Contacts of the helix formed by residues 600 - 606 (chain A) in PDB entry 5FO9
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 LYS 600 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233A GLU* 5.2 12.8 + - - +
260A LEU* 4.1 12.3 - - + +
598A VAL 4.4 0.2 - - - -
599A ASP* 1.3 74.1 + - - +
601A GLY* 1.3 62.0 + - - +
602A VAL 3.1 0.8 + - - -
603A PHE* 3.5 21.8 + - + +
604A VAL* 3.4 15.6 + - - +
801B THR* 3.1 39.6 + - + +
803B GLU* 3.4 34.8 - - + +
822B GLU* 2.5 39.1 + - - +
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Residues in contact with GLY 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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229A LEU* 4.3 15.2 - - - +
230A PRO* 3.8 13.6 - - - +
260A LEU* 3.9 16.2 - - - +
599A ASP* 2.7 21.0 + - - -
600A LYS* 1.3 70.0 - - - +
602A VAL* 1.3 64.5 + - - +
604A VAL* 3.3 25.6 - - - +
605A LEU* 3.9 4.3 + - - +
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Residues in contact with VAL 602 (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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136A LYS* 4.2 11.7 - - + -
137A THR* 3.7 27.4 - - - +
138A ILE* 3.8 18.3 - - + +
229A LEU* 4.4 9.8 - - + +
598A VAL* 3.9 15.0 - - + -
599A ASP* 3.4 17.7 - - + +
600A LYS 3.1 0.2 - - - -
601A GLY* 1.3 76.9 - - - +
603A PHE* 1.3 65.0 + - + +
605A LEU* 2.9 24.9 + - - +
606A ASN 3.2 8.7 + - - -
769B GLU* 4.1 30.1 - - + +
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Residues in contact with PHE 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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135A ASP 5.5 2.0 - - - -
137A THR* 4.3 11.7 - - + -
598A VAL* 4.0 35.0 - - + -
599A ASP 4.8 0.9 - - - -
600A LYS* 3.5 23.0 + - + +
601A GLY 3.4 0.4 - - - -
602A VAL* 1.3 79.5 - - + +
604A VAL* 1.3 65.5 + - - +
605A LEU 3.1 0.6 + - - -
606A ASN 3.4 20.3 - - - -
607A LYS* 3.1 42.7 + - + +
610A LYS* 4.1 28.9 - - + -
803B GLU* 3.1 46.7 - - + -
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Residues in contact with VAL 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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230A PRO* 4.4 8.3 - - + -
232A PHE 4.3 13.2 - - - +
233A GLU* 3.8 32.8 - - + +
234A VAL 5.1 2.7 - - - +
260A LEU* 4.5 5.6 - - + -
339A VAL* 4.5 13.2 - - + -
340A GLN 5.6 2.7 - - - +
600A LYS 3.4 13.9 - - - +
601A GLY* 3.3 21.3 - - - +
602A VAL 3.1 0.2 - - - -
603A PHE* 1.3 79.3 - - - +
605A LEU* 1.3 69.7 + - + +
607A LYS* 5.3 3.1 - - - +
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Residues in contact with LEU 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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138A ILE* 4.0 24.0 - - + -
223A GLU* 5.3 2.4 - - - +
225A LYS* 6.2 0.9 - - + -
227A TYR* 3.5 48.0 - - + -
228A VAL 4.8 4.0 - - - +
229A LEU* 5.5 1.8 - - + -
230A PRO* 3.9 29.4 - - + -
601A GLY 4.0 7.4 - - - +
602A VAL* 2.9 9.4 + - - +
603A PHE 4.1 0.2 - - - -
604A VAL* 1.3 88.1 - - + +
606A ASN* 1.3 59.5 + - - +
607A LYS 4.4 0.2 - - - -
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Residues in contact with ASN 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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137A THR* 2.6 62.8 + - - +
138A ILE* 4.5 8.3 - - + -
203A GLN* 5.3 4.8 + - - +
221A GLU 5.6 0.2 + - - -
222A PHE* 5.3 1.2 - - - +
223A GLU* 4.5 20.2 + - - +
602A VAL 3.2 3.2 + - - -
603A PHE* 3.4 15.8 - - - -
605A LEU* 1.3 81.1 - - - +
607A LYS* 1.3 58.8 + - - +
608A LYS* 2.8 43.7 + - - +
609A ASN* 4.8 5.7 + - - +
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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