Contacts of the helix formed by residues 610 - 618 (chain A) in PDB entry 5ZR1
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 GLY 610 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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605A PRO 3.8 0.2 + - - -
606A GLU* 3.4 21.5 + - - +
608A GLN 3.7 0.6 - - - -
609A LEU* 1.3 79.1 - - - +
611A ASN* 1.3 61.6 + - - -
612A LYS* 3.6 2.9 - - - -
613A ILE* 4.3 2.7 - - - -
614A THR* 2.8 27.9 + - - +
534B GLN* 3.7 19.5 - - - -
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Residues in contact with ASN 611 (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 GLU* 3.9 25.0 + - - +
610A GLY* 1.3 77.4 - - - -
612A LYS* 1.3 63.2 - - - +
613A ILE 3.4 0.4 - - - -
614A THR* 3.4 5.1 + - - -
615A SER* 3.3 23.7 + - - -
534B GLN* 4.8 4.6 + - - +
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Residues in contact with LYS 612 (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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610A GLY* 6.0 0.4 - - - -
611A ASN* 1.3 78.9 - - - +
613A ILE* 1.3 80.7 + - + +
615A SER* 3.0 18.7 + - - -
616A ARG* 3.3 17.9 + - - +
527B LEU* 4.8 13.3 - - + +
530B GLU* 5.3 8.7 - - - +
562B LEU* 5.2 8.3 + - - +
565B ALA* 6.3 0.8 - - - +
566B ASP* 3.8 26.7 + - - -
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Residues in contact with ILE 613 (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 TYR* 3.7 32.5 - - + -
609A LEU* 3.4 40.6 - - + +
610A GLY 4.2 1.6 + - - -
611A ASN 3.4 0.2 - - - -
612A LYS* 1.3 94.7 - - + +
614A THR* 1.3 59.6 + - - +
616A ARG* 3.0 27.1 + - - +
617A ILE* 3.2 27.7 + - + +
531B THR* 5.7 5.4 - - + -
558B LEU* 5.9 1.8 - - + -
562B LEU* 3.9 31.0 - - + -
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Residues in contact with THR 614 (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 PRO* 3.3 40.8 - - + +
606A GLU* 4.1 6.4 - - - +
609A LEU* 4.0 14.1 - - + -
610A GLY 2.8 25.0 + - - +
611A ASN* 3.4 8.0 + - - -
613A ILE* 1.3 74.4 - - - +
615A SER* 1.3 59.7 + - - +
617A ILE* 4.2 7.2 - - - -
618A GLY* 4.0 12.6 + - - -
619A PHE* 4.0 19.4 + - + -
621A ARG* 4.8 7.8 + - - -
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Residues in contact with SER 615 (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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611A ASN 3.3 16.8 + - - -
612A LYS* 3.0 17.7 + - - -
614A THR* 1.3 75.7 - - - +
616A ARG* 1.3 63.0 + - - +
617A ILE 3.4 0.7 - - - -
618A GLY* 4.0 8.7 + - - -
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Residues in contact with ARG 616 (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 TYR* 3.4 22.1 + - - -
584A ASN* 2.8 41.2 + - - +
587A THR* 3.8 24.6 + - - +
612A LYS* 3.3 15.9 + - - +
613A ILE* 3.0 15.8 + - - +
615A SER* 1.3 81.7 + - - +
617A ILE* 1.3 72.6 + - - +
565B ALA* 4.8 22.2 - - - +
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Residues in contact with ILE 617 (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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474A THR* 4.5 3.4 - - - +
580A TYR* 5.6 2.0 - - + -
583A PHE* 3.6 50.3 - - + +
584A ASN 5.1 0.2 - - - +
586A THR* 4.2 7.6 - - - +
587A THR* 4.0 18.0 - - + +
609A LEU* 4.2 11.2 - - + -
613A ILE* 3.2 34.5 + - + +
614A THR* 4.3 3.8 - - - +
615A SER 3.4 0.4 - - - -
616A ARG* 1.3 86.7 - - - +
618A GLY* 1.3 63.2 + - - +
619A PHE* 3.7 28.9 - - + +
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Residues in contact with GLY 618 (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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473A THR* 5.2 4.3 + - - -
474A THR 5.7 0.2 + - - -
614A THR 4.0 9.6 + - - -
615A SER 4.0 8.0 + - - -
616A ARG 3.5 1.6 - - - -
617A ILE* 1.3 81.9 - - - +
619A PHE* 1.3 62.7 + - - +
620A THR* 4.2 1.0 + - - +
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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