Contacts of the strand formed by residues 293 - 304 (chain C) in PDB entry 2UZX
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 GLU 293 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A LYS* 5.6 5.7 - - - +
274C ASP* 4.0 5.5 - - - +
291C THR* 3.0 16.1 + - - +
292C ASN* 1.3 90.0 - - + +
294C VAL* 1.3 76.4 + - - +
295C SER* 4.5 5.4 + - - -
316C THR* 3.3 26.9 - - - +
317C GLN 3.2 20.2 - - - +
318C PRO* 4.0 3.8 - - + -
319C LEU* 3.8 4.9 - - - -
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Residues in contact with VAL 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253C LEU* 4.3 7.9 - - + -
273C SER* 3.6 5.8 - - - +
274C ASP* 3.7 9.6 - - - +
285C TRP* 3.4 60.3 - - + +
287C LEU* 4.6 7.2 - - + -
291C THR* 4.5 7.2 - - + -
293C GLU* 1.3 83.7 - - - +
295C SER* 1.3 67.9 + - - +
317C GLN* 2.9 45.4 + - + +
319C LEU* 4.4 9.9 - - + -
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Residues in contact with SER 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C ILE* 3.9 0.3 - - - -
273C SER* 2.9 39.9 + - - -
285C TRP* 3.8 6.7 - - - -
293C GLU* 4.5 7.0 + - - -
294C VAL* 1.3 83.6 - - - +
296C PHE* 1.3 64.1 + - - +
297C ILE* 5.3 3.0 - - - +
314C ARG* 4.4 17.5 - - - -
315C VAL 3.0 21.5 - - - -
316C THR* 4.1 5.2 - - - -
317C GLN* 4.8 1.1 - - - +
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Residues in contact with PHE 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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255C VAL* 5.2 8.3 - - + -
256C PRO 5.2 1.6 - - - -
257C ASN* 3.6 32.1 - - - -
258C THR* 5.2 1.6 - - - -
259C VAL* 4.5 4.9 - - + -
269C PRO* 4.0 21.3 - - + -
271C ILE 3.1 16.6 - - - +
272C ILE* 3.9 15.9 - - + -
283C VAL* 3.9 29.6 - - + -
285C TRP* 4.3 8.5 - + - -
295C SER* 1.3 80.6 - - - +
297C ILE* 1.3 68.9 + - - +
298C PHE* 3.9 4.8 + - + -
313C GLY 4.1 0.2 - - - +
314C ARG* 3.6 0.3 - - - -
315C VAL* 3.0 60.8 + - + +
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Residues in contact with ILE 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269C PRO* 3.9 2.6 - - - +
270C GLU* 3.0 35.7 + - - +
271C ILE* 3.0 24.3 + - + +
273C SER 6.3 0.2 - - - +
295C SER* 5.3 2.9 - - - +
296C PHE* 1.3 81.1 - - - +
298C PHE* 1.3 71.9 + - - +
312C HIS* 3.9 6.7 - - + +
313C GLY 3.2 11.0 - - - +
314C ARG* 4.2 25.1 - - + +
331D ARG 4.0 9.4 - - - +
332D GLN 3.7 16.8 - - - +
333D ILE 5.1 0.2 - - - -
334D GLY* 3.4 36.3 - - - +
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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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220C ILE 4.7 2.0 - - - -
240C GLN* 4.5 6.7 - - + -
242C CYS* 5.0 4.5 - - - -
259C VAL* 3.9 33.4 - - + -
267C VAL* 4.5 18.8 - - + +
269C PRO* 4.5 10.3 - - + -
270C GLU* 4.0 6.1 - - - +
296C PHE* 4.6 6.1 - + + -
297C ILE* 1.3 76.9 - - - +
299C TYR* 1.3 61.3 + - - +
311C PHE* 3.5 51.8 - + - -
312C HIS* 3.1 35.9 - - - -
313C GLY* 2.8 53.2 + - - -
314C ARG 4.0 2.0 - - - -
315C VAL* 4.6 10.8 - - + -
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Residues in contact with TYR 299 (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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238C PHE* 4.6 4.3 - + - -
267C VAL* 4.6 3.5 - - - +
268C THR 4.8 4.6 + - - +
270C GLU* 3.2 30.2 - - + +
298C PHE* 1.3 77.9 - - - +
300C GLN* 1.3 67.6 + - - +
301C PRO* 3.7 29.2 - - + +
310C ARG* 3.0 39.5 + - + -
311C PHE 3.7 3.4 - - - -
312C HIS* 4.4 12.3 - + + -
427D VAL* 4.7 17.0 - - + +
469D ARG* 3.4 43.1 - - - -
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Residues in contact with GLN 300 (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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261C ASN* 3.6 25.6 + - - +
267C VAL* 3.6 36.3 - - + +
268C THR* 4.9 6.1 + - - -
298C PHE* 5.0 0.7 - - + -
299C TYR* 1.3 79.8 - - - +
301C PRO* 1.3 94.6 + - - +
302C VAL* 3.2 4.9 + - + +
310C ARG* 4.6 1.1 - - - -
311C PHE* 2.7 42.3 + - + +
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Residues in contact with PRO 301 (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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299C TYR* 3.7 29.6 - - + +
300C GLN* 1.3 108.4 + - - +
302C VAL* 1.3 59.8 + - - +
309C ALA 3.7 9.4 - - - +
310C ARG* 4.2 6.3 - - + -
301D THR* 6.2 4.7 - - + -
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Residues in contact with VAL 302 (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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223C LEU* 4.2 10.8 - - + -
235C LEU* 4.7 5.6 - - + -
237C LEU* 4.4 12.6 - - + -
261C ASN* 3.6 24.5 - - - +
262C THR* 5.0 4.5 - - + +
300C GLN* 3.4 13.9 - - + +
301C PRO* 1.3 75.8 - - - +
303C THR* 1.3 71.5 + - - +
304C ILE* 5.0 5.4 - - + -
308C LYS* 3.8 1.6 - - - +
309C ALA* 2.9 50.3 + - + +
311C PHE* 4.0 17.3 - - + +
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Residues in contact with THR 303 (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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262C THR* 5.5 2.6 + - - +
302C VAL* 1.3 81.9 + - - +
304C ILE* 1.3 66.8 + - - +
305C GLY 4.0 17.0 - - - +
306C LYS 5.0 0.7 - - - -
307C ALA 3.2 19.1 + - - +
308C LYS* 4.1 21.8 + - + +
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Residues in contact with ILE 304 (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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223C LEU* 5.4 3.8 - - + -
226C LEU* 3.6 40.8 - - + +
227C ALA* 4.3 8.5 - - - +
229C LEU 3.6 19.3 - - - +
232C LEU* 3.9 16.4 - - + +
235C LEU* 4.0 24.8 - - + +
262C THR* 3.8 29.4 - - + -
302C VAL* 5.0 3.4 - - + -
303C THR* 1.3 80.6 - - - +
305C GLY* 1.3 64.8 + - - +
306C LYS 2.9 0.9 + - - -
307C ALA* 2.9 34.2 + - + +
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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