Contacts of the strand formed by residues 210 - 219 (chain A) in PDB entry 2J2M
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 210 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202A LYS* 3.8 24.4 - - - +
203A TRP 3.3 7.9 - - - -
204A VAL* 3.7 15.5 - - + -
208A GLY 4.2 8.7 - - - +
209A ASN* 1.3 82.6 + - - +
211A VAL* 1.3 65.4 + - - +
266A ASP* 5.2 0.2 - - - +
267A PRO* 3.2 27.7 - - + +
403A GLN* 3.1 35.6 + - - +
404A PRO* 5.8 0.9 - - + -
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Residues in contact with VAL 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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75A TYR* 3.9 29.4 - - + +
202A LYS* 3.4 5.1 - - - -
203A TRP* 2.9 40.1 + - + +
209A ASN* 4.1 17.0 + - - +
210A THR* 1.3 80.6 - - - +
212A TYR* 1.3 60.7 + - - +
213A ILE* 3.8 14.4 - - + -
264A VAL* 3.6 31.0 - - + -
265A LEU 4.2 1.6 - - - +
266A ASP* 4.7 11.0 - - + +
267A PRO* 3.9 10.3 - - + -
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Residues in contact with TYR 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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200A SER* 3.9 14.1 - - - -
201A PHE 3.2 14.8 - - - -
202A LYS* 3.8 20.9 - - + -
211A VAL* 1.3 71.6 - - - +
213A ILE* 1.3 61.1 + - - +
263A GLN 3.5 0.3 - - - +
264A VAL* 3.4 4.5 - - - -
265A LEU* 2.8 52.1 + - + +
267A PRO* 3.8 35.6 - - + +
270A VAL* 3.9 20.4 - - + -
278A LEU* 3.6 18.8 - - + +
284A TRP* 3.9 15.2 - - + -
327A SER* 4.0 5.6 - - - -
328A GLU* 2.7 36.1 + - - -
28B ARG* 5.0 6.1 + - - -
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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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199A HIS 3.9 0.7 - - - +
200A SER* 3.1 6.9 - - - -
201A PHE* 2.8 53.0 + - + +
203A TRP* 3.6 56.3 - - + +
211A VAL* 3.8 23.8 - - + +
212A TYR* 1.3 81.2 - - - +
214A LYS* 1.3 61.0 + - - +
215A LEU* 3.6 33.4 - - + +
262A VAL* 3.9 8.1 - - + -
263A GLN 2.9 11.0 - - - +
264A VAL* 4.3 4.5 - - + -
284A TRP* 4.2 2.0 - - - -
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Residues in contact with LYS 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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132A PRO 4.6 3.6 + - - -
197A SER* 3.6 11.2 - - - +
198A VAL* 2.6 28.2 + - - +
199A HIS 3.3 20.6 - - - +
200A SER* 3.6 10.1 - - - +
213A ILE* 1.3 74.8 - - - +
215A LEU* 1.3 61.4 + - - +
216A ARG* 4.7 8.9 - - - +
262A VAL* 3.4 9.5 - - - +
263A GLN* 2.8 51.4 + - + +
277A PRO 4.6 4.4 + - - -
279A ASP 5.5 0.6 + - - -
282A LYS 3.5 20.8 + - - -
283A ASP* 4.6 2.0 + - - +
284A TRP* 3.2 52.8 - - + +
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Residues in contact with LEU 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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124A TRP* 3.7 31.0 - - + -
126A PHE* 3.7 25.6 - - + -
196A SER* 3.6 2.4 - - - -
197A SER* 2.8 37.1 + - - -
201A PHE* 5.3 5.4 - - + -
203A TRP* 3.9 13.0 - - + +
213A ILE* 3.6 25.6 - - + -
214A LYS* 1.3 80.4 - - - +
216A ARG* 1.3 67.6 + - - +
260A LEU* 3.9 21.5 - - + -
261A PHE 3.6 12.8 - - - +
262A VAL* 3.9 13.5 - - + -
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Residues in contact with ARG 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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132A PRO* 3.2 33.7 - - - +
194A ARG* 4.3 9.7 - - - +
195A GLY 3.7 4.2 + - - +
196A SER* 4.4 9.6 + - - -
214A LYS* 4.7 9.7 - - - +
215A LEU* 1.3 87.0 + - - +
217A TRP* 1.3 63.2 + - - +
218A VAL* 4.9 1.8 - - + -
259A ASP 3.3 1.4 - - - +
260A LEU* 3.3 7.4 - - - +
261A PHE* 2.8 56.5 + - + +
262A VAL* 5.5 0.2 - - - -
263A GLN* 2.6 40.7 + - + -
283A ASP* 3.3 14.5 + - - -
284A TRP* 3.2 20.4 + - - +
291A PHE* 3.3 36.4 - - + -
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Residues in contact with TRP 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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66A PHE* 3.9 24.5 - + - -
113A PHE* 3.4 34.9 - + + -
115A VAL* 4.3 10.5 - - + -
117A PHE* 4.0 23.3 - + - -
124A TRP* 5.9 0.7 - + - -
126A PHE* 3.3 46.1 - + + -
194A ARG* 3.3 11.6 - - - +
195A GLY* 2.9 33.9 + - - +
216A ARG* 1.3 74.5 - - - +
218A VAL* 1.3 63.2 + - - +
219A PRO 4.2 0.2 - - - -
258A TRP* 3.6 24.7 - - + -
259A ASP 3.2 10.3 - - - -
260A LEU* 3.7 26.2 - - + +
297A MET* 3.5 33.2 - - + -
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Residues in contact with VAL 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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194A ARG* 5.0 0.9 - - + -
216A ARG* 4.8 2.2 - - + +
217A TRP* 1.3 78.1 - - - +
219A PRO* 1.4 75.9 - - + +
220A LYS 3.6 0.2 + - - -
258A TRP* 3.3 2.2 - - - -
259A ASP* 2.9 34.9 + - + +
261A PHE* 3.6 36.6 - - + -
291A PHE* 4.6 17.7 - - + -
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Residues in contact with PRO 219 (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 ARG 3.8 16.4 - - - +
193A MET 3.5 30.5 - - - +
194A ARG* 4.0 13.5 - - + -
218A VAL* 1.4 93.6 - - + +
220A LYS* 1.3 65.4 + - - +
222A GLY* 3.1 37.7 + - - +
223A VAL* 3.8 7.4 - - + +
257A GLU 3.8 2.0 - - - +
258A TRP* 3.5 14.6 - - + +
259A ASP* 5.6 0.2 - - - -
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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