Contacts of the strand formed by residues 185 - 193 (chain L) in PDB entry 6BCH
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 185 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181L THR* 2.8 26.7 + - - +
182L ALA 5.6 0.2 - - - +
183L GLY 3.6 2.3 - - - +
184L GLU* 1.3 83.8 - - - +
186L SER* 1.3 60.6 + - - -
187L PHE* 5.2 5.4 - - - -
207L PHE* 4.9 2.9 - - - -
208L GLN 3.3 10.1 - - - -
209L ILE* 4.3 8.5 - - - -
274L LYS* 6.0 2.1 - - - +
16O G 4.4 4.5 - - - +
17O A 3.7 6.2 + - - -
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Residues in contact with SER 186 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184L GLU 5.1 0.7 - - - -
185L GLY* 1.3 72.8 - - - -
187L PHE* 1.3 66.9 + - - +
188L TYR* 3.4 24.3 - - - +
206L VAL 3.7 1.2 - - - +
207L PHE* 3.5 8.0 - - - -
208L GLN* 2.9 46.2 + - - +
310L ASN* 4.8 0.9 + - - -
16O G 4.0 13.8 - - - +
17O A 2.3 32.6 + - - -
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Residues in contact with PHE 187 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181L THR* 5.3 4.0 - - - -
185L GLY 5.2 2.5 - - - -
186L SER* 1.3 78.2 + - - +
188L TYR* 1.3 59.5 + - - +
206L VAL 3.6 3.1 - - - -
207L PHE* 3.3 36.3 - + - -
261L ILE* 4.5 0.7 - - + -
265L PHE* 4.0 16.4 - + - -
270L ILE* 4.2 24.0 - - + -
274L LYS* 4.9 8.3 - - + -
277L ASP* 5.1 3.4 - - + +
278L TYR* 3.4 45.5 - + + +
281L TRP* 3.4 49.4 - + + -
309L MET* 3.7 11.4 - - - +
310L ASN* 3.5 19.0 + - - +
17O A 4.5 0.6 + - - -
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Residues in contact with TYR 188 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186L SER* 3.4 19.1 - - - -
187L PHE* 1.3 75.3 - - - +
189L ILE* 1.3 74.0 + - - +
190L ARG* 3.8 20.3 + - + -
206L VAL* 2.9 72.9 + - + +
208L GLN* 3.1 36.4 + - + -
250L VAL* 5.3 2.1 - - - +
281L TRP* 3.3 2.9 + - - +
309L MET* 4.7 1.8 - - - -
310L ASN* 3.8 5.6 - - - +
17O A 4.1 12.1 - + + -
18O C 3.6 55.5 + + - +
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Residues in contact with ILE 189 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188L TYR* 1.3 80.1 - - - +
190L ARG* 1.3 64.0 + - - +
191L ILE* 3.8 10.6 + - + +
203L VAL* 4.1 13.7 - - + -
204L GLN 3.5 6.3 - - - +
205L SER* 3.8 17.0 - - - +
281L TRP* 3.5 28.0 - - + +
284L VAL* 3.7 35.4 - - + -
302L ILE* 3.9 24.9 - - + -
306L LYS* 4.7 17.7 - - + +
309L MET* 4.4 14.3 - - + +
18O C 5.3 2.3 + - - +
19O G 5.4 2.9 + - - -
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Residues in contact with ARG 190 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188L TYR* 3.8 29.9 + - + -
189L ILE* 1.3 72.2 - - - +
191L ILE* 1.3 64.8 + - - +
192L ALA* 5.0 2.0 - - + +
202L GLN 3.6 1.0 - - - +
203L VAL* 3.6 3.8 - - - -
204L GLN* 2.9 62.3 + - + +
206L VAL* 4.1 17.0 - - + +
250L VAL* 5.3 3.8 - - - +
252L THR* 4.0 19.0 - - - +
7N A 3.9 9.3 + - - +
8N A 3.6 21.0 + - - +
9N C 3.9 8.3 - - - +
18O C 4.7 1.6 - - - +
19O G 3.2 36.1 + - + +
20O T 3.4 30.7 + - + +
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Residues in contact with ILE 191 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189L ILE* 3.8 18.6 + - + +
190L ARG* 1.3 79.9 - - - +
192L ALA* 1.3 61.0 + - - +
193L LYS 4.2 0.7 + - - +
201L TYR* 4.6 22.9 - - + -
202L GLN 3.3 4.9 - - - +
203L VAL* 4.4 15.9 - - + -
299L LEU* 4.9 7.4 - - + -
302L ILE* 4.6 9.4 - - + -
303L GLN* 4.1 24.7 - - + +
306L LYS* 5.9 2.9 - - + -
19O G 4.1 30.3 + - - +
20O T 4.2 12.5 + - - +
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Residues in contact with ALA 192 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190L ARG* 4.2 2.4 - - + -
191L ILE* 1.3 74.6 - - - +
193L LYS* 1.3 63.1 + - - +
194L ASN* 3.2 1.4 + - + +
201L TYR* 3.1 6.4 - - - -
202L GLN* 2.9 44.7 + - + +
7N A 5.8 0.4 - - - +
20O T 3.5 32.1 - - + -
21O T 4.1 22.0 - - + +
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Residues in contact with LYS 193 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191L ILE 4.2 0.4 + - - -
192L ALA* 1.3 70.8 - - - +
194L ASN* 1.3 60.8 + - - +
200L GLY 3.6 1.6 - - - +
201L TYR* 3.5 27.3 - - + +
20O T 3.7 23.7 + - - +
21O T 3.9 18.7 + - - +
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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