Contacts of the strand formed by residues 217 - 224 (chain H) in PDB entry 1B6C
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 217 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213H LYS* 4.9 0.2 - - - -
214H GLY* 3.4 23.8 + - - -
215H ARG 3.6 5.1 + - - -
216H PHE* 1.3 78.7 - - - +
218H GLU* 1.3 63.6 + - - -
219H VAL* 4.1 4.9 + - - +
232H LYS* 4.9 1.5 - - - +
233H ILE 3.3 13.2 - - - -
235H SER* 3.8 11.3 + - - -
238H GLU* 3.4 7.4 + - - -
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Residues in contact with GLU 218 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210H SER* 2.8 26.0 + - - -
212H GLY 3.4 5.6 - - - +
213H LYS* 3.9 31.0 - - + +
217H GLY* 1.3 74.5 - - - -
219H VAL* 1.3 60.6 + - - +
220H TRP* 3.2 37.0 + - - +
231H VAL 3.7 0.7 - - - +
232H LYS* 3.4 3.1 - - - +
233H ILE* 2.7 41.1 + - + +
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Residues in contact with VAL 219 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210H SER* 3.7 2.4 + - - -
211H ILE* 2.7 49.5 + - + +
212H GLY* 2.9 22.1 + - - +
214H GLY 5.8 0.9 - - - +
217H GLY 4.7 3.8 - - - +
218H GLU* 1.3 75.6 - - - +
220H TRP* 1.3 63.6 + - - +
230H ALA* 4.9 8.1 - - + -
231H VAL 3.4 11.7 - - - +
232H LYS* 3.8 28.7 - - + -
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Residues in contact with TRP 220 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E SER* 4.6 9.6 - - - -
207H LEU* 4.0 44.9 - - + -
208H GLN 4.7 1.8 - - - -
209H GLU* 3.4 26.9 - - - -
210H SER* 3.7 18.6 - - - -
211H ILE* 3.9 4.6 - - - +
218H GLU* 3.2 48.8 + - + +
219H VAL* 1.3 80.8 - - - +
221H ARG* 1.3 61.7 + - - +
222H GLY 3.6 0.3 + - - -
230H ALA* 3.6 4.0 - - - -
231H VAL* 2.8 37.6 + - - +
233H ILE* 3.8 22.2 - - + +
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Residues in contact with ARG 221 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207H LEU* 4.0 1.0 - - - -
208H GLN* 2.8 52.8 + - + +
209H GLU* 2.2 52.2 + - - +
211H ILE* 3.6 22.9 - - + +
220H TRP* 1.3 75.0 - - - +
222H GLY* 1.3 62.4 + - - +
223H LYS* 3.1 35.2 - - - +
228H GLU* 2.6 31.3 + - + +
229H VAL 3.7 6.1 - - - +
282H TYR* 3.7 26.0 + - + -
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Residues in contact with GLY 222 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205H ILE* 4.2 7.2 - - - -
206H VAL 3.4 10.3 - - - -
207H LEU* 4.2 4.7 - - - -
208H GLN* 3.9 1.3 - - - -
220H TRP 3.6 2.0 + - - -
221H ARG* 1.3 76.3 - - - +
223H LYS* 1.3 61.4 + - - +
228H GLU* 3.4 4.7 - - - +
229H VAL* 2.5 52.5 + - - -
231H VAL* 4.8 1.1 - - - +
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Residues in contact with LYS 223 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205H ILE* 3.4 5.5 - - - -
206H VAL* 2.8 39.1 + - + +
208H GLN* 3.8 30.1 + - + +
221H ARG* 3.1 31.5 - - - +
222H GLY* 1.3 78.6 - - - +
224H TRP* 1.3 59.7 + - - +
225H ARG 4.1 0.9 - - - -
226H GLY* 3.8 29.4 - - - +
227H GLU 3.1 5.8 - - - +
228H GLU* 4.5 10.3 - - + -
229H VAL* 4.7 0.7 - - - -
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Residues in contact with TRP 224 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175H THR 5.0 9.4 - - - -
177H LEU* 3.2 46.9 - - + -
180H LEU* 4.0 15.3 - - + -
200H THR* 5.4 1.9 - - + +
201H ILE* 3.7 49.2 - - + +
204H THR* 3.9 28.1 - - + +
205H ILE* 4.3 11.2 - - + +
223H LYS* 1.3 73.1 - - - +
225H ARG* 1.3 118.0 + - + +
227H GLU* 2.8 29.9 + - + +
229H VAL* 5.2 2.9 - - + -
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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