Contacts of the helix formed by residues 656 - 666 (chain A) in PDB entry 3APO
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 656 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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597A GLU* 3.5 17.7 - - - +
654A ASN* 3.2 16.5 - - - +
655A ARG* 1.3 81.3 - - - +
657A ALA* 1.3 63.9 + - - +
658A TYR* 3.4 12.9 + - - +
659A SER* 2.9 43.6 + - - -
660A LEU* 3.1 20.8 + - - +
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Residues in contact with ALA 657 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597A GLU* 3.0 34.0 + - - +
600A ARG* 3.7 23.3 - - + +
601A MET* 3.8 21.4 - - + +
656A ASP* 1.3 71.7 - - - +
658A TYR* 1.3 66.4 + - + +
660A LEU* 3.2 3.7 + - - +
661A ARG* 2.8 32.7 + - - +
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Residues in contact with TYR 658 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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656A ASP* 3.4 9.9 + - - +
657A ALA* 1.3 80.7 - - + +
659A SER* 1.3 64.4 + - - +
661A ARG* 3.4 13.8 + - - +
662A SER* 2.9 26.2 + - - -
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Residues in contact with SER 659 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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650A TYR* 3.9 9.2 + - - -
654A ASN* 3.5 31.9 + - - +
656A ASP* 2.9 30.3 + - - -
658A TYR* 1.3 76.1 - - - +
660A LEU* 1.3 59.4 + - - +
662A SER* 3.6 5.4 - - - -
663A TRP* 2.9 28.8 + - - +
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Residues in contact with LEU 660 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580A MET* 3.7 10.8 - - + +
594A LEU* 3.7 20.2 - - + -
597A GLU* 5.1 2.5 - - + +
598A TRP* 4.0 13.5 - - + -
601A MET* 3.4 20.6 - - - -
634A ILE* 4.0 14.8 - - + -
650A TYR* 3.7 42.6 - - + -
655A ARG* 3.4 27.8 - - - +
656A ASP 3.1 13.7 + - - +
657A ALA* 3.9 2.5 - - - +
659A SER* 1.3 73.6 - - - +
661A ARG* 1.3 67.5 + - - +
663A TRP* 3.2 5.9 + - + +
664A GLY* 2.9 19.6 + - - -
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Residues in contact with ARG 661 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601A MET* 3.9 16.4 - - + +
604A THR* 2.5 58.4 + - + +
605A LEU* 4.1 16.8 - - + +
608A LEU* 4.4 2.6 - - - +
657A ALA 2.8 22.1 + - - +
658A TYR* 3.7 14.1 - - + +
660A LEU* 1.3 72.0 - - - +
662A SER* 1.3 58.5 + - - +
664A GLY* 3.2 0.7 + - - -
665A LEU* 2.9 41.1 + - + +
709A GLU* 2.9 42.2 + - - -
712A LEU* 3.4 21.2 - - - +
767A ASP* 4.6 7.6 + - - -
768A ALA* 4.9 0.8 - - - +
769A LYS* 6.3 0.6 - - - +
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Residues in contact with SER 662 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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658A TYR 2.9 19.3 + - - -
659A SER* 3.6 5.4 - - - -
661A ARG* 1.3 75.7 - - - +
663A TRP* 1.3 64.1 + - - +
665A LEU* 3.6 4.7 + - - -
666A GLY* 3.0 18.2 + - - -
704A GLN 4.8 0.2 + - - -
705A ASN* 3.1 35.1 + - - -
708A PRO* 3.5 20.4 - - - +
709A GLU 5.5 0.4 + - - +
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Residues in contact with TRP 663 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580A MET* 3.8 22.7 - - + -
634A ILE* 3.7 16.4 - - + -
635A ARG 4.6 0.4 - - - -
636A PHE* 3.7 21.3 - - + -
648A HIS* 3.5 19.1 - - + -
649A SER 3.7 6.0 + - - -
650A TYR* 3.3 72.6 - + + +
659A SER 2.9 17.5 + - - +
660A LEU* 3.6 5.2 - - + +
662A SER* 1.3 76.0 - - - +
664A GLY* 1.3 61.6 + - - +
666A GLY* 3.4 8.7 + - - -
667A PHE* 3.3 43.0 - + - -
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Residues in contact with GLY 664 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580A MET* 4.0 12.8 - - - -
609A ILE* 3.6 18.1 - - - +
636A PHE* 3.6 22.0 - - - -
660A LEU 2.9 13.4 + - - -
661A ARG 3.7 2.2 - - - -
663A TRP* 1.3 75.5 - - - +
665A LEU* 1.3 61.7 + - - +
666A GLY 3.0 5.8 + - - -
667A PHE* 3.1 13.8 + - - +
668A LEU* 4.1 2.4 + - - +
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Residues in contact with LEU 665 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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605A LEU* 4.0 20.2 - - + -
608A LEU* 4.6 5.6 - - + -
609A ILE* 3.9 1.5 - - + +
661A ARG* 2.9 58.9 + - + +
662A SER* 4.7 1.6 - - - +
664A GLY* 1.3 75.0 - - - +
666A GLY* 1.3 59.5 + - - +
668A LEU* 3.2 43.4 + - + +
708A PRO* 3.7 24.4 - - + +
709A GLU* 3.6 15.3 - - - +
711A GLU* 5.7 1.0 - - - +
712A LEU* 4.1 19.3 - - + -
715A ARG* 4.3 8.3 + - - +
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Residues in contact with GLY 666 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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662A SER 3.0 16.1 + - - -
663A TRP* 3.7 5.6 - - - -
664A GLY 3.0 1.8 - - - -
665A LEU* 1.3 76.7 - - - +
667A PHE* 1.3 61.7 + - - +
668A LEU 4.1 4.1 - - - +
708A PRO* 3.5 15.7 - - - +
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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