Contacts of the strand formed by residues 210 - 219 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202C LYS* 3.9 17.5 - - - +
203C TRP 3.1 9.4 - - - -
204C VAL* 3.8 13.9 - - + -
208C GLY 4.2 8.3 - - - +
209C ASN* 1.3 78.1 - - - +
211C VAL* 1.3 67.3 + - - +
267C PRO* 3.2 29.3 - - + +
401C ASP* 4.6 0.7 - - - +
403C GLN* 3.1 38.5 + - - +
404C PRO* 5.7 2.5 - - + -
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Residues in contact with VAL 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C TYR* 4.1 28.5 - - + +
202C LYS* 3.3 5.1 - - - -
203C TRP* 2.9 37.8 + - + +
209C ASN* 5.6 4.0 - - + +
210C THR* 1.3 83.1 - - - +
212C TYR* 1.3 62.9 + - - +
213C ILE* 3.9 14.4 - - + -
264C VAL* 3.8 28.9 - - + -
265C LEU 3.7 11.7 - - - +
266C ASP* 4.6 10.5 - - - +
267C PRO* 4.0 5.2 - - + -
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Residues in contact with TYR 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200C SER* 4.0 6.5 - - - -
201C PHE 3.3 10.3 - - - -
202C LYS* 3.5 21.7 + - + -
211C VAL* 1.3 73.2 - - - +
213C ILE* 1.3 64.2 + - - +
264C VAL* 3.5 0.3 - - - -
265C LEU* 2.8 42.6 + - + +
267C PRO* 3.9 25.6 - - + -
270C VAL* 3.8 30.5 - - + -
278C LEU* 3.7 29.4 - - + +
284C TRP* 3.8 18.8 - - + -
327C SER* 3.8 7.2 - - - -
328C GLU* 2.7 38.3 + - - -
28D ARG* 5.2 3.5 + - - -
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Residues in contact with ILE 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199C HIS 4.1 0.2 - - - +
200C SER* 2.9 6.1 - - - -
201C PHE* 2.7 56.0 + - + +
203C TRP* 3.5 48.5 - - + +
211C VAL* 3.9 22.7 - - + +
212C TYR* 1.3 81.4 - - - +
214C LYS* 1.3 65.8 + - - +
215C LEU* 4.0 23.8 - - + +
262C VAL* 3.5 16.2 - - + -
263C GLN 3.0 9.0 - - - +
264C VAL* 4.3 4.3 - - + -
284C TRP* 4.0 4.7 - - - -
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Residues in contact with LYS 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132C PRO 5.0 2.4 + - - -
197C SER* 3.5 16.8 - - - +
198C VAL* 2.7 26.0 + - - +
199C HIS* 3.7 10.0 - - - +
200C SER* 3.8 9.6 - - - +
213C ILE* 1.3 73.0 - - - +
215C LEU* 1.3 63.7 + - - +
216C ARG* 4.6 8.0 - - - +
261C PHE 3.9 0.2 - - - +
262C VAL* 3.3 7.1 - - - +
263C GLN* 2.9 44.8 + - + +
277C PRO 4.3 6.9 + - - -
279C ASP 5.0 2.6 + - - -
282C LYS 3.3 20.6 + - - -
283C ASP* 5.0 1.3 - - - +
284C TRP* 3.4 64.4 - - + +
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Residues in contact with LEU 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C TRP* 3.7 34.8 - - + -
126C PHE* 3.8 25.1 - - + -
196C SER* 3.7 1.3 - - - -
197C SER* 3.0 34.6 + - - -
201C PHE* 5.7 3.8 - - + -
203C TRP* 4.0 16.2 - - + +
213C ILE* 4.0 15.2 - - + +
214C LYS* 1.3 80.3 - - - +
216C ARG* 1.3 71.0 + - - +
260C LEU* 3.8 22.7 - - + -
261C PHE 3.5 13.2 - - - +
262C VAL* 3.8 20.0 - - + -
294C VAL* 5.3 0.2 - - + -
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Residues in contact with ARG 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132C PRO* 3.4 22.3 - - - +
194C ARG* 4.3 9.7 - - - +
195C GLY 3.6 4.7 + - - +
196C SER* 4.7 10.2 + - - -
214C LYS* 4.6 9.6 - - - +
215C LEU* 1.3 87.8 + - - +
217C TRP* 1.3 65.9 + - - +
218C VAL* 5.3 1.3 - - + -
259C ASP 3.4 1.4 - - - +
260C LEU* 3.2 9.7 - - - +
261C PHE* 2.8 54.9 + - + +
263C GLN* 2.6 39.8 + - + +
283C ASP* 3.1 23.4 + - - -
284C TRP* 3.3 18.6 + - - +
291C PHE* 3.4 34.9 - - + -
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Residues in contact with TRP 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C PHE* 3.6 28.7 - + - -
113C PHE* 3.4 32.0 - + + -
115C VAL* 4.4 9.2 - - + -
117C PHE* 3.9 22.0 - + - -
124C TRP* 6.1 0.4 - + - -
126C PHE* 3.2 45.5 - + - -
194C ARG* 3.3 11.4 - - - +
195C GLY* 2.8 42.6 + - - +
216C ARG* 1.3 74.8 - - - +
218C VAL* 1.3 62.6 + - - +
258C TRP* 3.5 26.9 - - + -
259C ASP 3.4 4.3 - - - -
260C LEU* 3.6 33.3 - - + +
297C MET* 3.6 28.5 - - + -
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Residues in contact with VAL 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194C ARG* 6.0 0.4 - - + -
216C ARG* 4.9 1.1 - - + +
217C TRP* 1.3 79.8 - - - +
219C PRO* 1.3 76.2 - - + +
220C LYS* 3.5 0.7 + - - -
258C TRP* 3.0 7.7 - - - -
259C ASP* 2.9 40.5 + - + +
261C PHE* 3.7 32.5 - - + -
291C PHE* 4.8 16.4 - - + -
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Residues in contact with PRO 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191C ARG 3.9 11.9 - - - +
193C MET 3.4 31.4 - - - +
194C ARG* 4.0 10.3 - - + -
218C VAL* 1.3 93.6 - - + +
220C LYS* 1.3 65.8 + - - +
222C GLY* 2.9 43.7 + - - +
223C VAL* 3.8 11.2 - - + -
257C GLU 3.8 1.8 - - - +
258C TRP* 3.4 14.5 - - + +
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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