Contacts of the strand formed by residues 209 - 215 (chain G) in PDB entry 2BDI
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 LEU 209 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45G VAL* 3.6 28.9 - - + -
47G VAL* 3.8 9.2 - - + -
53G LEU* 4.1 4.7 - - + -
121G ILE* 4.1 9.9 - - + +
122G SER 2.8 19.3 + - - +
123G ILE* 3.5 27.2 - - + +
124G ALA* 2.8 22.4 + - - +
198G PRO* 3.8 24.7 - - + -
199G LEU 3.9 0.9 - - - +
200G ILE* 3.9 9.2 - - + -
208G TYR* 1.4 68.7 - - - +
210G GLN* 1.3 59.2 + - - +
211G GLY 3.7 19.7 - - - +
212G LEU* 5.3 0.4 - - + -
231G LEU* 3.6 16.8 - - + +
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Residues in contact with GLN 210 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124G ALA* 3.7 15.9 - - - +
127G GLN 3.0 25.0 + - - +
128G CYS 3.8 0.4 - - - -
129G PRO* 3.4 35.1 - - + +
181G PHE* 3.9 12.4 - - + -
199G LEU* 2.7 20.1 + - + +
201G CYS* 3.1 47.6 + - + +
208G TYR* 3.2 1.6 + - - +
209G LEU* 1.3 72.3 - - - +
211G GLY* 1.3 56.5 + - - +
229G THR 3.8 0.7 - - - +
230G ASN* 4.4 0.9 - - - +
231G LEU* 3.4 25.6 + - - +
232G CYS* 4.3 4.3 + - - -
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Residues in contact with GLY 211 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181G PHE* 4.1 8.7 - - - -
197G GLY 3.4 2.4 - - - +
198G PRO* 3.5 3.1 - - - +
199G LEU* 2.9 38.7 + - - +
209G LEU* 3.7 6.4 - - - +
210G GLN* 1.3 79.9 - - - +
212G LEU* 1.3 60.7 + - - +
228G TYR* 4.6 0.4 - - - -
229G THR 3.3 12.6 - - - -
231G LEU* 3.4 10.0 - - - +
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Residues in contact with LEU 212 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45G VAL* 4.2 16.2 - - + -
53G LEU* 4.0 13.0 - - + +
54G SER* 3.5 30.7 - - - +
55G ALA* 4.4 2.0 - - + +
102G ASP 4.5 0.4 - - - +
103G LEU* 4.1 10.3 - - + -
196G GLY* 3.1 33.9 - - - +
197G GLY 3.0 7.2 - - - +
211G GLY* 1.3 79.7 - - - +
213G VAL* 1.3 67.5 + - - +
228G TYR* 3.0 10.6 - - - +
229G THR* 2.8 39.5 + - - +
231G LEU* 3.8 27.8 - - + -
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Residues in contact with VAL 213 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55G ALA* 4.1 3.8 - - - +
138G VAL* 4.2 11.9 - - + -
139G SER 5.4 0.2 - - - +
190G SER* 4.1 16.8 - - - +
194G ASP* 3.0 45.8 - - + +
195G SER* 3.3 7.6 - - - +
196G GLY* 2.6 26.5 + - - -
197G GLY* 2.8 19.3 + - - +
198G PRO 4.8 0.2 - - - +
212G LEU* 1.3 72.2 - - - +
214G SER* 1.3 56.9 + - - +
227G VAL 4.5 0.7 - - - +
228G TYR* 3.6 25.3 - - + -
707G PBZ 4.3 16.2 - - + -
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Residues in contact with SER 214 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186F GLN* 3.4 3.8 - - - -
55G ALA* 5.3 0.2 - - - -
57G HIS* 3.0 23.0 - - - -
99G LEU 4.5 1.2 + - - -
102G ASP* 2.8 32.6 + - - +
180G MET* 6.1 0.6 - - - +
195G SER* 3.9 0.5 + - - -
212G LEU 3.0 4.6 + - - -
213G VAL* 1.3 72.7 - - - +
215G PHE* 1.4 81.1 + - - +
227G VAL* 3.3 17.3 + - - -
228G TYR 4.3 1.1 - - - -
229G THR* 4.0 18.2 - - - -
707G PBZ 3.7 8.8 + - - -
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Residues in contact with PHE 215 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186F GLN* 3.5 19.5 - + + -
222F VAL* 4.5 8.5 - - + -
99G LEU* 3.9 39.5 - - + -
172G TYR* 3.8 18.6 - + + -
175G LEU* 5.2 8.5 - - + -
180G MET* 3.6 31.4 - - + -
214G SER* 1.4 94.0 - - - +
216G GLY* 1.3 60.6 + - - +
227G VAL* 2.7 65.7 + - + +
707G PBZ 3.3 19.6 - - - -
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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