Contacts of the strand formed by residues 213 - 219 (chain A) in PDB entry 5BZZ
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 PRO 213 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200A PHE* 4.3 7.2 - - + -
211A CYS* 3.3 17.0 - - - +
212A ASN* 1.3 84.7 - - - +
214A GLN* 1.3 57.7 + - - +
228A ASN 4.2 0.5 - - - +
230A GLY* 2.7 33.9 + - - +
231A PRO* 3.9 15.9 - - + -
239A MET* 3.9 12.1 - - - -
241A PHE* 3.3 38.5 - - + -
257A PHE* 4.2 10.8 - - + -
258A PHE 3.2 9.0 - - - +
270A MET* 4.4 8.5 - - - -
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Residues in contact with GLN 214 (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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212A ASN 4.8 1.1 - - - +
213A PRO* 1.3 76.6 - - - +
215A PHE* 1.3 83.6 + - - +
216A VAL* 4.0 3.4 - - - +
226A SER* 3.5 12.1 + - - -
227A SER* 3.0 37.6 + - - +
228A ASN 4.2 6.7 - - - +
229A SER* 4.5 11.2 - - - +
257A PHE* 3.3 6.2 - - - -
258A PHE* 2.7 54.6 + - + +
260A LYS* 5.0 6.5 - - + -
267A LYS* 3.1 30.1 + - + +
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Residues in contact with PHE 215 (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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198A MET* 3.6 25.6 - - + -
214A GLN* 1.3 82.4 + - - +
216A VAL* 1.3 67.3 + - - +
217A VAL* 3.8 13.9 - - + -
225A TYR* 3.6 33.9 - + - -
227A SER* 2.8 48.6 + - - -
241A PHE* 3.9 31.4 - + + -
242A GLU 6.0 0.9 - - - -
243A PHE* 3.6 20.2 - + - -
255A VAL* 4.6 1.8 - - + -
256A GLU 3.2 13.0 - - - +
257A PHE* 3.6 29.8 - + + -
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Residues in contact with VAL 216 (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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214A GLN* 4.0 11.4 - - - +
215A PHE* 1.3 79.6 - - - +
217A VAL* 1.3 70.8 + - - +
218A CYS* 4.1 21.3 - - - -
223A LYS* 4.5 12.1 - - + -
225A TYR 3.4 11.2 - - - +
226A SER* 4.3 10.5 - - - +
254A LYS 3.8 0.5 - - - +
255A VAL* 3.5 4.7 - - - +
256A GLU* 3.0 36.4 + - + +
258A PHE* 3.8 22.2 - - + -
267A LYS* 4.6 4.9 - - - +
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Residues in contact with VAL 217 (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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195A PHE* 4.8 3.4 - - + -
215A PHE* 3.8 26.7 - - + -
216A VAL* 1.3 77.4 - - - +
218A CYS* 1.3 60.2 + - - +
223A LYS* 3.6 2.9 - - - -
224A ILE* 2.8 48.5 + - + -
225A TYR* 2.8 25.2 + - + +
243A PHE* 4.3 4.7 - - + -
247A LEU* 4.0 16.4 - - + -
249A VAL* 4.9 2.2 - - + -
253A ILE* 3.9 26.0 - - + -
254A LYS 3.4 3.1 - - - +
255A VAL* 4.3 12.1 - - + -
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Residues in contact with CYS 218 (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 VAL* 4.1 14.1 - - - -
217A VAL* 1.3 82.9 - - - +
219A GLN* 1.3 60.9 + - - +
220A LEU 4.1 11.3 + - - +
221A LYS* 4.8 6.1 - - - -
222A VAL 3.2 7.4 - - - +
223A LYS* 3.9 17.7 - - - -
224A ILE* 4.5 0.2 - - - -
252A ASP 4.0 0.2 - - - +
253A ILE* 3.5 8.0 - - - +
254A LYS* 2.8 53.6 + - + +
256A GLU* 6.2 0.2 - - - -
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Residues in contact with GLN 219 (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 CYS* 1.3 72.1 - - - +
220A LEU* 1.3 73.6 + - + +
222A VAL* 2.8 33.2 + - - +
224A ILE* 4.0 26.8 - - + +
248A PRO 4.2 1.4 - - - +
249A VAL* 3.5 10.0 - - - -
250A CYS* 2.7 53.9 + - - +
252A ASP 3.7 4.5 - - - +
253A ILE* 3.7 7.8 - - + +
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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