Contacts of the helix formed by residues 568 - 583 (chain B) in PDB entry 4A9C
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 LYS 568 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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563B THR* 3.8 12.8 - - + -
564B SER 3.3 27.1 - - - +
565B GLY* 3.5 9.3 + - - +
566B ASN 3.4 2.4 - - - -
567B GLU* 1.3 90.2 + - - +
569B THR* 1.3 61.5 + - - +
570B ALA* 3.4 2.5 - - - +
571B ARG* 3.4 42.2 + - + +
572B ARG* 3.3 31.0 + - - +
1732B B5F 5.1 20.2 - - + +
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Residues in contact with THR 569 (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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566B ASN 3.8 2.8 + - - -
567B GLU* 3.5 4.7 + - - -
568B LYS* 1.3 70.8 - - - +
570B ALA* 1.4 60.1 + - - +
572B ARG* 3.3 11.7 + - - +
573B ASN* 3.1 34.3 + - - +
610B TYR* 4.2 9.4 - - + -
636B GLN* 3.2 38.3 + - + +
640B GLU* 3.6 39.0 - - + +
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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 GLU 5.2 1.1 + - - +
568B LYS* 3.4 0.8 - - - +
569B THR* 1.4 79.2 - - - +
571B ARG* 1.4 55.6 + - - +
573B ASN* 3.5 11.1 + - - +
574B GLN* 3.1 26.5 + - - +
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Residues in contact with ARG 571 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563B THR* 3.9 23.5 - - + +
568B LYS* 3.4 49.7 + - + +
569B THR 3.3 0.4 - - - -
570B ALA* 1.4 74.5 - - - +
572B ARG* 1.4 54.9 + - - +
574B GLN* 3.2 9.1 + - + +
575B ASN* 2.8 43.6 + - - +
1732B B5F 4.1 13.8 + - - -
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Residues in contact with ARG 572 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562B LEU* 3.8 10.9 - - + +
563B THR 2.9 37.0 + - - +
564B SER 3.7 6.7 - - - -
565B GLY 2.7 30.3 + - - -
566B ASN 3.8 2.0 + - - -
568B LYS 3.3 11.3 + - - +
569B THR* 3.3 23.9 + - - +
571B ARG* 1.4 72.6 - - - +
573B ASN* 1.4 59.1 + - - +
575B ASN* 3.3 10.0 + - - +
576B TYR* 3.1 25.5 + - - +
608B LEU 3.3 25.6 - - - +
609B ASN 3.1 20.4 + - - -
610B TYR* 3.6 35.3 + - + +
611B ARG* 4.3 1.6 - - - +
636B GLN* 2.8 25.4 + - - -
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Residues in contact with ASN 573 (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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569B THR 3.1 21.2 + - - +
570B ALA* 3.6 12.0 - - - +
571B ARG 3.3 0.2 - - - -
572B ARG* 1.4 72.9 - - - +
574B GLN* 1.3 58.7 + - - +
576B TYR* 3.4 4.0 + - - +
577B LEU* 3.1 37.1 + - + +
610B TYR* 2.8 31.2 + - - -
640B GLU* 2.8 33.6 + - - +
645B LYS* 4.1 15.8 - - + +
646B VAL* 3.6 23.7 - - + +
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Residues in contact with GLN 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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570B ALA 3.1 14.4 + - - +
571B ARG* 3.2 14.1 + - + +
573B ASN* 1.3 72.9 - - - +
575B ASN* 1.4 60.5 + - - +
577B LEU* 3.4 19.4 + - - +
578B ASP* 2.9 61.5 + - - +
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Residues in contact with ASN 575 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532B THR* 3.5 35.9 + - + +
562B LEU* 3.7 16.7 - - + -
563B THR* 2.6 44.6 + - - -
571B ARG* 2.8 20.8 + - - +
572B ARG* 3.3 8.4 + - - +
574B GLN* 1.4 77.7 - - - +
576B TYR* 1.4 56.1 + - - +
578B ASP* 3.2 8.3 + - - +
579B ILE* 2.9 35.4 + - - +
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Residues in contact with TYR 576 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562B LEU* 4.5 7.7 - - + +
572B ARG 3.1 12.9 + - - +
573B ASN 3.6 6.3 - - - +
574B GLN 3.4 0.2 - - - -
575B ASN* 1.4 75.5 - - - +
577B LEU* 1.4 66.7 + - + +
579B ILE* 3.4 10.2 + - - +
580B LEU* 2.9 57.2 + - + +
596B SER* 5.4 0.9 - - - -
604B TRP* 3.6 28.7 - + - -
610B TYR* 4.9 0.7 - - - +
645B LYS 5.0 0.2 - - - -
646B VAL* 3.7 26.5 - - + -
647B PHE* 3.3 72.7 + + + -
648B LEU* 4.0 3.8 + - + -
650B PHE* 3.7 13.3 - - - -
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Residues in contact with LEU 577 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573B ASN* 3.1 27.6 + - + +
574B GLN* 3.7 24.2 - - - +
575B ASN 3.3 0.2 - - - -
576B TYR* 1.4 89.1 - - + +
578B ASP* 1.4 62.7 + - - +
580B LEU* 3.6 14.2 + - + +
581B ARG* 3.2 24.1 + - - +
645B LYS 4.7 13.5 - - - +
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Residues in contact with ASP 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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530B VAL* 4.6 0.4 - - - -
531B LYS 5.9 0.2 - - - +
532B THR* 4.5 12.8 - - + +
574B GLN* 2.9 46.0 + - - +
575B ASN* 3.2 9.7 + - - +
577B LEU* 1.4 74.5 - - - +
579B ILE* 1.4 55.4 + - - +
581B ARG* 3.3 3.3 + - - -
582B LEU* 2.8 58.5 + - + +
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Residues in contact with ILE 579 (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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530B VAL* 3.9 12.8 - - + -
532B THR* 3.8 19.3 - - + -
542B GLY 4.5 2.0 - - - -
543B ALA* 3.7 35.0 - - + -
558B VAL* 4.2 7.2 - - + -
560B CYS* 4.3 4.0 - - + -
562B LEU* 3.7 26.9 - - + -
575B ASN 2.9 23.0 + - - +
576B TYR* 3.8 6.1 - - - +
578B ASP* 1.4 74.2 - - - +
580B LEU* 1.3 63.0 + - - +
583B LEU* 3.1 44.4 + - + +
595B ILE* 4.3 0.3 - - - +
604B TRP* 3.6 23.6 - - + -
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Residues in contact with LEU 580 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576B TYR* 2.9 46.2 + - + +
577B LEU* 3.7 15.9 - - + +
579B ILE* 1.3 75.1 - - - +
581B ARG* 1.3 56.8 + - - +
583B LEU 4.9 0.3 + - - +
594B ASP* 3.3 42.8 - - - +
595B ILE* 3.5 34.8 + - + +
596B SER* 4.0 15.5 - - - +
604B TRP* 3.7 22.6 - - + -
650B PHE* 5.4 1.6 - - + -
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Residues in contact with ARG 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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577B LEU 3.2 16.7 + - - +
578B ASP* 3.9 4.5 - - - +
579B ILE 3.2 0.4 - - - -
580B LEU* 1.3 78.4 - - - +
582B LEU* 1.3 68.2 + - + +
583B LEU 3.5 4.1 + - - +
594B ASP* 5.2 3.8 - - - +
598B ARG* 5.6 3.8 + - - -
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Residues in contact with LEU 582 (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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528B SER* 5.2 0.2 + - - -
530B VAL* 3.6 26.3 - - + +
531B LYS 5.1 5.4 - - - +
578B ASP* 2.8 43.7 + - + +
581B ARG* 1.3 77.9 - - + +
583B LEU* 1.4 62.0 + - - +
584B SER* 3.4 6.9 + - - -
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Residues in contact with LEU 583 (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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528B SER* 3.7 35.7 - - - +
529B SER* 4.1 3.1 - - - +
530B VAL* 3.5 21.4 - - + +
543B ALA* 4.7 2.9 - - + +
544B VAL 5.0 1.1 - - - -
545B GLY* 4.4 7.2 - - - +
558B VAL* 3.9 28.3 - - + -
579B ILE* 3.1 30.3 + - + +
580B LEU 5.0 0.7 - - - +
581B ARG 3.5 5.1 - - - +
582B LEU* 1.4 73.6 - - - +
584B SER* 1.3 59.4 + - - +
585B LEU* 3.5 23.5 + - + -
595B ILE* 3.5 32.0 - - + +
598B ARG* 3.7 6.8 + - - -
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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