Contacts of the strand formed by residues 210 - 218 (chain A) in PDB entry 2ADB
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 VAL 210 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201A HIS* 3.5 57.3 - - + +
204A PHE* 4.0 7.4 - - + -
205A SER* 3.8 19.1 - - - +
208A GLY 4.3 0.7 - - - +
209A THR* 1.3 80.8 - - - +
211A LEU* 1.3 63.9 + - - +
213A ILE* 3.6 28.0 - - + -
226A LEU* 4.0 13.2 - - + -
227A GLN 4.1 0.2 - - - -
228A TYR* 3.4 18.4 - - + -
275A TYR* 4.6 4.5 - - + +
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Residues in contact with LEU 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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209A THR* 4.5 6.1 - - + +
210A VAL* 1.3 78.6 - - - +
212A LYS* 1.3 78.1 + - + +
227A GLN* 2.7 34.9 + - + +
228A TYR 3.7 17.7 - - - +
229A ALA* 4.3 17.0 - - + +
274A ASP* 4.6 1.2 - - - +
275A TYR* 3.5 32.1 + - - +
276A THR* 4.9 16.0 + - + +
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Residues in contact with LYS 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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211A LEU* 1.3 94.0 - - + +
213A ILE* 1.3 66.3 + - - +
214A ILE* 5.9 0.9 - - - -
225A LEU 3.9 0.7 - - - +
226A LEU* 3.3 2.6 - - - -
227A GLN* 2.8 54.3 + - + +
263A LEU* 3.5 24.7 + - + +
264A ASN* 5.2 3.2 + - - +
265A VAL* 4.1 25.1 - - + +
273A ARG 3.9 3.6 - - - +
274A ASP* 2.7 39.6 + - + +
275A TYR* 5.0 0.2 - - - -
276A THR* 5.8 2.6 - - + +
277A ARG* 6.1 0.6 - - - +
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Residues in contact with ILE 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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197A LEU* 3.4 33.5 - - + +
200A LEU* 4.5 11.0 - - + -
210A VAL* 3.6 31.9 - - + -
212A LYS* 1.3 81.0 - - - +
214A ILE* 1.3 75.2 + - - +
224A ALA* 4.6 0.2 - - + -
225A LEU 3.4 7.6 - - - +
226A LEU* 3.7 22.9 - - + -
265A VAL* 4.4 1.5 - - - +
272A SER* 3.2 5.5 - - - -
273A ARG 3.0 34.8 + - - +
275A TYR* 3.5 34.3 - - + +
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Residues in contact with ILE 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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197A LEU* 4.8 0.4 - - - -
212A LYS 5.9 0.7 - - - -
213A ILE* 1.3 76.4 - - - +
215A THR* 1.3 65.8 + - - +
216A PHE* 3.6 24.2 - - + -
224A ALA* 3.1 9.8 - - - +
225A LEU* 2.7 56.9 + - + +
263A LEU* 4.5 5.6 - - + -
264A ASN 3.7 14.6 - - - +
265A VAL* 4.2 2.7 - - - +
271A LYS* 3.3 27.1 - - + +
272A SER* 3.5 17.5 - - - +
302B U 3.4 35.7 - - + +
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Residues in contact with THR 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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194A PRO* 3.7 27.7 - - + +
196A THR* 3.5 35.2 - - + -
197A LEU* 3.8 25.1 - - + +
214A ILE* 1.3 78.3 - - - +
216A PHE* 1.3 60.8 + - - +
222A PHE* 4.6 11.4 - - - -
223A GLN 3.7 6.7 - - - -
224A ALA* 4.2 1.1 - - + -
270A ASP 4.1 13.0 + - - +
271A LYS* 2.8 24.1 + - - +
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Residues in contact with PHE 216 (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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214A ILE* 3.6 22.9 - - + -
215A THR* 1.3 72.4 - - - +
217A THR* 1.3 62.1 + - - +
218A LYS* 3.1 22.6 + - + -
222A PHE* 4.4 5.6 - - - -
223A GLN* 2.9 64.6 + - + +
225A LEU* 4.1 17.3 - - + -
271A LYS* 4.1 17.5 - - + +
301B C 3.4 34.8 - - - -
302B U 3.0 38.1 - - - -
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Residues in contact with THR 217 (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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192A PHE 5.3 1.0 + - - -
216A PHE* 1.3 72.7 - - - +
218A LYS* 1.3 56.5 + - - +
219A ASN* 2.9 28.5 + - - +
220A ASN* 4.6 4.0 - - - +
221A GLN 3.1 19.1 - - - +
222A PHE* 3.9 19.2 - - + -
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Residues in contact with LYS 218 (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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216A PHE* 3.1 17.7 + - + -
217A THR* 1.3 65.6 - - - +
219A ASN* 1.3 73.6 - - - +
220A ASN* 2.8 17.5 + - - -
221A GLN* 2.9 42.4 + - + +
223A GLN* 3.9 19.1 - - + +
300B U 5.2 0.2 - - - -
301B C 2.8 45.6 + - - +
302B U 2.8 33.6 + - - +
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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