Contacts of the strand formed by residues 322 - 327 (chain C) in PDB entry 4J2X
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 MET 322 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315C TYR* 3.3 7.1 - - - -
316C LEU* 2.9 26.8 + - + -
319C THR* 3.1 27.5 + - + +
320C GLU* 3.5 20.4 - - + +
321C ARG* 1.3 74.9 - - - +
323C TYR* 1.3 59.6 + - - +
333C GLN* 3.5 38.1 - - + +
334C PHE* 3.7 5.2 - - - -
335C GLN* 3.5 42.4 - - + +
195D LYS* 4.6 21.1 - - + -
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Residues in contact with TYR 323 (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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291C ARG* 2.8 31.6 + - - -
298C ALA* 3.7 13.5 - - + +
300C LEU* 3.4 11.8 - - - +
313C ALA* 3.9 25.4 - - + -
314C PHE 3.5 5.8 - - - +
315C TYR* 3.5 28.9 - - + -
316C LEU* 3.7 3.4 - - - -
321C ARG 3.3 24.5 - - - -
322C MET* 1.3 75.2 - - - +
324C LEU* 1.4 65.1 + - - +
325C CYS* 3.1 4.9 + - - +
333C GLN* 3.7 0.7 - - - -
334C PHE 2.9 33.3 + - - +
336C ALA* 3.6 21.8 - - + -
346C GLU* 2.9 21.0 + - - -
348C ILE* 4.0 9.9 - - + -
352C ALA* 4.2 17.7 - - + +
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Residues in contact with LEU 324 (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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215C LEU* 6.0 0.7 - - + -
229C LEU* 4.5 11.0 - - + -
276C LEU* 5.0 1.3 - - + -
285C LEU* 3.7 41.5 - - + -
288C LEU* 4.5 9.2 - - + -
314C PHE* 3.0 40.6 + - + +
316C LEU* 3.4 9.5 - - + +
323C TYR* 1.4 68.9 - - - +
325C CYS* 1.3 58.3 + - - +
331C ILE* 3.6 27.8 - - + -
332C ILE 3.8 3.6 - - - -
352C ALA* 3.6 10.2 - - - +
354C TRP* 3.2 39.6 + - + +
193D PRO* 3.8 12.8 - - + -
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Residues in contact with CYS 325 (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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323C TYR 3.4 11.2 - - - +
324C LEU* 1.3 76.6 - - - +
326C LEU* 1.3 74.8 + - - +
331C ILE* 3.5 4.6 - - - +
332C ILE* 2.7 44.2 + - + +
334C PHE* 3.6 20.0 - - + -
349C ASN* 3.3 38.8 - - - -
351C GLY 3.4 14.4 - - - -
352C ALA* 3.8 4.7 - - + -
354C TRP* 4.6 4.5 - - - +
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Residues in contact with LEU 326 (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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217C ASN* 3.2 40.4 - - + +
227C ARG* 4.2 13.2 - - + +
238C ALA* 3.8 14.4 - - + -
325C CYS* 1.3 86.7 - - - +
327C SER* 1.3 60.9 + - - +
328C GLN* 3.4 23.3 - - - +
330C ARG 3.3 7.0 - - - +
331C ILE* 3.7 17.5 - - + -
332C ILE* 4.6 0.6 - - - +
349C ASN* 4.3 2.8 - - - +
351C GLY* 2.9 23.7 + - - +
354C TRP* 3.6 14.8 - - + -
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Residues in contact with SER 327 (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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326C LEU* 1.3 73.7 - - - +
328C GLN* 1.4 85.7 + - - +
330C ARG* 2.8 48.0 + - - +
332C ILE* 3.8 19.5 - - - -
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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