Contacts of the strand formed by residues 246 - 251 (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 CYS 246 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210A THR* 4.3 23.1 - - + -
211A GLN 3.8 2.2 - - - +
212A ASP* 4.1 18.4 - - - -
213A THR* 3.9 0.7 + - - -
232A ARG 4.0 0.2 - - - +
233A ILE* 3.8 2.6 - - - +
234A ARG* 2.9 37.2 + - + +
245A THR* 1.3 84.7 + - - +
247A VAL* 1.3 64.4 + - - +
248A ASP* 4.8 4.8 - - - +
14C A 4.3 23.3 - - - -
15C C 4.4 15.0 - - + -
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Residues in contact with VAL 247 (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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209A ILE 3.9 0.9 - - - +
210A THR* 3.5 2.8 - - - +
211A GLN* 2.8 37.1 + - - +
212A ASP 5.0 0.7 - - - +
213A THR* 3.8 28.9 - - + +
216A ILE* 4.0 20.0 - - + -
219A MET* 4.5 18.4 - - + +
231A ILE* 3.6 30.7 - - + -
232A ARG 3.5 3.8 - - - +
233A ILE* 3.9 16.8 - - + -
246A CYS* 1.3 78.9 - - - +
248A ASP* 1.3 69.9 + - - +
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Residues in contact with ASP 248 (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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208A GLN* 2.8 25.3 + - + +
209A ILE 3.3 3.4 - - - +
210A THR* 2.6 35.4 + - - +
219A MET* 4.4 0.2 - - - -
230A ASN 3.4 4.3 - - - +
231A ILE* 3.4 3.5 - - - -
232A ARG* 2.9 71.7 + - + +
234A ARG* 5.2 2.8 - - - +
246A CYS* 4.8 5.7 - - - +
247A VAL* 1.3 81.4 - - - +
249A LEU* 1.3 58.9 + - - +
250A VAL* 3.8 7.7 + - + +
16C G 4.7 2.1 - - - +
17C A 5.1 2.8 + - - -
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Residues in contact with LEU 249 (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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207A PHE* 4.4 16.6 - - + -
208A GLN* 3.2 6.9 - - - +
209A ILE* 2.9 45.4 + - + +
219A MET* 3.6 27.3 - - + +
222A LEU* 3.7 33.4 - - + +
223A ILE* 3.7 31.2 - - + +
226A LEU* 5.2 4.5 - - + -
228A CYS 4.8 1.8 - - - +
229A GLY* 4.8 2.0 - - - -
230A ASN 3.6 4.0 - - - -
231A ILE* 5.0 2.9 - - + +
248A ASP* 1.3 71.5 - - - +
250A VAL* 1.3 63.8 + - - +
251A VAL* 4.0 23.6 - - + -
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Residues in contact with VAL 250 (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* 5.3 1.6 - - - +
190A ARG* 5.3 4.7 - - - +
206A VAL* 4.0 17.5 - - + -
207A PHE 3.5 1.8 - - - +
208A GLN* 4.4 10.8 - - + +
229A GLY* 3.3 1.0 - - - -
230A ASN* 2.9 45.0 + - + +
232A ARG* 4.7 15.5 - - + -
248A ASP* 3.8 22.9 - - + +
249A LEU* 1.3 79.9 - - - +
251A VAL* 1.3 64.5 + - - +
252A THR* 3.7 26.3 + - + -
7B A 6.0 4.3 - - + -
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Residues in contact with VAL 251 (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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206A VAL* 3.6 5.2 - - - -
207A PHE* 2.9 61.4 + - + +
226A LEU* 5.9 0.7 - - + -
228A CYS* 4.1 13.0 - - + -
229A GLY* 3.7 24.7 - - - +
249A LEU* 4.0 9.4 - - + -
250A VAL* 1.3 71.9 - - - +
252A THR* 1.3 63.1 + - - +
253A ASN* 4.3 2.2 - - + +
256A ASP* 4.2 22.4 - - + -
257A ILE* 3.8 23.7 - - + +
261A ILE* 4.2 10.8 - - + -
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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