Contacts of the helix formed by residues 603 - 609 (chain B) in PDB entry 4UN5
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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598B LEU* 4.2 5.8 - - - +
601B ILE* 3.4 15.7 - - + +
602B LYS* 1.3 78.8 - - - +
604B LYS* 1.3 64.5 + - - +
605B ASP* 3.5 11.8 + - - +
606B PHE* 3.0 41.4 + - + +
607B LEU* 3.3 14.5 + - - +
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Residues in contact with LYS 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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550B ASP* 4.9 4.5 + - - +
554B LYS* 3.8 29.9 + - - +
555B THR* 5.2 5.2 - - - +
594B TYR* 2.9 29.0 + - + +
598B LEU* 4.0 23.3 - - + +
602B LYS 4.2 0.4 - - - -
603B ASP* 1.3 73.2 + - - +
605B ASP* 1.3 64.1 + - - +
607B LEU* 3.1 7.6 + - - +
608B ASP* 2.9 50.2 + - - +
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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
----------------------------------------------------------
603B ASP* 3.2 9.1 + - - +
604B LYS* 1.3 84.8 - - - +
606B PHE* 1.3 62.1 + - - +
608B ASP* 3.9 7.3 - - - +
609B ASN* 3.1 24.3 + - - +
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Residues in contact with PHE 606 (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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601B ILE* 3.6 18.6 - - + -
603B ASP* 3.0 33.8 + - + +
605B ASP* 1.3 80.1 - - - +
607B LEU* 1.3 64.2 + - + +
608B ASP 3.5 0.5 + - - -
609B ASN* 3.5 4.7 + - - -
612B ASN* 2.9 62.3 + - + +
615B ILE* 5.0 5.8 - - + -
616B LEU* 4.0 22.6 - - + +
642B LEU* 4.5 24.7 - - + -
643B PHE* 4.0 29.4 - + - -
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Residues in contact with LEU 607 (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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513B LEU* 5.2 4.0 - - + +
517B TYR* 4.7 5.9 + - - -
594B TYR* 3.6 49.0 - - + +
597B LEU* 4.0 17.0 - - + +
598B LEU* 3.7 34.1 - - + +
601B ILE* 3.7 20.2 - - + -
603B ASP 3.3 8.5 + - - +
604B LYS* 3.1 7.5 + - - +
606B PHE* 1.3 76.5 - - + +
608B ASP* 1.3 61.7 + - - +
609B ASN 3.6 3.1 + - - +
616B LEU* 3.9 33.9 - - + +
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Residues in contact with ASP 608 (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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554B LYS* 2.9 25.1 + - - +
594B TYR* 2.8 21.7 + - - -
604B LYS* 2.9 45.0 + - - +
605B ASP* 4.1 9.1 - - - +
606B PHE 3.2 0.2 - - - -
607B LEU* 1.3 75.5 - - - +
609B ASN* 1.3 64.3 + - - +
610B GLU* 3.4 4.0 + - - +
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Residues in contact with ASN 609 (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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605B ASP 3.1 17.8 + - - +
606B PHE 3.9 1.0 - - - +
607B LEU 3.4 4.5 - - - +
608B ASP* 1.3 76.3 - - - +
610B GLU* 1.3 73.3 + - - +
611B GLU* 3.1 34.7 + - - +
612B ASN* 3.2 34.6 + - - +
613B GLU* 4.2 2.1 + - - -
616B LEU* 5.7 0.5 - - - +
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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