Contacts of the strand formed by residues 309 - 317 (chain C) in PDB entry 1JZ3
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 TYR 309 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260C LEU* 3.6 30.3 - - + -
261C TRP 3.3 18.6 - - - +
262C GLN* 3.7 25.2 + - + +
267C VAL* 4.1 18.2 - - + -
295C VAL* 4.5 4.1 - - + +
297C ASN 4.6 0.3 + - - -
298C PRO* 3.4 8.0 - - + +
299C LYS* 2.8 56.3 + - + +
307C ASN* 5.1 1.8 - - + -
308C LEU* 1.3 84.5 - - - +
310C ARG* 1.4 56.8 + - - +
329C ASP* 3.4 6.6 - - - +
330C VAL* 2.7 38.7 + - + +
332C PHE* 3.5 28.0 - + - -
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Residues in contact with ARG 310 (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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36C TRP* 3.5 13.3 - - - -
42C ALA 2.9 25.7 + - - -
43C ARG* 3.2 22.6 + - + +
45C ASP* 2.9 42.8 + - - +
259C SER 3.6 1.6 - - - +
260C LEU* 3.4 6.5 - - - -
261C TRP* 2.9 45.6 + - + +
309C TYR* 1.4 72.5 - - - +
311C ALA* 1.4 61.7 + - - +
312C VAL* 4.1 15.5 - - + -
327C ALA* 3.6 13.7 - - - +
328C CYS* 3.6 9.1 - - - +
329C ASP* 2.8 45.7 + - - +
404C ARG* 4.0 1.0 - - - +
8404C DMS 3.6 6.3 - - - +
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Residues in contact with ALA 311 (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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227C VAL* 4.9 7.0 - - + -
240C LEU* 4.9 5.6 - - + -
258C VAL* 4.6 13.5 - - + -
259C SER 3.4 7.6 - - - +
260C LEU* 4.3 7.0 - - + -
310C ARG* 1.4 71.0 - - - +
312C VAL* 1.3 60.9 + - - +
313C VAL* 4.8 5.3 - - + +
327C ALA* 3.1 7.6 - - - +
328C CYS* 2.8 43.4 + - - +
330C VAL* 3.7 24.1 - - + +
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Residues in contact with VAL 312 (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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39C SER* 4.5 8.5 - - - +
42C ALA* 4.3 13.9 - - + -
43C ARG* 3.7 34.3 - - + +
257C THR 3.5 2.6 - - - +
258C VAL* 3.4 5.5 - - - +
259C SER* 3.0 41.9 + - - +
261C TRP* 4.1 12.6 - - + +
310C ARG* 4.1 8.1 - - + -
311C ALA* 1.3 77.3 - - - +
313C VAL* 1.3 64.0 + - - +
314C GLU* 4.2 22.1 - - + +
325C ALA* 4.8 2.0 - - + -
326C GLU 3.7 7.9 - - - +
327C ALA* 4.0 2.9 - - + -
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Residues in contact with VAL 313 (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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222C ILE* 3.5 22.4 - - + +
225C PHE* 4.2 30.1 - - + -
242C ALA* 5.7 2.7 - - + -
244C VAL* 3.9 30.7 - - + -
256C VAL* 4.2 9.6 - - + -
257C THR 3.7 2.0 - - - -
258C VAL* 4.5 15.7 - - + +
311C ALA* 4.8 6.7 - - + +
312C VAL* 1.3 76.4 - - - +
314C GLU* 1.3 63.1 + - - +
325C ALA* 3.1 4.3 - - - -
326C GLU* 2.8 47.1 + - + +
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Residues in contact with GLU 314 (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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39C SER* 2.4 36.2 + - - +
222C ILE* 4.6 1.6 - - - -
256C VAL* 3.2 9.0 - - - +
257C THR* 2.8 63.2 + - - +
259C SER* 4.8 5.8 + - - -
312C VAL* 4.2 15.0 - - + +
313C VAL* 1.3 76.5 - - - +
315C LEU* 1.3 58.4 + - - +
316C HIS* 3.4 12.8 - - + -
322C LEU* 3.8 15.4 - - + +
324C GLU 3.7 3.8 - - - -
325C ALA* 4.4 2.7 - - + -
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Residues in contact with LEU 315 (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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220C THR* 3.5 33.2 - - + +
221C GLN* 3.5 26.0 - - - +
222C ILE* 3.9 16.1 - - + +
246C MET* 5.1 0.7 - - + -
254C LEU* 4.6 13.2 - - + -
255C ARG 3.5 14.4 - - - +
256C VAL* 4.4 2.9 - - + +
274C PHE* 3.7 30.5 - - + -
313C VAL 4.1 0.6 + - - -
314C GLU* 1.3 71.6 - - - +
316C HIS* 1.3 63.3 + - - +
322C LEU* 3.6 1.4 - - - +
323C ILE* 2.9 34.6 + - + -
324C GLU* 2.8 22.1 + - + +
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Residues in contact with HIS 316 (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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254C LEU* 3.6 5.4 - - - +
255C ARG* 2.8 56.4 + - + +
257C THR* 2.8 32.9 + - - -
271C THR* 4.2 4.7 - - + -
314C GLU* 3.4 29.4 - - + -
315C LEU* 1.3 76.3 - - - +
317C THR* 1.3 84.4 + - - +
318C ALA* 5.4 0.7 - - - -
320C GLY* 4.9 6.2 - - - -
321C THR 3.0 18.2 - - - +
322C LEU* 3.7 10.8 - - + -
323C ILE* 3.9 8.1 - - - +
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Residues in contact with THR 317 (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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253C TYR* 3.3 40.2 - - + -
254C LEU* 4.4 0.2 - - + -
255C ARG* 4.2 0.7 - - - -
316C HIS* 1.3 91.6 + - - +
318C ALA* 1.3 60.8 + - - +
319C ASP* 2.9 29.5 + - - +
320C GLY* 2.7 18.2 + - - -
321C THR* 2.9 24.2 + - + +
323C ILE* 4.3 13.7 - - + -
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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