Contacts of the strand formed by residues 208 - 215 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121A ILE* 4.3 1.3 - - - -
122A SER* 3.6 22.9 - - - -
123A ILE 4.3 4.0 - - - -
124A ALA* 3.7 35.2 - - + -
125A SER 5.5 2.2 - - - -
200A ILE* 2.9 9.5 - - - +
201A CYS 2.7 39.4 + - - +
202A ASN* 3.0 28.5 - - + -
203A GLY* 1.3 82.1 - - - +
209A LEU* 1.3 60.0 + - - +
210A GLN* 3.2 2.4 + - - +
27K GLN* 6.3 0.9 - - - -
137K LEU* 6.1 2.3 - - - +
159K ASN* 6.0 0.3 + - - -
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Residues in contact with LEU 209 (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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45A VAL* 3.6 30.1 - - + -
47A VAL* 3.8 8.7 - - + -
53A LEU* 4.1 5.2 - - + -
121A ILE* 4.2 9.6 - - + +
122A SER 2.8 18.6 + - - +
123A ILE* 3.5 28.1 - - + +
124A ALA* 2.7 26.7 + - - +
198A PRO* 3.8 24.7 - - + -
199A LEU 4.1 0.2 - - - +
200A ILE* 3.8 11.0 - - + -
208A TYR* 1.3 68.4 - - - +
210A GLN* 1.3 59.7 + - - +
211A GLY 3.7 19.7 - - - +
212A LEU* 5.3 0.9 - - + -
231A LEU* 3.6 17.0 - - + +
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Residues in contact with GLN 210 (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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124A ALA* 3.7 15.2 - - - +
127A GLN 2.9 26.4 + - - +
128A CYS 5.2 0.4 - - - -
129A PRO* 3.4 36.5 - - + +
181A PHE* 3.9 11.9 - - + -
199A LEU* 2.6 17.6 + - + +
201A CYS* 3.0 46.4 + - + +
208A TYR* 3.2 1.8 + - - +
209A LEU* 1.3 73.5 - - - +
211A GLY* 1.3 57.2 + - - +
229A THR 3.8 0.9 - - - +
230A ASN* 4.4 0.9 - - - +
231A LEU* 3.5 24.7 + - - +
232A CYS* 4.3 4.0 + - - +
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Residues in contact with GLY 211 (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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181A PHE* 4.0 9.2 - - - -
197A GLY 3.5 1.9 - - - +
198A PRO* 3.6 3.3 - - - +
199A LEU* 2.9 37.0 + - - +
209A LEU* 3.7 6.6 - - - +
210A GLN* 1.3 80.5 - - - +
212A LEU* 1.3 60.7 + - - +
228A TYR* 4.5 0.7 - - - -
229A THR 3.3 13.2 - - - -
231A LEU* 3.4 10.2 - - - +
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Residues in contact with LEU 212 (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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45A VAL* 4.2 15.9 - - + -
53A LEU* 4.0 12.6 - - + +
54A SER* 3.5 31.4 - - - +
55A ALA* 4.5 1.3 - - + +
102A ASP 4.6 0.7 - - - +
103A LEU* 4.1 9.9 - - + -
196A GLY* 3.0 34.1 - - - +
197A GLY 3.0 6.3 - - - +
209A LEU* 5.3 0.2 - - + -
211A GLY* 1.3 79.0 - - - +
213A VAL* 1.3 67.5 + - - +
214A SER 2.9 4.0 + - - -
228A TYR* 3.1 8.2 - - - +
229A THR* 2.9 36.7 + - - +
231A LEU* 3.8 28.3 - - + -
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Residues in contact with VAL 213 (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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55A ALA* 4.2 4.2 - - - +
138A VAL* 4.2 16.4 - - + -
139A SER 5.4 0.2 - - - +
190A SER* 4.1 11.9 - - - +
194A ASP* 3.0 44.0 - - + +
195A SER* 3.3 7.8 - - - +
196A GLY* 2.7 26.5 + - - +
197A GLY* 2.8 20.0 + - - +
198A PRO 4.8 0.7 - - - +
212A LEU* 1.3 70.1 - - - +
214A SER* 1.3 57.1 + - - +
227A VAL 5.4 0.4 - - - +
228A TYR* 3.6 23.1 - - + -
701A PBZ 4.0 18.2 - - + -
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Residues in contact with SER 214 (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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55A ALA* 5.3 0.2 - - - -
57A HIS* 3.1 23.0 - - - -
99A LEU 4.5 1.2 + - - -
102A ASP* 2.7 33.5 + - - +
180A MET* 6.2 0.7 - - - -
212A LEU 2.9 4.1 + - - -
213A VAL* 1.3 71.1 - - - +
215A PHE* 1.3 80.7 + - - +
227A VAL* 3.2 16.9 + - - -
228A TYR 4.3 0.7 - - - -
229A THR* 3.9 18.4 - - - -
701A PBZ 3.2 12.2 + - - -
186D GLN* 3.4 0.7 - - - -
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Residues in contact with PHE 215 (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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99A LEU* 3.9 38.8 - - + -
172A TYR* 3.8 18.8 - + - -
175A LEU* 5.2 8.1 - - + -
180A MET* 3.5 31.9 - - + -
214A SER* 1.3 95.2 - - - +
216A GLY* 1.3 73.1 + - - +
226A GLY* 3.8 0.3 - - - -
227A VAL* 2.6 65.3 + - + +
701A PBZ 3.1 20.1 - - - -
186D GLN* 3.4 21.3 - + + +
222D VAL* 4.6 7.4 - - + -
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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