Contacts of the strand formed by residues 229 - 233 (chain A) in PDB entry 3U3D
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 ILE 229 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A LYS* 5.0 0.2 - - - +
203A LEU* 3.6 18.4 - - + -
205A VAL* 3.8 24.9 - - + -
219A CYS* 4.1 7.0 - - + +
222A ALA* 3.7 26.5 - - + -
223A CYS* 3.9 17.0 - - - +
227A LYS 3.9 11.9 - - - +
228A LYS* 1.3 77.2 - - - +
230A VAL* 1.3 66.3 + - - +
239A ILE* 4.7 5.8 - - + -
243A MET* 3.7 21.1 - - + +
244A SER* 3.9 20.4 - - - -
245A ASP* 2.8 37.3 + - - +
246A TYR 3.2 8.1 + - - +
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Residues in contact with VAL 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ILE* 4.4 1.1 - - + -
21A LEU* 4.0 19.1 - - + -
24A ILE* 4.7 5.6 - - + -
202A LEU* 3.7 24.5 - - + -
203A LEU 2.9 9.9 + - - -
204A LEU* 3.4 15.9 - - + +
205A VAL 2.7 30.9 + - - -
228A LYS* 4.8 0.7 - - + -
229A ILE* 1.3 80.9 - - - +
231A GLU* 1.3 67.7 + - - +
232A ILE* 3.8 3.3 + - + +
246A TYR* 3.6 32.1 - - + +
248A VAL* 3.9 20.0 - - + -
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Residues in contact with GLU 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A VAL* 3.2 12.3 - - + +
208A THR* 5.9 1.0 - - + +
229A ILE 4.2 0.6 - - - -
230A VAL* 1.3 75.4 - - - +
232A ILE* 1.3 62.0 + - - +
233A ASN* 3.8 3.7 + - + +
237A THR* 3.0 37.3 + - - +
239A ILE* 3.7 21.9 - - + +
240A THR* 2.6 26.4 + - - +
244A SER* 2.9 22.7 + - - -
246A TYR 3.2 9.0 + - - +
247A HIS* 3.3 26.6 + - + +
248A VAL* 2.9 29.1 + - - +
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Residues in contact with ILE 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU* 5.2 2.7 - - + -
21A LEU* 4.1 28.7 - - + -
204A LEU* 4.2 21.5 - - + -
205A VAL 2.8 9.9 + - - +
206A ILE* 3.4 38.6 - - + +
207A GLY 3.2 24.8 + - - -
230A VAL* 4.4 1.6 - - + +
231A GLU* 1.3 75.8 - - - +
233A ASN* 1.3 63.1 + - - +
248A VAL* 3.5 12.6 - - + +
250A ALA* 3.9 30.0 - - + +
251A LYS 5.1 2.7 - - - +
252A PHE 5.4 0.7 - - - +
255A LEU* 4.3 20.9 - - + -
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Residues in contact with ASN 233 (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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205A VAL 5.1 1.4 + - - -
206A ILE* 5.0 0.2 - - - +
207A GLY* 3.3 13.8 - - - +
208A THR* 3.1 39.6 + - - +
231A GLU* 3.8 8.4 + - + +
232A ILE* 1.3 72.2 + - - +
234A ILE* 1.3 76.4 + - - +
235A SER* 3.0 30.7 + - - +
237A THR* 4.1 10.0 - - - +
247A HIS* 3.5 8.2 + - - +
248A VAL 3.0 7.3 + - - +
249A CYS* 3.0 12.3 - - - -
250A ALA 3.0 23.5 + - - -
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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
------------------------------------------------------------
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