.1 17.3 + - - +
569B VAL* 1.3 80.3 - - - +
571B TYR* 1.3 61.7 + - - +
573B ALA* 3.5 1.2 + - - +
574B ALA* 3.0 26.9 + - - +
621B PHE* 3.8 7.3 - - + -
623B PRO* 3.9 12.3 - - + -
655B THR* 3.4 24.7 - - - +
691B VAL* 5.5 0.4 - - + -
696B PHE* 3.6 25.3 - - + -
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Residues in contact with TYR 571 (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 ILE* 3.8 29.4 - - + +
562B ILE* 3.9 15.9 - - + -
566B TYR* 3.7 27.6 - + + -
567B ASP 3.2 16.6 + - - +
568B ASN* 3.6 4.9 - - + +
569B VAL 3.1 0.2 - - - -
570B ALA* 1.3 80.2 - - - +
572B ASP* 1.3 74.5 + - - +
574B ALA* 3.9 1.2 - - - +
575B TYR* 2.9 56.1 + + + +
587B VAL* 3.4 23.7 - - + +
603B VAL* 3.4 31.9 - - + +
621B PHE* 4.7 4.7 - - - -
623B PRO* 4.0 8.2 - - + +
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Residues in contact with ASP 572 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568B ASN* 2.9 37.5 + - - +
569B VAL* 3.8 5.2 - - - +
571B TYR* 1.3 95.0 - - - +
573B ALA* 1.3 62.4 + - - +
575B TYR* 3.8 3.4 - - - +
576B ALA* 3.1 26.5 + - - +
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Residues in contact with ALA 573 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569B VAL* 3.0 16.9 + - + +
570B ALA 3.7 3.6 - - - +
571B TYR 3.3 0.2 - - - -
572B ASP* 1.3 78.3 - - - +
574B ALA* 1.3 61.1 + - - +
576B ALA* 3.6 3.9 + - - +
577B ALA* 3.1 24.8 + - - +
696B PHE* 3.6 39.3 - - + +
710B LEU* 3.9 6.7 - - + +
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Residues in contact with ALA 574 (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 ILE* 4.9 1.8 - - + -
570B ALA 3.0 18.1 + - - +
571B TYR 4.0 1.8 - - - +
573B ALA* 1.3 73.6 - - - +
575B TYR* 1.3 61.3 + - - +
577B ALA* 3.2 1.2 + - - +
578B ILE* 2.8 45.0 + - + +
621B PHE* 3.5 34.3 - - + -
696B PHE* 5.8 0.4 - - + -
710B LEU* 4.2 20.1 - - + +
713B PHE* 6.1 1.1 - - + -
714B PHE* 6.2 0.2 - - + -
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Residues in contact with TYR 575 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560B ILE* 3.9 22.6 - - + +
571B TYR* 2.9 41.1 + + + +
572B ASP* 3.8 6.1 - - - +
574B ALA* 1.3 76.3 - - - +
576B ALA* 1.3 63.1 + - - +
578B ILE* 3.8 4.0 - - - +
579B SER* 3.1 36.5 + - - -
585B PRO* 3.6 25.8 - - + +
587B VAL* 3.8 22.0 - - + -
606B HIS* 3.9 17.9 + - - -
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Residues in contact with ALA 576 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572B ASP 3.1 19.0 + - - +
573B ALA* 4.0 3.6 - - - +
575B TYR* 1.3 78.7 - - - +
577B ALA* 1.3 58.5 + - - +
579B SER* 3.4 5.1 + - - -
580B ALA* 2.8 33.1 + - - +
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Residues in contact with ALA 577 (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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573B ALA 3.1 18.2 + - - +
574B ALA 3.7 2.2 - - - +
576B ALA* 1.3 74.2 - - - +
578B ILE* 1.3 66.0 + - - +
580B ALA* 4.4 3.1 - - - -
581B ASN* 2.6 35.9 + - - +
700B VAL* 4.8 6.7 - - + -
710B LEU* 3.6 23.6 - - + -
714B PHE* 3.4 17.1 - - + -
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Residues in contact with ILE 578 (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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558B VAL* 3.7 32.5 - - + -
560B ILE* 4.0 21.1 - - + -
574B ALA* 2.8 31.9 + - + +
575B TYR 3.8 3.8 - - - +
577B ALA* 1.3 76.9 - - - +
579B SER* 1.3 61.4 + - - +
581B ASN* 3.2 7.1 + - - -
583B ALA* 3.0 49.2 + - + +
584B ILE 3.9 2.5 - - - +
585B PRO* 3.7 27.4 - - + -
621B PHE* 5.5 0.4 - - + -
713B PHE* 5.4 2.2 - - + -
714B PHE* 3.9 23.1 - - + -
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Residues in contact with SER 579 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575B TYR* 3.1 25.5 + - - -
576B ALA* 3.7 5.4 - - - -
578B ILE* 1.3 80.2 - - - +
580B ALA* 1.3 57.2 + - - +
582B GLN* 3.1 22.3 + - - -
583B ALA 3.8 9.5 - - - +
585B PRO* 3.8 17.7 - - - +
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Residues in contact with ALA 580 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576B ALA 2.8 22.7 + - - +
577B ALA* 4.0 6.3 - - - +
578B ILE 3.3 0.4 - - - -
579B SER* 1.3 72.1 - - - +
581B ASN* 1.3 63.0 + - - +
582B GLN* 3.1 18.1 + - - +
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Residues in contact with ASN 581 (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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552B THR* 5.2 0.3 + - - -
553B ILE* 3.6 31.9 + - + +
554B LYS* 4.0 5.2 + - - -
577B ALA* 2.6 30.9 + - - +
578B ILE 3.8 0.7 - - - +
579B SER 3.1 1.4 - - - -
580B ALA* 1.3 83.9 + - - +
582B GLN* 1.3 78.3 + - - +
583B ALA 3.2 2.5 + - - -
700B VAL* 4.3 15.7 - - - +
702B ILE* 4.0 17.1 - - + +
714B PHE* 3.5 17.3 - - - -
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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
------------------------------------------------------------
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