Contacts of the strand formed by residues 229 - 234 (chain W) in PDB entry 5IY6
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 ALA 229 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68W THR* 3.3 8.4 + - - -
69W LYS* 3.2 19.1 - - + +
71W ILE* 5.1 4.3 - - + +
225W LEU* 3.8 26.9 - - + -
228W LYS* 1.4 78.9 - - - +
230W VAL* 1.3 72.0 + - - +
451W PHE 3.4 4.9 + - - -
452W GLN* 3.1 15.5 - - + +
453W SER* 3.0 23.7 + - - -
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Residues in contact with VAL 230 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32W LEU* 4.6 22.2 - - + -
56W ILE* 5.9 4.3 - - + -
68W THR* 4.4 17.9 - - + +
69W LYS 2.8 12.4 + - - +
70W LEU* 3.7 11.0 - - + +
71W ILE* 2.8 31.0 + - - +
229W ALA* 1.3 78.3 - - - +
231W VAL* 1.3 63.4 + - - +
452W GLN* 4.6 0.4 - - - -
453W SER* 3.2 20.0 - - - +
454W VAL 4.8 1.3 - - - -
455W ILE* 3.9 31.4 - - + -
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Residues in contact with VAL 231 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71W ILE* 3.4 18.2 - - + -
73W CYS* 3.7 18.6 - - - -
212W LEU* 4.2 6.3 - - + -
230W VAL* 1.3 75.6 - - - +
232W VAL* 1.4 62.2 + - - +
233W PHE* 3.6 25.6 - - + -
447W VAL* 3.9 5.8 - - + -
452W GLN* 3.4 30.3 - - - +
453W SER 2.9 17.6 + - - +
454W VAL* 3.3 21.8 - - + +
455W ILE* 2.9 30.8 + - - +
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Residues in contact with VAL 232 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40W LEU* 5.6 1.1 - - + -
52W LEU* 3.7 17.5 - - + -
70W LEU* 4.3 3.5 - - + +
71W ILE 2.9 10.9 + - - +
72W TYR* 2.4 66.6 - - + -
73W CYS* 3.2 26.7 + - - +
209W TYR* 3.5 0.3 + - - -
230W VAL 4.3 0.2 - - - -
231W VAL* 1.4 74.3 - - - +
233W PHE* 1.4 71.6 + - - +
234W ASP* 3.7 3.9 + - + +
455W ILE* 3.3 26.9 - - + +
457W THR* 4.4 13.9 - - + -
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Residues in contact with PHE 233 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37W HIS* 5.9 0.4 - - - -
73W CYS* 4.0 1.8 - - - -
209W TYR* 2.1 47.8 - + + +
212W LEU* 3.8 14.4 - - + -
213W LEU* 3.6 21.8 - - + -
231W VAL* 3.6 24.9 - - + -
232W VAL* 1.4 67.1 - - - +
234W ASP* 1.3 56.6 + - - +
236W ALA* 3.7 16.6 - - + -
239W ILE* 3.9 24.2 - - + -
447W VAL* 3.9 23.3 - - + -
454W VAL* 3.6 16.2 - - + -
455W ILE 3.1 5.3 + - - -
456W ILE* 3.4 23.5 - - + -
457W THR* 3.3 29.8 + - - +
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Residues in contact with ASP 234 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48W LYS* 2.8 44.9 + - - +
49W THR* 4.3 11.6 + - + -
72W TYR* 5.5 7.6 - - + -
73W CYS 3.9 10.4 + - - +
74W SER* 5.6 0.3 - - - -
75W ARG* 5.1 4.7 + - - +
209W TYR* 2.2 28.7 + - - -
232W VAL* 3.7 8.2 + - + +
233W PHE* 1.3 64.1 - - - +
235W GLU* 1.3 80.0 + - - +
457W THR* 4.0 10.0 - - + +
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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