Contacts of the strand formed by residues 205 - 213 (chain A) in PDB entry 2ATW
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 205 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A GLU* 3.0 28.6 + - + +
200A ILE* 3.5 39.7 - - + +
203A GLY* 4.0 6.8 - - - -
204A SER* 1.3 84.6 - - - +
206A GLU* 1.3 71.8 + - - +
222A VAL* 4.4 1.8 - - + -
223A ARG 3.4 10.1 - - - +
224A SER* 4.4 1.3 - - - -
229A LEU* 4.0 11.9 - - + -
231A ALA* 3.6 36.1 - - + +
234A ALA* 4.5 2.5 - - + -
235A CYS* 4.2 13.7 - - - -
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Residues in contact with GLU 206 (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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200A ILE* 5.4 0.9 - - - -
203A GLY* 6.2 0.9 - - - -
205A VAL* 1.3 77.7 - - - +
207A ILE* 1.3 67.1 + - - +
208A VAL* 3.6 8.6 + - + +
222A VAL* 3.1 7.1 - - - +
223A ARG* 2.8 80.1 + - + +
225A ASN* 3.0 24.7 + - - +
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Residues in contact with ILE 207 (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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190A ARG* 3.1 57.2 + - + +
193A PHE* 3.9 30.1 - - + -
200A ILE* 4.0 25.6 - - + +
206A GLU* 1.3 77.2 - - - +
208A VAL* 1.3 57.8 + - - +
209A ALA 3.8 9.0 - - - +
210A VAL* 3.7 24.5 - - + -
220A ILE* 4.7 9.9 - - + -
221A ALA 3.4 5.6 - - - +
222A VAL* 4.2 9.6 - - + -
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Residues in contact with VAL 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A ARG* 4.1 6.7 + - - -
206A GLU* 4.2 8.5 - - - +
207A ILE* 1.3 74.7 - - - +
209A ALA* 1.3 64.6 + - + +
221A ALA* 2.8 15.2 + - + +
223A ARG* 3.7 37.9 - - + -
260A TYR* 3.8 41.3 - - + -
267A PHE* 5.6 0.4 - - + -
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Residues in contact with ALA 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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190A ARG* 3.8 6.7 - - - +
207A ILE* 3.4 2.9 - - - +
208A VAL* 1.3 87.5 - - + +
210A VAL* 1.3 67.3 + - - +
220A ILE* 3.3 3.6 - - - -
221A ALA* 2.7 36.2 + - + -
267A PHE* 5.1 2.2 - - + -
316A LEU* 3.6 31.2 - - + +
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Residues in contact with VAL 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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186A PRO* 4.2 31.2 - - + +
189A VAL* 4.6 9.0 - - + -
190A ARG* 3.7 32.1 - - + +
207A ILE* 3.7 20.2 - - + -
209A ALA* 1.3 82.3 - - - +
211A ALA* 1.3 69.5 + - - +
212A ARG* 4.2 6.8 + - + -
218A SER* 4.9 1.1 - - - +
219A LYS 3.4 7.9 - - - +
220A ILE* 4.0 15.3 - - + -
315A ARG* 4.5 4.7 + - - +
316A LEU* 3.9 2.6 - - - -
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Residues in contact with ALA 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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210A VAL* 1.3 74.1 - - - +
212A ARG* 1.3 59.7 + - - +
218A SER* 3.3 2.6 - - - -
219A LYS* 2.9 34.7 + - + +
312A LEU* 3.4 43.5 - - + +
315A ARG* 3.9 22.9 - - + +
316A LEU* 3.7 12.5 - - + +
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Residues in contact with ARG 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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152A VAL* 4.7 3.2 - - - +
155A GLU* 5.2 3.2 + - - -
183A ARG 2.9 29.0 + - - -
184A THR 3.0 25.8 + - - +
185A HIS 3.3 9.9 + - - -
186A PRO* 4.0 17.5 - - + +
188A LEU* 4.2 6.9 - - - +
189A VAL* 3.6 18.2 - - - +
210A VAL* 4.1 10.2 + - + +
211A ALA* 1.3 74.6 - - - +
213A GLU* 1.3 64.7 + - - +
214A ALA* 3.6 18.8 + - + +
215A GLY 4.4 0.6 - - - +
218A SER* 3.1 17.7 - - - +
250A LEU* 3.7 18.9 - - - +
253A GLU* 2.8 34.5 + - - +
312A LEU* 4.0 0.9 - - - -
315A ARG* 2.9 32.1 + - - +
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Residues in contact with GLU 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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212A ARG* 1.3 76.2 - - - +
214A ALA* 1.3 56.4 + - - +
215A GLY 3.2 0.2 + - - -
216A HIS* 2.8 46.1 + - + -
217A ARG 2.9 25.8 + - - +
253A GLU* 4.0 0.9 - - - -
308A GLN* 3.8 14.1 + - - +
311A ARG* 2.8 51.6 + - - +
312A LEU* 4.2 11.6 - - + +
315A ARG* 4.1 10.9 + - - +
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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