Contacts of the strand formed by residues 246 - 251 (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 CYS 246 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210D THR* 4.2 22.4 - - + -
211D GLN 3.8 2.7 - - - +
212D ASP* 4.1 20.2 - - - -
213D THR* 3.9 2.0 - - - +
232D ARG 4.0 0.2 - - - +
233D ILE* 3.8 1.7 - - - -
234D ARG* 2.9 36.9 + - + +
245D THR* 1.3 83.6 + - - +
247D VAL* 1.3 63.8 + - - +
248D ASP* 4.8 4.8 - - - +
14F A 4.3 22.9 - - - -
15F C 4.4 15.0 - - + -
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Residues in contact with VAL 247 (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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209D ILE 3.8 0.7 - - - +
210D THR* 3.5 3.1 - - - +
211D GLN 2.8 38.3 + - - +
212D ASP 4.9 0.4 - - - +
213D THR* 3.5 28.3 - - + -
216D ILE* 3.7 26.0 - - + -
219D MET* 4.3 21.9 - - + +
231D ILE* 3.6 29.6 - - + -
232D ARG 3.4 4.0 - - - +
233D ILE* 4.1 12.8 - - + -
246D CYS* 1.3 74.9 - - - +
248D ASP* 1.3 70.3 + - - +
249D LEU 4.3 0.2 - - - -
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Residues in contact with ASP 248 (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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208D GLN* 2.7 25.2 + - + +
209D ILE 3.3 3.1 - - - +
210D THR* 2.6 35.7 + - - +
230D ASN 3.4 4.0 - - - +
231D ILE* 3.4 3.8 - - - -
232D ARG* 2.9 70.1 + - + +
234D ARG* 5.1 3.5 - - - +
246D CYS* 4.8 5.2 - - - +
247D VAL* 1.3 82.0 + - - +
249D LEU* 1.3 60.0 + - - +
250D VAL* 3.7 8.1 + - + +
16F G 4.7 1.9 - - - +
17F A 5.1 2.4 + - - -
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Residues in contact with LEU 249 (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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207D PHE* 4.4 16.6 - - + -
208D GLN* 3.2 6.6 - - - +
209D ILE* 2.9 46.0 + - + +
219D MET* 3.6 26.2 - - + +
222D LEU* 3.6 30.5 - - + +
223D ILE* 3.6 34.3 - - + +
226D LEU* 5.2 5.4 - - + -
228D CYS 4.8 2.7 - - - +
229D GLY* 4.8 0.9 - - - -
230D ASN 3.6 3.8 - - - -
231D ILE* 5.0 2.0 - - + +
248D ASP* 1.3 71.4 - - - +
250D VAL* 1.3 62.7 + - - +
251D VAL* 4.0 23.6 - - + -
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Residues in contact with VAL 250 (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* 5.3 1.6 - - - +
190D ARG* 5.4 3.6 - - - +
206D VAL* 4.0 16.6 - - + -
207D PHE 3.5 1.6 - - - +
208D GLN* 4.6 9.2 - - + +
229D GLY* 3.3 0.7 - - - -
230D ASN* 2.9 44.2 + - + +
232D ARG* 4.6 14.8 - - + -
248D ASP* 3.8 24.9 - - + +
249D LEU* 1.3 79.0 - - - +
251D VAL* 1.3 65.1 + - - +
252D THR* 3.8 28.2 + - + +
7E A 5.6 3.8 + - + -
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Residues in contact with VAL 251 (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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205D SER 3.9 1.4 - - - +
206D VAL* 3.6 4.9 - - - +
207D PHE* 2.9 60.4 + - + +
226D LEU* 5.9 0.7 - - + -
228D CYS* 4.1 13.9 - - + +
229D GLY* 3.7 21.5 - - - +
249D LEU* 4.0 9.4 - - + -
250D VAL* 1.3 74.9 - - - +
252D THR* 1.3 62.5 + - - +
253D ASN* 4.3 2.2 - - + +
256D ASP* 4.1 23.8 - - + +
257D ILE* 3.9 21.7 - - + +
261D ILE* 4.2 10.3 - - + -
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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