Contacts of the strand formed by residues 230 - 235 (chain A) in PDB entry 3L4U
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 SER 230 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A ARG* 2.8 16.5 + - - -
221A LEU* 4.5 3.1 - - - -
222A CYS 3.1 13.9 - - - -
223A LEU* 3.5 14.3 - - - +
224A GLU* 3.1 10.6 + - - -
228A GLY 2.8 19.3 + - - -
229A LEU* 1.3 72.7 + - - +
231A PHE* 1.3 59.9 + - - +
267A GLY 3.0 18.7 + - - -
269A THR 4.1 0.9 - - - -
270A PRO* 3.4 21.0 - - - +
273A VAL* 3.5 16.6 - - - -
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Residues in contact with PHE 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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151A LEU* 3.4 53.4 - - + -
152A PHE* 4.7 2.0 - + - -
170A THR* 6.1 0.4 - - + -
172A LEU* 4.0 10.1 - - + -
173A PRO* 3.5 28.0 - - + -
220A PHE* 4.6 4.9 - + - -
221A LEU* 3.5 2.9 - - - +
222A CYS* 2.8 55.8 + - + +
224A GLU* 3.7 17.3 - - + +
230A SER* 1.3 77.1 - - - +
232A GLY* 1.3 69.1 + - - +
233A VAL* 3.9 19.5 - - + -
264A VAL* 4.2 7.9 - - + -
265A PHE 3.1 15.9 - - - +
266A LEU* 4.3 1.6 - - + -
273A VAL* 3.7 9.8 - - - +
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Residues in contact with GLY 232 (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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219A PHE* 4.1 2.7 - - - -
220A PHE* 3.1 15.3 - - - -
222A CYS 4.7 0.2 - - - -
231A PHE* 1.3 78.0 - - - +
233A VAL* 1.3 68.7 + - - +
264A VAL* 3.4 3.8 - - - +
265A PHE* 2.8 36.6 + - - +
273A VAL* 3.6 14.1 - - - +
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Residues in contact with VAL 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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152A PHE* 4.1 24.0 - - + -
170A THR* 5.5 0.4 - - + -
218A THR 3.8 2.3 - - - +
219A PHE* 3.3 8.1 - - - -
220A PHE* 3.1 57.5 + - + -
231A PHE* 3.9 16.2 - - + -
232A GLY* 1.3 78.8 - - - +
234A PHE* 1.3 64.2 + - - +
253A TYR* 4.1 14.7 + - + +
262A PHE* 3.8 29.4 - - + -
263A TYR 3.3 7.9 - - - +
264A VAL* 4.2 7.0 - - + -
265A PHE* 4.5 0.7 - - - -
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Residues in contact with PHE 234 (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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218A THR* 3.1 28.3 - - + -
219A PHE* 4.1 7.2 - - + +
233A VAL* 1.3 79.6 - - - +
235A LEU* 1.3 66.7 + - - +
236A MET* 3.9 41.7 - - + -
261A ASP 3.9 0.7 - - - +
262A PHE* 3.5 5.2 - - - -
263A TYR* 2.9 50.4 + + + +
265A PHE* 3.8 19.3 - - + -
277A TYR* 3.7 24.9 - + + -
280A LEU* 4.2 5.8 - - + -
281A ILE* 4.0 8.5 - - + -
529A PHE* 5.0 3.1 - + - -
530A ALA* 3.4 35.0 - - + -
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Residues in contact with LEU 235 (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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218A THR* 2.7 37.1 + - - +
234A PHE* 1.3 80.3 - - - +
236A MET* 1.3 57.8 + - - +
237A ASN* 3.2 25.6 + - + +
241A MET* 3.9 20.6 - - + -
253A TYR* 3.7 36.7 + - + -
255A THR* 5.1 3.6 - - + -
260A LEU* 4.1 13.9 - - + -
261A ASP 3.4 32.3 - - - +
262A PHE* 3.9 24.0 - - + -
529A PHE* 5.4 0.9 - - - -
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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