Contacts of the strand formed by residues 185 - 193 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181A THR* 2.8 25.5 + - - +
182A ALA 5.6 0.3 - - - +
183A GLY 3.6 2.0 - - - +
184A GLU* 1.3 83.1 - - - +
186A SER* 1.3 60.7 + - - -
187A PHE* 5.2 5.4 - - - -
207A PHE* 4.8 4.7 - - - -
208A GLN 3.3 10.5 - - - -
209A ILE* 4.2 8.7 - - - -
16C G 4.3 4.3 - - - +
17C A 3.6 7.1 + - - -
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Residues in contact with SER 186 (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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184A GLU 5.1 0.4 - - - -
185A GLY* 1.3 72.6 - - - -
187A PHE* 1.3 66.3 + - - +
188A TYR* 3.5 23.4 - - - +
206A VAL 3.7 1.2 - - - +
207A PHE* 3.4 8.4 - - - -
208A GLN* 2.9 46.0 + - - +
310A ASN* 4.8 0.7 + - - -
16C G 3.9 13.9 - - - +
17C A 2.4 33.6 + - - +
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Residues in contact with PHE 187 (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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181A THR* 5.3 4.3 - - - -
185A GLY 5.2 2.7 - - - -
186A SER* 1.3 78.9 + - - +
188A TYR* 1.3 59.1 + - - +
206A VAL 3.5 3.4 - - - -
207A PHE* 3.3 36.8 - + - -
261A ILE* 4.6 0.2 - - + -
265A PHE* 4.0 16.2 - + - -
270A ILE* 4.2 22.7 - - + -
274A LYS* 4.8 8.5 - - + -
277A ASP* 4.8 4.5 - - + +
278A TYR* 3.4 45.3 - + + +
281A TRP* 3.4 52.6 - + + -
309A MET* 3.7 8.8 - - - +
310A ASN* 3.5 18.5 + - - +
17C A 4.5 0.8 + - - -
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Residues in contact with TYR 188 (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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186A SER* 3.5 18.2 - - - -
187A PHE* 1.3 75.5 - - - +
189A ILE* 1.3 69.0 + - - +
190A ARG* 3.8 21.1 + - + -
206A VAL* 2.9 74.0 + - + +
208A GLN* 3.1 36.8 + - + -
250A VAL* 5.3 1.9 - - - +
281A TRP* 3.3 7.6 + - - +
309A MET* 4.8 1.8 - - - -
310A ASN* 3.8 5.8 - - - +
17C A 4.2 12.1 - + + -
18C C 3.7 54.3 + + - +
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Residues in contact with ILE 189 (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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188A TYR* 1.3 80.5 - - - +
190A ARG* 1.3 63.0 + - - +
191A ILE* 3.8 10.7 + - + +
203A VAL* 4.1 13.7 - - + -
204A GLN 3.5 6.5 - - - +
205A SER* 3.8 17.9 - - - +
281A TRP* 3.5 29.2 - - + +
284A VAL* 3.6 33.7 - - + -
288A ILE* 5.0 0.4 - - + -
302A ILE* 3.9 24.2 - - + -
306A LYS* 4.7 17.4 - - + +
309A MET* 4.5 13.4 - - + +
18C C 5.3 1.2 + - - -
19C G 5.4 2.8 + - - -
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Residues in contact with ARG 190 (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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188A TYR* 3.8 30.3 + - + -
189A ILE* 1.3 72.2 - - - +
191A ILE* 1.3 65.2 + - - +
192A ALA* 5.0 1.8 - - + +
202A GLN 3.6 1.2 - - - +
203A VAL* 3.5 3.3 - - - -
204A GLN* 2.9 63.0 + - + +
206A VAL* 4.2 16.0 - - + +
250A VAL* 5.3 3.6 - - - +
252A THR* 4.0 18.8 - - - +
7B A 3.9 9.5 + - - +
8B A 3.6 20.6 + - - +
9B C 3.9 8.7 - - - +
18C C 4.8 1.6 - - - +
19C G 3.3 36.5 + - + +
20C T 3.4 29.8 + - + -
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Residues in contact with ILE 191 (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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189A ILE* 3.8 20.1 + - + +
190A ARG* 1.3 78.7 - - - +
192A ALA* 1.3 61.1 + - - +
193A LYS 4.2 0.5 + - - -
201A TYR* 4.6 22.0 - - + -
202A GLN 3.3 4.5 - - - +
203A VAL* 4.5 15.9 - - + -
299A LEU* 4.9 7.9 - - + -
302A ILE* 4.9 7.6 - - + -
303A GLN* 3.9 26.2 - - + +
306A LYS* 5.9 2.9 - - + -
19C G 4.1 29.7 + - - +
20C T 4.2 12.5 + - - +
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Residues in contact with ALA 192 (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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190A ARG* 4.2 2.4 - - + -
191A ILE* 1.3 74.3 - - - +
193A LYS* 1.3 63.1 + - - +
194A ASN* 3.2 1.2 + - + +
201A TYR* 3.1 6.9 - - - -
202A GLN* 2.9 45.4 + - + +
7B A 5.9 0.4 - - - +
20C T 3.5 32.1 - - + -
21C T 4.2 21.8 - - + +
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Residues in contact with LYS 193 (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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191A ILE 4.2 0.6 + - - -
192A ALA* 1.3 70.8 - - - +
194A ASN* 1.3 59.9 + - - +
200A GLY 3.6 1.3 - - - +
201A TYR* 3.5 27.5 - - + +
20C T 3.7 24.4 + - - +
21C T 3.9 17.8 + - - +
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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