Contacts of the strand formed by residues 283 - 297 (chain C) in PDB entry 4PAR
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 ALA 283 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192C LYS 3.1 7.5 - - - +
274C ARG* 3.8 33.0 - - + +
275C VAL 3.7 6.5 - - - -
276C LYS* 4.9 1.5 - - - +
282C ARG* 1.3 95.6 + - - +
284C MET* 1.3 59.3 + - - +
285C TYR* 4.1 5.5 - - + +
15E G 3.7 22.4 + - - +
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Residues in contact with MET 284 (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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172C TYR* 3.5 38.6 - - + -
190C VAL* 3.8 16.6 - - + -
191C LEU 3.5 27.1 - - - +
192C LYS* 3.7 10.8 - - + +
273C ALA 3.4 0.7 - - - +
274C ARG* 3.5 1.2 - - - -
275C VAL* 2.8 43.4 + - + +
277C ASP* 3.9 29.4 - - + +
282C ARG* 3.7 21.3 - - - +
283C ALA* 1.3 79.2 - - - +
285C TYR* 1.3 70.9 + - - +
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Residues in contact with TYR 285 (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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190C VAL* 3.2 3.8 - - - +
191C LEU 2.8 36.4 + - - +
192C LYS 4.1 3.8 - - - -
193C THR* 3.6 24.7 - - - -
194C THR* 3.7 18.3 - - + +
197C VAL* 4.2 11.9 - - + -
225C PHE* 4.2 14.4 - + + -
272C PHE* 3.9 29.7 - - + -
273C ALA 3.3 3.4 - - - +
274C ARG* 3.6 47.7 + - + -
283C ALA* 4.1 3.9 - - + +
284C MET* 1.3 83.9 - - - +
286C ARG* 1.3 61.7 + - - +
14E A 3.8 8.5 - - - -
15E G 2.5 41.2 + - - -
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Residues in contact with ARG 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C GLN* 5.7 1.0 + - - -
63C TYR* 4.9 8.1 - - - -
111C ASP* 2.6 42.4 + - - -
113C ILE* 3.8 22.0 - - - +
188C ASN* 2.4 47.0 + - - +
189C VAL 3.7 10.8 - - - +
190C VAL* 4.0 20.0 - - + +
272C PHE* 3.1 2.9 - - - -
273C ALA 2.8 38.7 + - - +
275C VAL* 4.6 8.3 - - + -
284C MET 4.2 0.2 - - - -
285C TYR* 1.3 72.8 - - - +
287C PHE* 1.3 73.9 + - - +
288C MET* 3.2 27.1 + - + +
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Residues in contact with PHE 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183C ILE* 3.7 21.1 - - + -
184C SER 3.7 22.2 - - - -
185C LEU* 3.1 29.4 - - + +
189C VAL* 3.0 19.8 + - + +
270C ILE* 4.1 2.5 - - + -
271C VAL 3.6 5.6 - - - -
272C PHE* 3.4 38.9 - + + -
286C ARG* 1.3 76.1 - - - +
288C MET* 1.3 58.2 + - - +
289C GLY* 3.5 33.9 - - - -
309C SER 3.5 24.7 - - - -
311C VAL* 3.6 35.9 - - + -
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Residues in contact with MET 288 (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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112C ILE 4.6 13.5 - - - +
113C ILE* 6.0 1.8 - - - -
185C LEU* 3.7 16.0 - - - +
228C LEU* 4.2 15.5 - - + -
238C ILE* 4.2 14.6 - - + -
242C GLY* 6.4 0.2 - - - -
245C ILE* 5.0 0.2 - - + -
271C VAL* 2.8 24.4 + - + +
273C ALA* 3.9 27.4 - - + -
275C VAL* 5.2 6.1 - - + -
286C ARG* 3.2 33.4 + - + +
287C PHE* 1.3 76.5 - - - +
289C GLY* 1.3 58.0 + - - +
291C TYR* 3.7 23.9 + - + +
306C ARG* 3.7 10.2 + - - -
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Residues in contact with GLY 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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185C LEU* 4.9 0.2 - - - -
269C ARG 3.8 0.5 - - - +
270C ILE* 3.7 1.0 - - - -
271C VAL* 2.9 27.0 + - - +
287C PHE* 3.5 31.1 - - - -
288C MET* 1.3 82.2 - - - +
290C LEU* 1.3 60.5 + - - -
291C TYR* 3.9 6.7 - - - -
306C ARG* 4.4 2.7 - - - -
308C LYS 3.9 6.7 - - - -
309C SER* 4.9 2.5 - - - -
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Residues in contact with LEU 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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218C LYS* 6.3 0.4 - - - +
221C THR* 3.9 10.5 - - + +
268C LYS* 4.0 25.8 - - + +
269C ARG 3.4 32.5 - - - +
270C ILE* 3.8 14.6 - - + +
287C PHE* 4.4 0.8 - - - -
289C GLY* 1.3 72.2 - - - -
291C TYR* 1.3 63.1 + - - +
306C ARG* 4.2 1.0 - - - -
307C VAL* 3.3 10.8 + - + +
308C LYS* 2.9 60.0 + - + +
310C GLU 4.9 1.1 - - - +
311C VAL* 3.7 20.6 - - + -
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Residues in contact with TYR 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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238C ILE* 4.0 7.4 - - - +
242C GLY* 2.5 27.1 + - - -
243C LEU 4.1 2.7 - - - -
245C ILE* 3.5 34.2 - - + +
267C GLN 4.1 0.2 - - - +
268C LYS* 3.4 4.2 - - - +
269C ARG* 2.9 35.5 + - + +
271C VAL* 3.7 20.6 - - + -
288C MET* 3.7 34.9 + - + +
289C GLY* 3.9 4.5 - - - -
290C LEU* 1.3 80.5 - - - +
292C GLU* 1.3 60.7 + - - +
304C TRP* 3.3 37.4 - - + -
305C LYS 3.3 5.4 - - - +
306C ARG* 3.4 30.5 - - + -
307C VAL* 4.0 0.9 - - - -
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Residues in contact with GLU 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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267C GLN* 3.3 11.9 - - + +
268C LYS* 4.2 21.1 - - + -
291C TYR* 1.3 74.8 - - - +
293C PHE* 1.3 70.8 + - - +
294C GLN* 3.1 6.4 + - + -
304C TRP* 3.9 3.6 - - - -
305C LYS* 2.9 27.4 + - + +
307C VAL* 3.4 28.7 - - + +
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Residues in contact with PHE 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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262C TRP* 3.8 26.5 - - + +
263C LYS* 4.4 19.7 - - + -
267C GLN* 3.0 36.0 + - - +
292C GLU* 1.3 77.5 - - - +
294C GLN* 1.3 61.0 + - - +
295C LYS* 3.1 42.4 - - - -
296C ALA* 3.6 13.7 - - + -
302C ALA* 4.2 8.3 - - + -
303C VAL 4.0 2.5 - - - -
304C TRP* 3.5 42.4 - + + -
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Residues in contact with GLN 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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292C GLU* 3.1 4.6 + - + +
293C PHE* 1.3 78.0 - - - +
295C LYS* 1.3 94.8 + - + +
303C VAL* 2.9 17.8 + - + +
305C LYS* 3.5 53.4 - - + +
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Residues in contact with LYS 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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293C PHE* 3.1 25.3 - - - -
294C GLN* 1.3 109.9 + - + +
296C ALA* 1.3 58.8 + - - +
297C ASP* 3.1 26.5 - - - +
302C ALA* 3.4 0.9 - - - -
303C VAL* 2.9 48.1 + - + +
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Residues in contact with ALA 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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259C LEU* 3.7 31.7 - - + +
262C TRP* 5.2 1.1 - - + -
263C LYS* 3.7 30.6 + - + +
293C PHE* 3.6 12.8 - - + -
295C LYS* 1.3 77.1 - - - +
297C ASP* 1.3 66.0 + - - +
298C LEU 4.1 0.8 + - - -
301C GLY 4.0 5.2 - - - -
302C ALA* 4.8 4.5 - - - -
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Residues in contact with ASP 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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295C LYS* 3.1 34.7 - - - +
296C ALA* 1.3 76.8 - - - +
298C LEU* 1.3 60.4 + - - +
299C LYS 3.3 2.7 - - - -
300C ASP* 2.8 35.6 + - + +
301C GLY 2.9 15.6 + - - +
303C VAL* 5.5 2.3 - - - +
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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