Contacts of the helix formed by residues 600 - 605 (chain A) in PDB entry 5UO5
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 VAL 600 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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596A THR* 2.9 23.0 + - + +
599A GLY* 1.3 78.9 - - - +
601A ARG* 1.3 62.3 + - - +
604A CYS* 3.1 28.3 + - - +
605A ASP* 3.3 5.9 + - - +
635A LEU* 3.8 19.1 - - + -
639A ASN* 3.3 27.8 - - - +
687A PRO* 3.9 17.5 - - + +
688A MET* 3.8 16.2 - - + -
691B SER* 3.0 27.8 - - - +
692B ILE* 4.7 3.3 - - + +
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Residues in contact with ARG 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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596A THR 3.2 12.3 + - - +
597A GLU* 3.7 12.6 - - - +
600A VAL* 1.3 74.2 - - - +
602A ASP* 1.3 69.2 + - - +
605A ASP* 3.0 59.6 + - - +
608A ARG* 3.6 7.9 - - - +
687A PRO* 3.7 19.1 - - + -
801A HEM 4.5 6.5 + - - +
802A H4B 3.2 41.0 + - - -
803A M4R 5.6 7.5 + - - -
691B SER* 3.6 23.7 - - - -
696B PHE* 3.8 14.3 - - - -
697B HIS* 3.5 16.8 + - - -
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Residues in contact with ASP 602 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A ARG* 5.2 0.2 + - - -
566A TRP* 3.3 43.1 + - + -
593A TYR* 4.2 6.1 + - - -
597A GLU* 2.9 22.8 + - - +
598A ILE* 3.2 21.2 + - - +
601A ARG* 1.3 77.7 - - - +
603A TYR* 1.3 60.2 + - + +
608A ARG* 3.1 45.9 + - - +
609A TYR* 3.3 16.8 + - - -
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Residues in contact with TYR 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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522A PHE* 5.1 3.4 - + - -
551A ILE* 3.5 15.3 - - + +
564A LEU* 4.0 20.9 - - + -
565A LYS 2.9 31.7 + - - -
566A TRP* 3.5 30.6 - + - +
598A ILE* 3.1 30.9 + - + +
599A GLY 4.2 7.9 - - - +
602A ASP* 1.3 83.2 - - + +
604A CYS* 1.3 58.9 + - - +
605A ASP 3.7 0.4 - - - -
609A TYR* 3.5 13.6 - + + -
610A ASN 2.7 26.5 + - - -
611A ILE* 2.9 38.5 + - + +
638A ILE* 4.0 13.5 - - + -
642A VAL* 4.1 13.0 - - + -
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Residues in contact with CYS 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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599A GLY 3.4 19.1 - - - -
600A VAL 3.1 15.7 + - - +
603A TYR* 1.3 82.3 - - - +
605A ASP* 1.3 66.1 + - - +
606A ASN* 3.4 7.4 + - - +
610A ASN* 4.5 5.5 - - - +
611A ILE* 4.4 1.3 - - - +
612A LEU* 3.6 46.1 - - + +
635A LEU* 3.7 14.8 - - + -
638A ILE* 3.6 19.5 - - - -
692B ILE* 4.4 12.9 - - + +
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Residues in contact with ASP 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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600A VAL 3.3 2.0 + - - +
601A ARG* 3.0 66.3 + - - +
603A TYR 3.7 0.2 - - - -
604A CYS* 1.3 79.0 - - - +
606A ASN* 1.3 64.7 + - - +
607A SER* 4.2 8.0 + - - +
608A ARG* 3.1 31.3 + - + +
610A ASN* 3.4 15.0 + - - -
312B GLU* 5.5 0.9 - - - +
691B SER* 4.4 7.7 + - - +
692B ILE* 6.1 0.3 - - - +
697B HIS* 3.7 18.0 + - - -
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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