Contacts of the strand formed by residues 227 - 231 (chain A) in PDB entry 5LU9
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 THR 227 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A TRP* 3.3 24.2 + - - +
41A TYR* 3.5 17.9 + - - -
43A TYR* 3.6 32.4 - - + +
221A TYR* 3.6 13.0 - - - -
222A ASP* 2.8 29.0 + - - +
225A ARG* 4.0 20.2 - - + +
226A SER* 1.3 80.8 - - - +
228A TYR* 1.3 71.8 + - - +
229A LEU* 4.8 1.6 - - + -
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Residues in contact with TYR 228 (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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41A TYR 5.6 0.9 - - - -
43A TYR* 3.8 4.2 - - - -
44A ARG* 3.4 33.3 + - - +
218A ALA* 3.7 16.2 - - + -
219A CYS 3.4 25.6 - - - +
220A TYR 3.5 2.7 - - - -
221A TYR* 3.8 37.3 - + + +
227A THR* 1.3 84.5 + - - +
229A LEU* 1.3 60.4 + - - +
230A GLY 3.5 0.2 - - - -
300C ACE 3.0 32.6 - - + +
301C TYR* 3.6 12.4 + + - -
302C VAL* 3.5 47.5 + - + +
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Residues in contact with LEU 229 (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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43A TYR* 3.8 23.8 - - + -
44A ARG* 3.6 4.1 - - - -
47A ALA* 3.6 13.3 - - - +
87A ILE* 3.9 17.0 - - + +
88A ASN* 2.7 32.5 + - - -
89A ARG* 3.5 31.2 - - - +
90A PRO* 3.6 12.3 - - + -
220A TYR* 2.9 27.2 + - + +
221A TYR 5.4 0.2 - - - +
222A ASP* 3.6 32.5 - - + +
225A ARG* 3.9 16.2 - - - -
227A THR* 4.5 2.2 - - + +
228A TYR* 1.3 73.7 - - - +
230A GLY* 1.3 51.7 + - - +
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Residues in contact with GLY 230 (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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44A ARG* 3.3 19.8 - - - +
48A ASP* 3.4 13.5 - - - -
88A ASN* 3.6 4.3 - - - -
219A CYS* 3.0 27.8 + - - +
220A TYR* 4.4 1.4 - - - +
229A LEU* 1.3 80.0 - - - +
231A ASP* 1.3 64.8 + - - -
235A VAL* 4.0 8.5 - - - -
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Residues in contact with ASP 231 (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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44A ARG* 3.0 15.4 + - - +
45A HIS* 3.4 15.1 + - - -
48A ASP* 2.4 33.6 + - - +
187A GLU* 3.2 26.0 - - - +
217A TYR 3.6 7.6 - - - +
218A ALA* 3.8 2.5 - - - +
219A CYS* 3.5 6.2 - - - -
230A GLY* 1.3 76.3 - - - +
232A TRP* 1.3 58.9 + - - +
233A TYR 3.4 0.4 - - - -
234A SER* 3.1 2.6 + - - +
235A VAL* 2.7 34.0 + - - +
304C ASP* 2.7 31.8 - - - +
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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