Contacts of the helix formed by residues 600 - 605 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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691A SER* 2.9 28.8 + - - +
692A ILE* 5.0 1.7 - - + +
596B THR* 2.9 26.6 + - + +
599B GLY* 1.3 77.9 - - - +
601B ARG* 1.3 60.8 + - - +
604B CYS* 3.1 29.9 + - - +
605B ASP* 3.5 3.3 + - - +
635B LEU* 3.9 17.3 - - + -
639B ASN* 3.3 27.6 - - - +
687B PRO* 3.8 18.8 - - + +
688B MET* 3.6 16.8 - - + -
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Residues in contact with ARG 601 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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691A SER* 3.7 14.6 - - - -
696A PHE* 3.8 10.9 - - - -
697A HIS* 3.3 18.0 + - - -
596B THR 3.1 10.5 + - - +
597B GLU* 3.6 12.1 - - - +
600B VAL* 1.3 73.8 - - - +
602B ASP* 1.3 69.0 + - - +
605B ASP* 3.0 63.1 + - - +
608B ARG* 3.6 5.2 - - - +
687B PRO* 3.7 30.5 - - + +
801B HEM 4.4 6.8 + - - +
802B H4B 3.0 43.4 + - - -
803B M4R 4.8 13.8 + - - -
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Residues in contact with ASP 602 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486B ARG* 4.9 1.0 + - - -
566B TRP* 3.2 37.7 + - + -
593B TYR* 3.9 9.2 + - - -
597B GLU 2.9 22.5 + - - +
598B ILE* 3.3 17.6 + - - +
601B ARG* 1.3 80.1 - - - +
603B TYR* 1.3 59.8 + - + +
608B ARG* 3.0 39.5 + - - +
609B TYR* 3.4 31.5 + - - -
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Residues in contact with TYR 603 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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522B PHE* 4.9 4.7 - + - -
551B ILE* 3.7 12.2 - - + +
564B LEU* 4.4 15.0 - - + -
565B LYS 2.6 36.0 + - - -
566B TRP* 3.4 31.2 - + - +
598B ILE* 2.9 30.9 + - + +
599B GLY* 3.9 9.9 - - - +
600B VAL 4.2 0.2 + - - -
602B ASP* 1.3 84.3 - - + +
604B CYS* 1.3 58.2 + - - +
605B ASP 3.8 0.2 - - - -
609B TYR* 3.5 17.2 - + + +
610B ASN 2.8 26.4 + - - -
611B ILE* 3.0 39.3 + - + +
638B ILE* 4.1 13.0 - - + -
642B VAL* 4.2 10.5 - - + -
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Residues in contact with CYS 604 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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692A ILE* 4.5 11.4 - - + +
599B GLY 3.4 19.3 - - - -
600B VAL 3.1 15.3 + - - +
603B TYR* 1.3 80.6 - - - +
605B ASP* 1.3 70.1 + - - +
606B ASN* 3.4 6.6 + - - +
610B ASN* 4.5 6.8 - - - +
611B ILE* 4.5 0.4 - - - -
612B LEU* 3.7 40.1 - - + +
635B LEU* 3.6 21.1 - - + -
638B ILE* 3.7 15.9 - - - -
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Residues in contact with ASP 605 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312A GLU* 5.2 1.3 - - - +
691A SER* 4.4 7.6 + - - +
692A ILE* 6.1 0.6 - - - +
697A HIS* 3.8 17.1 + - + -
600B VAL 3.5 2.3 + - - +
601B ARG* 3.0 69.6 + - - +
604B CYS* 1.3 80.0 - - - +
606B ASN* 1.3 65.0 + - - +
607B SER* 4.1 8.2 + - - +
608B ARG* 3.0 31.8 + - + +
610B ASN* 3.6 14.2 + - - -
803B M4R 5.8 1.4 - - - -
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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