Contacts of the strand formed by residues 227 - 234 (chain A) in PDB entry 6BHG
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 227 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223A THR* 3.5 7.7 - - - +
224A VAL* 2.8 30.3 + - - +
225A GLY 3.3 2.2 + - - -
226A PRO* 1.3 82.8 - - - +
228A LYS* 1.3 66.4 + - - -
229A LYS* 5.7 0.2 - - - -
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Residues in contact with LYS 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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192A LEU* 3.6 25.4 - - + -
195A ASP* 3.3 45.8 + - + +
221A ILE* 4.3 6.3 - - + -
222A GLN 3.3 7.4 - - - +
223A THR* 4.1 14.7 + - + +
227A GLY* 1.3 77.2 - - - -
229A LYS* 1.3 68.1 + - - +
230A TYR* 3.6 27.7 - - + +
243A SER* 4.3 7.8 + - - -
244A GLY 4.5 0.9 + - - -
509A UNX 4.4 1.6 - - - -
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Residues in contact with LYS 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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220A ALA 4.1 0.2 - - - +
221A ILE* 3.4 6.2 - - - +
222A GLN* 2.8 35.9 + - + +
224A VAL* 4.4 22.2 - - + +
227A GLY 5.4 0.4 - - - +
228A LYS* 1.3 79.6 - - - +
230A TYR* 1.3 63.6 + - - +
231A LYS 4.2 0.6 + - - -
241A LEU* 3.7 41.0 + - + +
242A LEU 3.5 16.4 - - - +
243A SER* 2.8 30.9 + - - +
515A UNX 4.0 7.3 - - - -
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Residues in contact with TYR 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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195A ASP* 2.6 26.6 + - + -
198A LEU* 3.6 24.3 - - + +
218A LEU* 3.7 15.7 - - + -
220A ALA 3.6 3.6 - - - -
221A ILE* 4.0 31.4 - - + -
228A LYS* 3.6 28.1 - - + +
229A LYS* 1.3 74.0 - - - +
231A LYS* 1.3 61.1 + - - +
232A VAL* 3.7 1.4 + - - +
240A SER 3.6 2.1 - - - +
241A LEU* 4.0 1.6 - - - -
242A LEU* 2.8 48.8 + - - +
243A SER 3.9 0.2 - - - -
244A GLY* 3.5 31.0 - - - -
247A ILE* 3.7 23.8 - - + -
315A ARG* 4.3 3.3 - - - +
509A UNX 3.6 5.9 - - - -
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Residues in contact with LYS 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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218A LEU* 3.5 4.9 - - - +
219A ILE* 2.7 56.8 + - + -
220A ALA* 2.8 35.5 + - + +
229A LYS 4.2 0.2 - - - -
230A TYR* 1.3 71.1 - - - +
232A VAL* 1.3 61.3 + - - +
239A LYS* 4.9 10.8 - - + -
240A SER 3.4 11.4 - - - +
241A LEU* 4.0 23.6 - - + +
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Residues in contact with VAL 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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204A ILE* 3.8 33.9 - - + -
206A GLY* 4.8 2.9 - - - +
216A GLY* 4.3 1.3 - - - -
217A THR 3.4 6.3 - - - +
218A LEU* 4.5 5.8 - - + -
219A ILE* 4.6 2.0 - - - -
230A TYR 4.2 3.1 - - - +
231A LYS* 1.3 78.0 - - - +
233A LYS* 1.4 69.9 + - - +
234A PHE* 3.9 26.7 + - + -
239A LYS* 3.1 7.2 - - - +
240A SER 2.9 36.2 + - - +
242A LEU* 4.0 13.7 - - + -
247A ILE* 3.9 24.0 - - + -
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Residues in contact with LYS 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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216A GLY* 3.2 0.5 - - - -
217A THR* 2.8 37.9 + - - +
219A ILE* 3.9 25.8 - - + +
232A VAL* 1.4 71.7 - - - +
234A PHE* 1.3 71.7 + - - +
235A ASP* 4.6 0.3 - - - +
238A GLY 3.7 8.3 - - - +
239A LYS* 4.1 16.8 - - + -
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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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206A GLY* 3.5 29.2 - - - -
207A LYS 4.6 1.8 - - - -
208A LYS* 3.6 31.0 - - + +
214A HIS* 3.4 41.5 - - + -
215A LYS 3.6 5.6 - - - +
232A VAL* 4.0 16.6 - - + -
233A LYS* 1.3 83.8 - - - +
235A ASP* 1.3 65.0 + - - +
236A ASN* 4.3 3.7 - - + +
237A LYS 3.3 21.0 + - - +
238A GLY* 3.0 25.5 + - - +
239A LYS 4.4 0.4 - - - -
240A SER* 3.4 35.2 - - - -
242A LEU* 4.6 1.1 - - + -
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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