Contacts of the strand formed by residues 228 - 234 (chain A) in PDB entry 5INQ
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 ASN 228 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122A SER* 6.0 2.6 - - - +
224A SER* 3.2 3.8 - - - -
225A LEU 2.9 31.7 + - - +
226A GLY* 3.2 24.7 + - - -
227A GLY* 1.3 81.9 + - - +
229A GLU* 1.3 70.1 + - - +
230A PHE* 3.4 19.0 - - + -
266A THR* 5.5 2.9 + - - +
368A VAL* 3.6 35.3 + - + +
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Residues in contact with GLU 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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202A LYS* 2.4 42.3 + - - +
223A VAL 3.5 0.9 - - - -
224A SER* 3.4 16.4 - - - -
227A GLY 4.8 2.4 - - - -
228A ASN* 1.3 82.1 + - - +
230A PHE* 1.3 61.6 + - - +
264A SER* 4.6 5.5 + - - +
265A THR* 3.8 18.2 - - + +
266A THR* 3.0 28.1 + - - -
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Residues in contact with PHE 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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124A ILE* 4.1 23.8 - - + -
202A LYS* 5.4 0.5 - - - -
221A VAL 3.8 0.3 - - - +
222A ASN* 3.4 6.2 - - - +
223A VAL* 2.9 42.7 + - + +
225A LEU* 3.5 40.6 - - + -
228A ASN* 3.4 20.4 - - + -
229A GLU* 1.3 73.4 - - - +
231A CYS* 1.3 58.5 + - - +
232A LEU* 3.8 17.7 - - + -
265A THR* 3.7 5.5 - - - +
266A THR* 3.2 36.1 - - + +
268A ILE* 4.1 17.0 - - + -
337A LEU* 5.0 0.7 - - + -
368A VAL* 3.7 29.2 - - + -
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Residues in contact with CYS 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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205A GLU* 6.1 0.2 - - - -
220A CYS* 4.2 15.3 - - - -
221A VAL 3.7 2.9 - - - -
222A ASN* 3.6 21.5 - - - +
230A PHE* 1.3 71.9 - - - +
232A LEU* 1.3 61.2 + - - +
233A MET* 4.1 23.3 - - - -
257A LYS* 5.1 8.7 - - - -
261A ALA* 4.8 7.9 - - + -
265A THR* 3.4 13.8 - - + +
266A THR 2.8 8.5 + - - -
267A VAL* 3.3 16.2 - - + +
268A ILE 3.0 26.0 + - - +
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Residues in contact with LEU 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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124A ILE* 4.4 7.0 - - + -
157A VAL* 3.8 35.9 - - + -
159A PHE* 3.8 17.7 - - + -
192A ILE* 3.5 11.1 - - + +
194A LEU* 4.5 7.6 - - + -
220A CYS* 3.3 3.3 - - - -
221A VAL* 2.8 43.5 + - + +
223A VAL* 3.8 21.5 - - + -
230A PHE* 3.8 31.4 - - + -
231A CYS* 1.3 76.9 - - - +
233A MET* 1.3 60.1 + - - +
268A ILE* 3.4 21.8 - - + -
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Residues in contact with MET 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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159A PHE* 3.6 6.2 - - - -
192A ILE* 4.4 0.2 - - - -
218A LEU* 3.7 30.5 - - + -
219A LEU 3.3 5.6 - - - +
220A CYS* 3.7 16.6 - - - -
231A CYS* 4.1 11.7 - - - +
232A LEU* 1.3 77.2 - - - +
234A THR* 1.3 63.8 + - - +
254A VAL* 3.7 30.1 - - + +
257A LYS* 3.9 14.4 - - + -
258A MET* 3.8 13.5 - - + -
267A VAL* 3.7 25.8 - - - -
268A ILE 2.7 13.2 + - - +
269A PHE* 3.9 9.4 - - + -
270A ALA 2.9 26.5 + - - +
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Residues in contact with THR 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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159A PHE* 3.8 9.0 - - + -
160A LEU 4.6 0.4 - - - +
161A GLN* 3.1 19.6 + - - +
190A THR* 3.8 25.8 + - - +
191A ALA 4.2 6.1 - - - +
192A ILE* 3.8 24.7 - - + -
217A ASN 4.1 0.3 - - - +
218A LEU* 3.6 2.0 - - - +
219A LEU* 2.9 36.8 + - + +
233A MET* 1.3 72.9 - - - +
235A SER* 1.3 70.3 + - - +
269A PHE* 3.8 5.8 - - - -
270A ALA 2.7 23.6 + - - -
271A GLY* 3.6 0.3 - - - -
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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