Contacts of the helix formed by residues 599 - 610 (chain A) in PDB entry 4AYT
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 THR 599 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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597A SER 4.2 7.2 - - - +
598A VAL* 1.3 76.0 - - - +
600A ALA* 1.3 64.0 + - - +
601A GLU* 3.7 16.7 + - - +
602A GLU* 2.8 50.3 + - - +
603A ILE* 3.3 13.1 + - - +
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Residues in contact with ALA 600 (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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598A VAL 4.1 0.2 + - - -
599A THR* 1.3 71.6 - - - +
601A GLU* 1.4 61.4 + - - +
603A ILE* 3.4 13.1 + - - +
604A GLN* 2.9 33.9 + - - +
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Residues in contact with GLU 601 (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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599A THR* 3.7 15.1 - - - +
600A ALA* 1.4 86.2 + - - +
602A GLU* 1.4 58.6 + - + +
604A GLN* 3.5 9.1 + - - +
605A ARG* 2.9 29.3 + - - +
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Residues in contact with GLU 602 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597A SER 3.9 3.5 - - - +
598A VAL* 3.6 20.2 - - + +
599A THR* 2.8 47.5 + - - +
601A GLU* 1.4 73.2 - - + +
603A ILE* 1.4 64.0 + - - +
605A ARG* 3.4 13.2 + - - +
606A VAL* 3.3 28.8 + - - +
649A LEU* 4.1 16.2 - - + +
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Residues in contact with ILE 603 (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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585A ALA* 3.9 29.6 - - + +
588A ILE* 3.9 34.0 - - + +
589A ALA* 4.2 12.6 - - + +
598A VAL* 4.3 22.7 - - + +
599A THR 3.3 15.3 + - - +
600A ALA* 3.7 10.1 - - - +
602A GLU* 1.4 74.1 - - - +
604A GLN* 1.4 62.2 + - - +
606A VAL* 3.3 9.8 - - - +
607A ALA* 3.2 23.0 + - - +
623A PHE* 3.9 16.8 - - + -
649A LEU* 5.0 2.7 - - + -
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Residues in contact with GLN 604 (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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600A ALA 2.9 18.0 + - - +
601A GLU* 3.8 9.7 - - - +
603A ILE* 1.4 75.4 - - - +
605A ARG* 1.3 64.7 + - - +
607A ALA* 3.5 6.5 + - - +
608A GLU* 2.8 50.5 + - - +
613A VAL* 4.5 5.8 - - + -
617A ARG* 3.5 24.8 + - - +
623A PHE* 4.4 11.9 - - + -
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Residues in contact with ARG 605 (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 GLU 2.9 18.5 + - - +
602A GLU* 3.6 11.5 + - - +
603A ILE 3.4 0.4 - - - -
604A GLN* 1.3 74.6 - - - +
606A VAL* 1.3 83.5 + - - +
608A GLU* 3.0 31.7 + - - +
609A VAL* 3.2 34.1 + - + +
648A LEU* 4.4 15.4 + - - +
649A LEU* 5.3 1.4 - - - +
651A ASN* 5.4 2.8 + - - -
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Residues in contact with VAL 606 (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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588A ILE* 3.6 26.0 - - + -
602A GLU 3.4 13.5 - - - +
603A ILE* 3.3 16.8 - - - +
605A ARG* 1.3 101.4 - - - +
607A ALA* 1.4 54.8 + - - +
609A VAL* 4.4 2.7 - - - -
610A ALA* 2.9 32.9 + - - +
645A ALA* 3.6 13.9 - - + +
648A LEU* 3.4 27.0 - - + +
649A LEU* 3.8 19.3 - - + +
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Residues in contact with ALA 607 (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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588A ILE* 4.5 3.6 - - + -
603A ILE 3.2 20.7 + - - +
604A GLN 3.7 6.1 - - - +
605A ARG 3.2 0.2 - - - -
606A VAL* 1.4 73.2 - - - +
608A GLU* 1.3 58.9 + - - +
611A ASN 3.5 1.0 + - - -
612A ALA* 2.8 36.7 + - - +
613A VAL* 2.8 13.2 + - + -
616A ILE* 4.1 10.1 - - + -
623A PHE* 3.7 27.8 - - + -
645A ALA* 4.6 5.2 - - - -
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Residues in contact with GLU 608 (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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604A GLN* 2.8 43.1 + - - +
605A ARG* 3.0 16.7 + - - +
607A ALA* 1.3 77.1 - - - +
609A VAL* 1.4 59.2 + - + +
611A ASN* 3.1 27.4 + - - +
613A VAL* 3.9 25.9 - - + +
617A ARG* 3.6 8.9 + - - +
678A ARG* 3.7 1.7 + - - -
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Residues in contact with VAL 609 (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 ARG* 3.2 37.9 + - + +
606A VAL* 4.5 0.2 - - - -
608A GLU* 1.4 77.0 - - + +
610A ALA* 1.4 55.5 + - - +
611A ASN 3.2 1.0 + - - -
648A LEU* 3.7 27.8 - - + -
675A ALA* 3.9 4.5 - - - +
678A ARG* 2.7 54.0 + - + +
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Residues in contact with ALA 610 (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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606A VAL 2.9 19.5 + - - +
607A ALA 3.9 2.7 + - - +
608A GLU 3.4 0.2 - - - -
609A VAL* 1.4 73.7 - - - +
611A ASN* 1.4 67.1 + - - +
612A ALA* 3.3 1.8 - - + +
641A ARG* 3.3 39.1 - - - +
644A ILE* 3.7 10.8 - - + -
645A ALA* 3.6 17.5 - - + +
648A LEU* 4.0 1.1 - - + -
675A ALA* 3.3 19.5 - - - +
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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