Contacts of the strand formed by residues 185 - 193 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181D THR* 2.8 26.4 + - - +
182D ALA 5.6 0.3 - - - +
183D GLY 3.6 2.1 - - - +
184D GLU* 1.3 82.0 - - - +
186D SER* 1.3 60.3 + - - -
187D PHE* 5.2 4.5 - - - -
207D PHE* 4.8 3.6 - - - -
208D GLN 3.3 10.1 - - - -
209D ILE* 4.3 8.5 - - - -
274D LYS* 6.0 1.6 - - - +
16F G 4.3 4.9 - - - +
17F A 3.6 6.6 + - - -
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Residues in contact with SER 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184D GLU 5.1 0.4 - - - -
185D GLY* 1.3 72.5 - - - -
187D PHE* 1.3 66.2 + - - +
188D TYR* 3.4 23.2 + - - +
206D VAL 3.7 1.0 - - - +
207D PHE* 3.4 7.6 - - - -
208D GLN* 2.9 46.6 + - - +
310D ASN* 4.8 0.7 + - - -
16F G 3.9 14.4 - - - +
17F A 2.3 33.0 + - - -
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Residues in contact with PHE 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181D THR* 5.3 2.9 - - - -
185D GLY 5.2 3.6 - - - -
186D SER* 1.3 78.2 + - - +
188D TYR* 1.3 59.5 + - - +
206D VAL 3.5 3.8 - - - -
207D PHE* 3.3 37.9 - + - -
261D ILE* 4.6 0.4 - - + -
265D PHE* 4.0 15.7 - + - -
270D ILE* 4.2 23.1 - - + -
274D LYS* 4.9 7.9 - - + -
277D ASP* 5.1 3.0 - - + +
278D TYR* 3.4 45.5 - + + +
281D TRP* 3.4 48.7 - + + -
309D MET* 3.7 11.8 - - - +
310D ASN* 3.5 18.6 + - - +
17F A 4.5 0.8 + - - -
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Residues in contact with TYR 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186D SER* 3.4 19.5 - - - -
187D PHE* 1.3 74.7 - - - +
189D ILE* 1.3 72.9 + - - +
190D ARG* 3.9 20.0 + - + -
206D VAL* 2.9 72.4 + - + +
208D GLN* 3.1 38.0 + - + -
250D VAL* 5.3 2.1 - - - +
281D TRP* 3.3 2.1 + - - -
309D MET* 4.8 2.0 - - - -
310D ASN* 3.8 5.8 - - - +
17F A 4.1 12.1 - + + -
18F C 3.6 55.8 + + - +
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Residues in contact with ILE 189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188D TYR* 1.3 80.1 - - - +
190D ARG* 1.3 64.1 + - - +
191D ILE* 3.8 12.0 + - + +
203D VAL* 4.1 13.9 - - + -
204D GLN 3.5 6.1 - - - +
205D SER* 3.7 20.2 - - - -
281D TRP* 3.6 26.0 - - + +
284D VAL* 3.7 35.7 - - + -
288D ILE* 4.9 0.2 - - + -
302D ILE* 3.9 24.2 - - + -
306D LYS* 4.7 17.0 - - + +
309D MET* 4.5 12.4 - - - +
18F C 5.3 2.5 + - - +
19F G 5.4 2.8 + - - -
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Residues in contact with ARG 190 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188D TYR* 3.9 28.5 + - + -
189D ILE* 1.3 72.5 - - - +
191D ILE* 1.3 62.8 + - - +
192D ALA* 5.0 1.8 - - + +
202D GLN 3.6 1.2 - - - +
203D VAL* 3.6 4.2 - - - -
204D GLN* 2.9 63.4 + - + +
206D VAL* 4.1 16.8 - - + +
250D VAL* 5.4 3.4 - - - +
252D THR* 4.0 18.8 - - - +
7E A 3.8 10.1 + - - -
8E A 3.5 22.0 + - - +
9E C 3.8 8.1 - - - +
18F C 4.8 2.3 - - - +
19F G 3.3 36.3 + - + +
20F T 3.3 29.9 + - + +
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Residues in contact with ILE 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189D ILE* 3.8 19.2 + - + +
190D ARG* 1.3 80.2 - - - +
192D ALA* 1.3 61.3 + - - +
193D LYS 4.2 0.6 + - - +
201D TYR* 4.7 21.3 - - + -
202D GLN 3.4 4.7 - - - +
203D VAL* 4.5 15.9 - - + -
299D LEU* 4.9 7.6 - - + -
302D ILE* 4.8 8.1 - - + -
303D GLN* 4.0 24.5 - - - +
306D LYS* 5.9 3.1 - - + -
19F G 4.1 29.2 + - - +
20F T 4.2 12.9 + - - +
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Residues in contact with ALA 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190D ARG* 4.1 2.7 - - + -
191D ILE* 1.3 75.8 - - - +
193D LYS* 1.3 63.5 + - - +
194D ASN* 3.8 1.4 - - + +
201D TYR* 3.1 7.2 - - - -
202D GLN* 2.9 44.0 + - + +
7E A 5.8 0.9 - - - +
20F T 3.5 30.1 - - + -
21F T 4.2 22.4 - - + +
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Residues in contact with LYS 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191D ILE* 4.2 0.8 + - - +
192D ALA* 1.3 70.1 - - - +
194D ASN* 1.3 59.5 + - - +
200D GLY 3.6 1.3 - - - +
201D TYR* 3.5 28.6 - - + +
20F T 3.7 23.8 + - - +
21F T 3.9 18.6 + - - +
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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