Contacts of the strand formed by residues 205 - 215 (chain A) in PDB entry 2JK4
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 205 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201A VAL 4.3 2.3 + - - -
202A ASN* 2.3 79.0 + - + +
204A LYS* 1.3 117.0 - - + +
206A GLU* 1.3 61.6 + - - +
207A THR* 5.2 2.9 - - + -
228A TYR* 3.8 22.9 - - + +
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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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199A GLN 4.4 3.6 - - - +
200A LYS* 4.6 16.0 + - + +
202A ASN 3.8 7.4 - - - +
203A LYS 3.5 10.1 - - - +
205A LEU* 1.3 80.6 - - - +
207A THR* 1.3 70.7 + - - +
226A ALA* 3.4 4.7 - - - +
227A LYS* 2.8 64.2 + - + +
228A TYR* 4.1 4.9 - - - -
229A GLN* 2.9 30.4 + - - -
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Residues in contact with THR 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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19A ASP* 5.7 1.7 - - - -
198A TYR* 4.0 3.1 - - - +
199A GLN* 3.1 58.6 + - - +
201A VAL* 6.1 1.6 - - + +
202A ASN* 6.0 0.7 - - - +
205A LEU* 5.2 2.7 - - + -
206A GLU* 1.3 85.4 - - - +
208A ALA* 1.3 67.7 + - - +
209A VAL* 5.8 2.2 - - - +
225A ALA 3.9 9.2 - - - -
226A ALA* 4.1 8.1 - - + +
228A TYR* 5.5 4.9 - - + -
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Residues in contact with ALA 208 (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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16A SER* 3.9 12.6 - - - +
19A ASP* 3.4 25.1 - - - +
197A ILE 3.4 13.7 - - - +
198A TYR* 4.4 7.2 - - + -
199A GLN* 5.8 0.2 - - - -
207A THR* 1.3 82.0 - - - +
209A VAL* 1.3 73.0 + - - +
210A ASN* 4.4 1.8 - - - +
225A ALA* 2.8 32.6 + - + +
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Residues in contact with VAL 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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196A SER* 3.5 0.2 - - - -
197A ILE* 3.0 48.2 + - + +
207A THR* 5.8 1.6 - - - +
208A ALA* 1.3 88.2 - - - +
210A ASN* 1.3 69.3 + - - +
211A LEU* 5.6 2.0 - - + -
222A PHE* 5.9 4.5 - - + -
223A GLY 3.0 19.3 - - - +
224A ILE* 4.2 21.8 - - + -
225A ALA 5.0 0.2 - - - +
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Residues in contact with ASN 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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16A SER* 3.8 17.0 + - - -
20A VAL* 4.3 19.8 - - - +
195A GLY 3.9 5.8 - - - -
196A SER* 4.4 13.0 - - - +
197A ILE* 6.0 0.7 - - - -
208A ALA* 4.4 1.9 - - - +
209A VAL* 1.3 87.5 + - - +
211A LEU* 1.3 68.0 + - - +
222A PHE 4.8 0.4 - - - -
223A GLY* 2.9 41.5 + - - +
225A ALA* 5.1 5.8 - - - +
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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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194A GLY* 3.5 0.7 - - - -
195A GLY 3.0 31.6 + - - +
209A VAL* 5.6 2.5 - - + -
210A ASN* 1.3 80.1 - - - +
212A ALA* 1.3 81.9 + - - +
213A TRP* 4.5 1.6 - - + +
220A THR* 3.4 22.2 - - + -
221A ARG* 2.8 29.6 - - - +
222A PHE* 3.1 46.4 - - + +
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Residues in contact with ALA 212 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188A ASN* 6.0 1.6 - - - +
193A PHE 3.2 11.9 - - - +
194A GLY* 3.5 8.3 - - - -
211A LEU* 1.3 94.0 - - - +
213A TRP* 1.3 53.1 + - - +
220A THR* 4.3 1.0 - - - +
221A ARG* 2.3 58.4 + - + +
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Residues in contact with TRP 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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192A GLU* 4.1 0.2 - - - +
193A PHE* 2.4 68.9 + - + +
194A GLY* 4.2 0.6 - - - +
211A LEU* 5.6 0.9 - - + -
212A ALA* 1.3 68.7 - - - +
214A THR* 1.3 99.6 + - - +
215A ALA* 3.6 15.8 + - - -
216A GLY 4.2 0.7 - - - -
217A ASN* 3.4 24.7 - - - -
218A SER 3.2 23.1 - - - -
219A ASN 3.8 2.2 - - - -
220A THR* 3.2 29.7 + - + -
221A ARG* 3.7 0.9 - - - +
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Residues in contact with THR 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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192A GLU* 2.9 29.8 + - - +
213A TRP* 1.3 92.5 - - - +
215A ALA* 1.3 70.9 + - - +
218A SER* 3.2 27.0 - - - +
219A ASN 5.0 1.6 + - - -
221A ARG* 2.8 31.9 + - - +
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Residues in contact with ALA 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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191A THR* 3.0 46.0 + - + +
192A GLU* 4.8 1.3 - - - +
193A PHE* 4.9 2.4 - - + +
213A TRP* 3.6 14.3 + - - -
214A THR* 1.3 88.6 - - - +
216A GLY* 1.3 60.1 + - - +
217A ASN 3.5 0.2 - - - -
218A SER* 3.3 10.4 + - - -
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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