Contacts of the strand formed by residues 288 - 296 (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 ARG 288 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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425B ARG* 5.2 4.6 + - - +
428B ASP* 4.8 6.5 + - - +
8420B DMS 4.4 17.0 - - - +
243C GLU* 3.9 23.9 + - + -
244C VAL 3.1 10.1 - - - +
245C GLN* 3.6 40.4 + - + +
274C PHE* 3.7 3.8 - - - -
275C GLY 2.8 26.0 + - - -
276C GLY* 3.1 12.3 + - - +
285C TYR* 3.4 65.9 + - + -
286C ALA 3.4 1.0 + - - -
287C ASP* 1.3 90.9 + - - +
289C VAL* 1.3 63.6 + - - +
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Residues in contact with VAL 289 (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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242C ALA 3.7 1.0 - - - +
243C GLU* 3.5 0.6 - - - -
244C VAL* 2.7 43.3 + - + +
256C VAL* 4.0 27.1 - - + -
272C ALA* 3.8 18.8 - - + +
273C PRO 3.4 26.2 - - - +
274C PHE* 4.1 7.6 - - + -
275C GLY 4.6 2.5 - - - +
276C GLY* 5.0 0.4 - - - -
288C ARG* 1.3 78.1 - - - +
290C THR* 1.3 67.7 + - - +
291C LEU* 3.9 15.0 + - + -
8412C DMS 3.5 20.0 - - + +
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Residues in contact with THR 290 (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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241C GLU* 3.2 41.1 - - + +
242C ALA 3.2 9.6 - - - +
243C GLU* 3.9 19.8 + - + +
272C ALA* 5.6 0.3 - - - +
277C GLU* 5.5 2.8 + - - -
289C VAL* 1.3 78.7 + - - +
291C LEU* 1.3 64.5 + - - +
292C ARG* 3.8 20.2 + - - +
8405C DMS 4.0 4.9 + - - -
8412C DMS 2.8 33.0 + - - +
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Residues in contact with LEU 291 (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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240C LEU* 3.6 1.6 - - - +
241C GLU* 3.5 3.3 - - - -
242C ALA* 2.9 35.5 + - + +
244C VAL* 4.9 0.7 - - + -
256C VAL* 4.1 11.4 - - + +
258C VAL* 3.7 36.6 - - + +
270C GLY 3.5 32.3 - - - +
271C THR* 3.8 14.8 - - - +
272C ALA* 4.0 4.9 - - + +
289C VAL* 3.9 26.7 - - + +
290C THR* 1.3 79.5 - - - +
292C ARG* 1.3 61.5 + - - +
293C LEU* 4.3 6.1 - - + -
8405C DMS 3.2 16.8 - - + +
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Residues in contact with ARG 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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239C VAL* 4.2 15.3 - - + -
240C LEU 3.2 4.9 - - - +
241C GLU* 2.4 41.2 + - + +
277C GLU* 5.1 11.7 + - - -
290C THR* 3.8 15.8 + - - +
291C LEU* 1.3 76.6 - - - +
293C LEU* 1.3 63.3 + - - +
294C ASN* 4.3 4.5 + - - +
8405C DMS 2.8 35.9 + - + +
8412C DMS 3.5 28.5 - - - +
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Residues in contact with LEU 293 (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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239C VAL* 3.4 3.0 - - - +
240C LEU* 2.7 52.3 + - + +
258C VAL* 3.7 31.2 - - + +
260C LEU* 4.1 25.8 - - + -
268C ALA* 4.1 16.6 - - + +
269C SER* 3.6 9.0 - - - +
270C GLY* 3.6 31.4 - - - +
291C LEU* 5.1 4.5 - - + -
292C ARG* 1.3 83.6 - - - +
294C ASN* 1.3 63.8 + - - +
295C VAL* 3.7 2.9 + - + +
8405C DMS 4.8 2.7 - - + -
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Residues in contact with ASN 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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237C ARG* 5.4 9.4 - - - +
238C ALA 3.7 4.3 + - - +
239C VAL* 3.9 21.6 - - - +
268C ALA* 4.1 9.4 - - - +
292C ARG 5.0 3.3 - - - +
293C LEU* 1.3 73.1 - - - +
295C VAL* 1.3 64.3 + - - +
296C GLU* 4.2 11.4 - - - +
8601C DMS 3.6 21.4 - - + +
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Residues in contact with VAL 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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237C ARG* 3.6 2.3 - - - -
238C ALA* 2.9 35.3 + - + +
240C LEU* 4.7 2.0 - - + -
260C LEU* 3.5 26.5 - - + -
267C VAL* 4.0 20.0 - - + -
268C ALA* 5.1 0.4 - - + -
293C LEU* 3.9 11.9 - - + +
294C ASN* 1.3 82.7 - - - +
296C GLU* 1.3 71.4 + - - +
298C PRO* 3.8 25.1 - - + +
309C TYR* 4.5 8.3 - - + +
332C PHE* 3.8 21.1 - - + -
8601C DMS 3.6 2.2 - - - +
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Residues in contact with GLU 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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236C SER 4.0 2.2 - - - +
237C ARG* 2.9 52.8 + - - +
238C ALA 5.4 0.3 - - - +
294C ASN* 4.7 9.0 - - - +
295C VAL* 1.3 81.4 + - - +
297C ASN* 1.3 81.5 + - - +
298C PRO* 3.2 2.1 - - - +
8601C DMS 2.6 36.4 + - + +
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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