Contacts of the strand formed by residues 207 - 217 (chain A) in PDB entry 1J71
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 THR 207 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202A ILE 3.6 1.4 - - - +
203A ASN* 3.1 2.3 - - - -
204A PHE* 2.7 40.6 + - - +
205A ASP 3.4 3.4 + - - -
206A GLY* 1.3 74.8 - - - +
208A SER* 1.3 69.3 + - - +
209A VAL* 3.8 1.4 + - + +
237A ILE* 4.0 32.9 - - + +
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Residues in contact with SER 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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201A SER* 4.4 14.0 + - - -
202A ILE 3.9 2.9 - - - -
203A ASN* 3.8 19.3 + - - +
206A GLY 3.3 2.9 + - - -
207A THR* 1.3 78.2 - - - +
209A VAL* 1.3 64.2 + - - +
210A SER 4.2 1.3 + - - -
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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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201A SER* 3.2 3.9 - - - -
202A ILE 3.0 41.2 + - - +
204A PHE* 4.0 8.5 - - + -
207A THR* 4.2 2.2 - - + +
208A SER* 1.3 80.0 + - - +
210A SER* 1.3 65.7 + - - +
211A THR* 3.5 1.7 + - - +
233A LYS* 3.6 31.4 - - + +
234A PHE* 3.5 30.1 - - + -
237A ILE* 3.3 33.7 - - + -
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Residues in contact with SER 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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200A GLY 3.9 9.8 + - - -
201A SER* 4.0 4.7 - - - -
208A SER* 4.2 1.6 + - - -
209A VAL* 1.3 75.2 - - - +
211A THR* 1.3 61.4 + - - +
212A ASN* 4.3 10.7 + - - +
230A THR* 4.5 1.0 + - - +
233A LYS* 2.9 31.7 + - - +
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Residues in contact with THR 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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199A LEU* 3.0 31.0 + - + +
200A GLY 3.0 12.2 + - - -
201A SER* 3.4 2.6 + - - -
202A ILE* 4.0 17.7 - - + -
209A VAL 3.5 8.3 + - - +
210A SER* 1.3 77.1 - - - +
212A ASN* 1.3 72.9 + - - +
213A ALA* 3.2 8.9 + - - +
226A PHE* 4.6 8.1 - - + -
230A THR* 4.0 16.4 + - + +
234A PHE* 3.8 29.8 - - + -
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Residues in contact with ASN 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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198A HIS* 2.9 33.5 + - - -
199A LEU 3.4 6.1 - - - -
200A GLY* 3.0 8.3 + - - +
210A SER* 4.4 9.9 - - - +
211A THR* 1.3 83.7 + - - +
213A ALA* 1.3 58.8 + - - +
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Residues in contact with ALA 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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198A HIS* 3.9 3.0 - - - -
199A LEU* 2.8 37.6 + - + +
211A THR* 3.6 10.1 - - - +
212A ASN* 1.3 78.1 - - - +
214A ASP* 1.3 66.2 + - - +
215A VAL* 3.4 9.9 + - + +
226A PHE* 4.9 8.1 - - + -
297A ASN* 3.8 27.8 - - - +
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Residues in contact with ASP 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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190A THR* 3.3 37.5 + - - +
196A ARG* 2.9 30.2 + - - -
197A VAL 3.4 4.5 - - - -
198A HIS* 3.5 25.8 + - - +
213A ALA* 1.3 69.5 - - - +
215A VAL* 1.3 60.7 + - - +
297A ASN* 4.0 8.9 + - - +
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Residues in contact with VAL 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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196A ARG* 3.0 5.3 - - - -
197A VAL* 2.9 44.1 + - + +
199A LEU* 4.0 16.2 - - + -
213A ALA* 4.0 9.4 - - + +
214A ASP* 1.3 76.3 - - - +
216A VAL* 1.3 62.0 + - - +
217A LEU* 3.8 1.7 + - + +
226A PHE* 3.8 32.8 - - + -
264A PHE* 4.4 0.4 - - + -
297A ASN* 3.3 18.4 - - + +
299A LEU* 3.7 33.4 - - + -
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Residues in contact with VAL 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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33A THR 5.2 0.7 - - - +
34A GLY* 5.0 7.9 - - - -
194A GLU* 4.4 7.2 - - + -
195A LEU* 3.5 25.8 - - + +
196A ARG* 3.4 22.7 - - + +
215A VAL* 1.3 72.7 - - - +
217A LEU* 1.3 70.3 + - - +
218A ASP* 3.1 11.1 + - + +
297A ASN 3.1 15.4 + - - +
298A ILE* 3.7 23.8 - - + -
299A LEU* 3.0 25.1 + - - -
336B THR* 3.9 18.6 - - + -
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Residues in contact with LEU 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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33A THR* 2.7 26.0 + - - +
195A LEU* 3.2 14.8 + - - +
197A VAL* 4.6 15.5 - - + -
215A VAL 4.5 4.7 - - - +
216A VAL* 1.3 74.2 - - - +
218A ASP* 1.3 52.6 + - - +
219A SER 3.9 0.2 - - - -
264A PHE* 5.0 1.1 - - + -
299A LEU* 3.6 38.4 - - + -
303A PHE* 4.2 8.5 - - + -
304A LEU* 3.9 7.4 - - + -
309A ILE* 4.1 13.9 - - + -
311A TYR* 3.0 24.1 + - + +
318A ILE* 3.9 30.1 - - + -
320A LEU* 4.0 21.1 - - + -
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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