Contacts of the strand formed by residues 208 - 215 (chain E) 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 TYR 208 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121E ILE* 4.3 0.9 - - - -
122E SER* 3.6 23.6 - - - -
123E ILE 4.3 4.0 - - - -
124E ALA* 3.7 34.8 - - + -
125E SER 5.4 2.0 - - - -
200E ILE* 2.9 8.8 - - - +
201E CYS 2.7 34.0 + - - +
202E ASN* 3.0 29.6 - - + -
203E GLY* 1.3 81.7 - - - +
209E LEU* 1.3 59.6 + - - +
210E GLN* 3.2 2.7 + - - +
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Residues in contact with LEU 209 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E VAL* 3.6 30.1 - - + -
47E VAL* 3.8 19.7 - - + -
53E LEU* 4.1 4.9 - - + -
121E ILE* 4.2 10.1 - - + +
122E SER 2.8 19.4 + - - +
123E ILE* 3.5 16.0 - - + +
124E ALA* 2.8 23.3 + - - +
198E PRO* 3.8 24.7 - - + -
199E LEU 4.1 0.2 - - - +
200E ILE* 3.9 9.6 - - + -
208E TYR* 1.3 68.1 - - - +
210E GLN* 1.3 58.0 + - - +
211E GLY 3.7 20.0 - - - +
212E LEU* 5.3 0.9 - - + -
231E LEU* 3.7 16.3 - - + +
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Residues in contact with GLN 210 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124E ALA* 3.6 15.6 - - - +
127E GLN 2.9 26.3 - - - +
128E CYS 3.8 0.4 - - - -
129E PRO* 3.4 36.9 - - + +
181E PHE* 3.8 11.9 - - + -
199E LEU* 2.7 19.2 + - + +
201E CYS* 3.5 43.2 + - - +
208E TYR* 3.2 1.8 + - - +
209E LEU* 1.3 72.0 - - - +
211E GLY* 1.3 56.2 + - - +
229E THR 3.8 0.9 - - - +
230E ASN* 4.7 0.9 - - - +
231E LEU* 3.5 23.3 + - - +
232E CYS* 4.4 4.7 + - - +
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Residues in contact with GLY 211 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181E PHE* 4.1 8.7 - - - -
197E GLY 3.5 1.7 - - - +
198E PRO* 3.6 3.1 - - - +
199E LEU* 3.0 34.9 + - - +
209E LEU* 3.7 7.0 - - - +
210E GLN* 1.3 80.7 - - - +
212E LEU* 1.3 61.8 + - - +
228E TYR* 4.7 0.2 - - - -
229E THR 3.3 12.8 - - - -
231E LEU* 3.4 10.5 - - - -
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Residues in contact with LEU 212 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E VAL* 4.2 14.8 - - + -
53E LEU* 4.0 12.3 - - + +
54E SER* 3.5 31.6 - - - +
55E ALA* 4.4 1.6 - - + +
102E ASP 4.5 0.9 - - - +
103E LEU* 4.2 9.2 - - + -
196E GLY* 3.0 34.3 - - - +
197E GLY 3.0 7.9 - - - +
209E LEU* 5.3 0.4 - - + -
211E GLY* 1.3 78.8 - - - +
213E VAL* 1.3 65.6 + - - +
214E SER 3.0 1.6 + - - -
228E TYR* 3.0 9.5 - - - +
229E THR* 2.9 39.4 + - - +
231E LEU* 3.8 28.3 - - + -
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Residues in contact with VAL 213 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55E ALA* 4.2 3.6 - - - +
138E VAL* 4.2 16.4 - - + -
139E SER 5.4 0.4 - - - +
190E SER* 4.1 5.6 - - - +
194E ASP* 3.0 43.3 - - + +
195E SER* 3.3 3.9 - - - -
196E GLY* 2.6 27.2 + - - -
197E GLY* 2.8 23.1 + - - +
198E PRO 4.8 0.2 - - - +
212E LEU* 1.3 71.1 - - - +
214E SER* 1.3 56.4 + - - +
227E VAL 5.4 0.7 - - - +
228E TYR* 3.7 24.0 - - + -
705E PBZ 3.4 31.4 - - + -
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Residues in contact with SER 214 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57E HIS* 3.1 22.3 - - - -
99E LEU 4.5 1.7 + - - -
102E ASP* 2.8 33.3 + - - +
180E MET* 6.2 0.4 - - - -
195E SER* 3.9 0.2 + - - -
212E LEU 3.0 4.4 + - - -
213E VAL* 1.3 73.4 - - - +
215E PHE* 1.3 81.9 + - - +
227E VAL* 3.2 17.3 + - - -
228E TYR 4.3 0.7 - - - -
229E THR* 4.0 18.2 - - - -
705E PBZ 3.8 8.0 + - - -
186H GLN* 3.4 4.2 - - - -
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Residues in contact with PHE 215 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99E LEU* 3.9 38.4 - - + -
172E TYR* 3.8 18.8 - + + -
175E LEU* 5.2 8.1 - - + -
180E MET* 3.5 30.5 - - + -
214E SER* 1.3 91.8 - - - +
216E GLY* 1.3 62.4 + - - +
226E GLY* 3.8 1.0 - - - -
227E VAL* 2.7 65.4 + - + +
705E PBZ 4.1 17.4 + - - -
186H GLN* 2.9 31.9 - + + +
222H VAL* 4.3 7.6 - - + -
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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