Contacts of the helix formed by residues 603 - 609 (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 ASP 603 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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601A THR* 2.6 24.7 + - - +
602A MET* 1.3 72.5 - - - +
604A LEU* 1.3 59.8 + - - +
605A PRO* 3.4 2.9 - - - -
606A GLU* 3.3 27.4 + - + +
607A ARG* 3.0 52.9 + - - +
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Residues in contact with LEU 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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476A TYR* 3.5 12.1 - - - +
568A LEU* 4.2 8.7 - - + +
569A ASP* 3.2 34.1 - - - +
572A VAL* 4.0 12.6 - - + -
579A MET* 3.9 19.0 - - + +
599A ALA* 3.8 20.0 - - + -
601A THR* 3.7 10.0 - - + +
602A MET 3.4 0.6 - - - -
603A ASP* 1.3 80.2 + - - +
605A PRO* 1.3 62.8 - - - +
607A ARG* 3.6 22.0 - - - +
608A GLN* 3.4 42.6 + - + +
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Residues in contact with PRO 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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476A TYR* 3.5 30.7 - - + +
579A MET* 3.7 21.8 - - + -
583A PHE* 4.8 4.0 - - + -
602A MET 3.9 7.2 - - - +
603A ASP 3.7 3.1 - - - -
604A LEU* 1.3 86.8 - - + +
606A GLU* 1.3 57.4 + - - +
609A LEU* 3.0 37.0 + - + +
614A THR* 3.3 9.2 - - + +
619A PHE* 3.6 35.4 - - + -
621A ARG* 4.2 6.5 - - - +
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Residues in contact with GLU 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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602A MET 5.4 0.4 - - - +
603A ASP* 3.3 30.3 - - + +
605A PRO* 1.3 77.3 - - + +
607A ARG* 1.3 81.9 + - - +
610A GLY* 3.4 27.9 + - - +
611A ASN* 3.9 23.2 + - - +
614A THR* 4.1 7.2 - - - +
621A ARG* 5.4 7.4 - - - +
534B GLN* 3.9 4.0 + - - -
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Residues in contact with ARG 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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569A ASP* 5.2 0.6 + - - -
601A THR* 3.4 27.0 - - - +
603A ASP* 3.0 41.4 + - - +
604A LEU* 3.6 22.6 - - - +
606A GLU* 1.3 91.5 - - - +
608A GLN* 1.3 66.5 + - + +
534B GLN* 2.9 23.9 + - - +
538B ASN* 3.4 27.1 + - - +
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Residues in contact with GLN 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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572A VAL* 3.6 22.5 + - + +
576A GLN* 3.3 49.0 - - + +
579A MET* 4.5 10.3 - - + -
604A LEU* 3.4 41.1 + - + +
605A PRO 4.5 0.2 - - - +
607A ARG* 1.3 86.7 - - + +
609A LEU* 1.3 63.8 + - + +
534B GLN* 4.1 8.1 - - - +
535B ASN* 4.4 2.8 - - - +
538B ASN* 3.1 30.9 + - - +
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Residues in contact with LEU 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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576A GLN* 4.0 15.0 - - - +
579A MET* 4.5 10.8 - - + +
580A TYR* 3.7 41.3 - - + +
583A PHE* 4.0 28.9 - - + -
605A PRO* 3.0 15.4 + - + +
608A GLN* 1.3 83.6 - - + +
610A GLY* 1.3 58.1 + - - +
613A ILE* 3.4 40.6 - - + +
614A THR* 4.0 20.6 - - + -
617A ILE* 4.2 4.7 - - + -
531B THR* 5.9 2.4 - - - +
534B GLN* 4.1 8.9 - - - +
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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