Contacts of the strand formed by residues 225 - 232 (chain A) in PDB entry 5M5U
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 GLY 225 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220A VAL* 3.6 1.9 - - - +
221A ARG* 4.2 9.6 - - - -
222A GLY* 3.0 28.1 + - - -
223A GLN 3.0 9.7 + - - -
224A ALA* 1.3 80.2 - - - +
226A GLY* 1.3 63.5 + - - -
227A LYS* 3.6 4.7 + - - +
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Residues in contact with GLY 226 (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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220A VAL 3.2 8.5 - - - -
221A ARG* 4.2 3.0 - - - +
224A ALA 4.8 0.3 - - - +
225A GLY* 1.3 73.0 - - - -
227A LYS* 1.3 63.8 + - - +
249A ASP* 3.4 11.1 - - - +
250A VAL* 2.8 42.9 + - - +
252A PHE* 4.0 14.0 - - - -
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Residues in contact with LYS 227 (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 PHE 3.9 0.5 - - - +
219A ALA* 3.2 3.1 - - - -
220A VAL* 2.8 51.2 + - + +
224A ALA* 4.3 22.5 + - + +
225A GLY 4.5 5.6 - - - +
226A GLY* 1.3 77.0 + - - +
228A LEU* 1.3 59.8 + - - +
229A HIS* 3.9 21.8 - - + +
247A ALA* 4.8 7.9 - - + -
248A VAL* 3.3 25.1 - - - +
249A ASP* 2.9 24.3 + - - -
250A VAL* 3.5 6.5 - - - +
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Residues in contact with LEU 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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217A CYS* 3.6 24.5 - - - -
218A PHE 3.3 4.9 - - - +
219A ALA* 4.1 7.4 - - + -
227A LYS* 1.3 75.9 - - - +
229A HIS* 1.3 63.4 + - - +
230A ILE* 4.1 22.6 - - + +
246A LYS 4.0 0.7 - - - +
247A ALA* 3.3 3.5 - - - -
248A VAL* 2.8 54.4 + - + +
250A VAL* 3.6 13.9 - - + -
264A MET* 3.9 16.6 - - + -
273A VAL* 4.6 3.4 - - + -
275A LEU* 5.0 1.1 - - + -
285A TYR* 3.8 37.5 - - + -
290A GLY 4.6 0.4 - - - +
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Residues in contact with HIS 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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216A PHE 3.8 1.1 - - - +
217A CYS* 3.2 5.9 - - - -
218A PHE* 2.8 78.0 + + + -
220A VAL* 4.8 3.1 - - + +
227A LYS* 3.9 27.8 - - + +
228A LEU* 1.3 77.6 - - - +
230A ILE* 1.3 66.4 + - - +
231A ILE* 4.2 9.2 - - + +
246A LYS 3.3 6.7 + - - +
247A ALA* 3.8 24.4 - - + +
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Residues in contact with ILE 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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215A LEU* 3.9 17.5 - - + -
216A PHE 3.5 4.9 - - - +
217A CYS* 3.9 16.4 - - + -
228A LEU* 4.1 12.8 - - + +
229A HIS* 1.3 80.5 - - - +
231A ILE* 1.3 64.6 + - - +
243A PHE* 3.7 16.8 - - + -
245A LYS* 3.5 2.6 - - - -
246A LYS* 2.9 43.9 + - + -
273A VAL* 5.1 1.1 - - + -
286A ASP 3.9 4.9 - - - +
287A LEU* 3.4 39.7 - - + +
290A GLY* 3.7 28.7 - - - +
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Residues in contact with ILE 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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183A LEU* 5.6 3.1 - - + -
194A ILE* 6.1 2.0 - - + -
215A LEU* 3.2 8.0 - - - -
216A PHE* 2.7 69.9 + - + +
218A PHE* 5.4 5.2 - - + -
229A HIS* 4.7 10.5 - - + +
230A ILE* 1.3 84.5 - - - +
232A GLU* 1.3 65.3 + - - +
233A VAL* 4.2 9.6 - - + -
243A PHE* 4.6 2.9 - - - -
245A LYS* 4.0 29.2 - - + -
246A LYS 5.0 0.9 - - - +
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Residues in contact with GLU 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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213A SER* 3.7 27.7 + - - -
214A THR 3.4 14.3 + - - +
215A LEU* 3.8 4.4 - - + +
231A ILE* 1.3 84.9 - - - +
233A VAL* 1.3 70.3 + - - +
234A GLY 3.9 7.9 + - - +
235A THR 4.8 0.3 - - - -
236A PRO* 3.6 30.9 - - - +
237A PRO* 4.1 3.8 - - - +
240A ASN* 5.0 0.2 + - - -
241A GLN 5.0 0.9 - - - +
242A PRO* 3.3 12.4 - - - +
243A PHE* 2.9 43.9 + - + +
245A LYS* 5.6 0.8 - - - +
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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