Contacts of the strand formed by residues 291 - 298 (chain C) in PDB entry 2JJD
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 ARG 291 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222C VAL 3.8 3.0 + - - -
223C TRP* 3.1 83.4 + - + +
226C LYS* 3.4 31.1 - - - +
227C SER 4.3 14.3 + - - -
228C ALA* 5.8 2.2 - - + +
278C CYS* 3.4 4.6 - - - -
279C ILE* 2.9 37.8 + - + +
289C ALA 4.5 2.1 + - - +
290C PRO* 1.3 77.1 - - - +
292C LEU* 1.3 71.2 + - - +
293C VAL* 3.8 3.8 + - + -
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Residues in contact with LEU 292 (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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228C ALA* 3.9 14.7 - - - +
264C GLU* 4.7 8.3 - - + -
276C LYS* 4.2 28.0 - - + -
277C PHE 3.0 26.5 - - - +
278C CYS* 4.3 12.6 - - + -
291C ARG* 1.3 81.7 - - - +
293C VAL* 1.3 62.3 + - - +
294C SER* 4.2 0.7 + - - -
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Residues in contact with VAL 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219C TRP* 4.8 1.6 - - + -
222C VAL* 4.0 6.5 - - + -
227C SER 3.6 22.2 - - - +
228C ALA 3.4 10.1 - - - +
230C ILE* 3.9 33.2 - - + -
276C LYS* 3.8 1.5 - - - -
277C PHE* 2.7 55.0 + - + +
279C ILE* 3.7 32.8 - - + -
291C ARG* 3.8 3.9 + - - +
292C LEU* 1.3 75.8 - - - +
294C SER* 1.3 63.9 + - - +
295C GLN 4.7 0.4 - - - +
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Residues in contact with SER 294 (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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228C ALA 2.9 11.3 + - - -
229C THR* 3.3 13.7 + - - +
230C ILE 3.1 20.5 + - - -
274C ILE* 5.9 1.3 - - - -
275C ARG 3.3 5.4 - - - -
276C LYS* 3.3 39.3 + - - +
292C LEU 4.2 1.3 + - - -
293C VAL* 1.3 72.8 - - - +
295C GLN* 1.3 62.2 + - - +
296C LEU* 4.3 1.7 - - - +
323C LEU* 4.0 26.8 + - - +
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Residues in contact with GLN 295 (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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230C ILE* 3.3 20.4 - - + +
232C MET* 3.7 11.1 - - + -
247C TYR* 2.9 29.8 + - + +
248C TRP* 3.4 26.0 - - - -
273C THR 4.0 0.2 - - - +
274C ILE* 3.5 4.9 - - - +
275C ARG* 2.7 72.4 + - + +
277C PHE* 3.7 24.0 - - + -
293C VAL 4.0 1.4 + - - -
294C SER* 1.3 72.2 - - - +
296C LEU* 1.3 69.0 + - - +
297C HIS* 3.9 10.2 + - - +
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Residues in contact with LEU 296 (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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229C THR* 3.6 30.7 - - + -
230C ILE 2.8 9.9 + - - +
231C VAL* 3.4 3.3 - - - -
232C MET 2.8 25.9 + - - +
272C TYR* 4.8 3.4 - - + -
273C THR 3.9 3.4 - - - -
274C ILE* 3.7 30.1 - - + -
294C SER* 4.3 4.5 - - - +
295C GLN* 1.3 73.3 - - - +
297C HIS* 1.3 60.0 + - - +
298C PHE 4.0 0.4 - - - -
316C PHE* 3.8 25.2 - - + -
319C LYS* 4.0 21.3 - - + -
320C VAL* 3.7 28.7 - - + -
323C LEU* 4.1 15.5 - - + -
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Residues in contact with HIS 297 (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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232C MET* 3.4 34.6 - - + -
234C THR 2.7 29.8 + - - -
235C ASN* 3.8 17.0 + - - -
236C LEU* 5.1 4.3 - - + -
248C TRP* 4.4 4.2 - + - -
272C TYR* 3.4 2.4 - - - -
273C THR* 2.8 42.4 + - - +
275C ARG* 2.9 31.8 + - - +
295C GLN* 3.9 9.1 - - - +
296C LEU* 1.3 72.3 - - - +
298C PHE* 1.3 70.1 + - - +
299C THR* 3.3 8.8 + - - -
316C PHE* 4.3 1.0 - - - -
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Residues in contact with PHE 298 (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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232C MET 2.8 16.1 + - - +
233C LEU* 4.0 19.9 - - + +
234C THR 4.3 3.1 - - - +
235C ASN* 4.9 1.0 + - - +
271C ASP* 3.7 17.0 - - + -
272C TYR* 3.9 4.0 - - + -
296C LEU 3.9 1.0 + - - -
297C HIS* 1.3 76.5 + - - +
299C THR* 1.3 60.9 + - - +
300C SER* 3.7 15.0 - - - -
301C TRP* 3.4 53.2 + + + +
307C PRO* 4.4 10.8 - - + -
312C GLY* 4.3 4.5 - - - -
313C MET* 4.1 29.2 - - + -
316C PHE* 3.6 49.3 - + + -
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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