Contacts of the strand formed by residues 283 - 295 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192A LYS 3.2 17.2 - - - +
274A ARG* 3.8 34.8 - - + +
275A VAL 3.8 4.7 - - - -
276A LYS* 4.5 2.9 - - - +
282A ARG* 1.3 82.1 + - - +
284A MET* 1.3 64.2 + - - +
285A TYR* 4.6 2.8 - - - +
7F A 3.9 19.0 + - - +
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Residues in contact with MET 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A TYR* 3.6 34.1 - - + +
190A VAL* 3.6 27.4 - - + -
191A LEU 3.5 19.5 - - - +
192A LYS* 3.8 13.0 - - + +
274A ARG* 3.3 5.9 - - - -
275A VAL* 2.7 47.7 + - + +
277A ASP* 3.4 45.1 - - + +
282A ARG* 4.0 7.2 - - + +
283A ALA* 1.3 80.0 - - - +
285A TYR* 1.3 67.3 + - - +
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Residues in contact with TYR 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A VAL* 3.4 3.0 - - - -
191A LEU* 2.7 39.0 + - + +
192A LYS 4.6 1.3 - - - -
193A THR* 3.6 28.7 - - - +
194A THR* 3.5 22.6 - - + +
197A VAL* 4.7 4.5 - - + -
225A PHE* 4.0 17.3 - + + -
272A PHE* 3.5 32.4 - - + -
273A ALA 3.3 2.9 - - - +
274A ARG* 3.5 47.3 + - + -
283A ALA 4.6 1.3 - - - -
284A MET* 1.3 83.1 - - - +
286A ARG* 1.3 60.4 + - - +
6F G 3.8 6.9 + - - -
7F A 3.0 39.7 + - - -
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Residues in contact with ARG 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A GLN* 5.6 2.0 + - - -
63A TYR* 6.1 1.4 - - - -
111A ASP* 3.0 36.7 + - - -
113A ILE* 4.0 20.0 - - - +
185A LEU* 5.7 1.6 + - - +
188A ASN* 2.9 48.7 + - - +
189A VAL 3.6 5.3 - - - +
190A VAL* 3.4 25.0 - - + +
272A PHE* 3.1 3.0 - - - -
273A ALA* 2.7 39.9 + - - +
275A VAL* 4.1 10.8 - - + -
284A MET 4.2 0.6 - - - -
285A TYR* 1.3 72.6 - - - +
287A PHE* 1.3 76.0 + - - +
288A MET* 3.2 27.3 + - + +
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Residues in contact with PHE 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A ILE* 3.4 33.4 - - + -
184A SER 4.0 7.6 - - - -
185A LEU* 3.1 29.8 - - + +
189A VAL* 3.0 18.6 + - + +
270A ILE* 3.9 5.8 - - + -
271A VAL 3.4 15.3 - - - -
272A PHE* 3.5 33.1 - + + -
286A ARG* 1.3 81.3 + - - +
288A MET* 1.3 58.5 + - - +
289A GLY* 3.3 39.5 - - - -
290A LEU 4.1 1.8 - - - -
309A SER 3.6 19.1 - - - -
311A VAL* 3.6 32.1 - - + -
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Residues in contact with MET 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A ILE 4.5 15.0 - - - +
113A ILE* 5.9 0.7 - - - -
185A LEU* 3.6 15.6 - - - +
228A LEU* 4.3 17.7 - - + -
238A ILE* 4.7 10.3 - - + -
245A ILE* 5.0 1.1 - - + -
271A VAL* 2.9 18.2 + - + +
273A ALA* 3.7 35.2 - - + +
275A VAL* 5.1 5.4 - - + -
286A ARG* 3.7 28.7 - - + +
287A PHE* 1.3 78.4 - - - +
289A GLY* 1.3 58.1 + - - +
291A TYR* 3.4 30.2 + - + +
306A ARG* 3.6 10.4 + - - -
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Residues in contact with GLY 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A LEU* 4.5 2.7 - - - -
270A ILE* 3.6 0.7 - - - -
271A VAL 2.9 25.5 + - - -
287A PHE* 3.3 31.6 - - - -
288A MET* 1.3 82.0 - - - +
290A LEU* 1.3 59.8 + - - -
291A TYR* 3.6 8.8 - - - -
306A ARG* 4.3 1.6 - - - -
308A LYS 3.7 7.9 - - - -
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Residues in contact with LEU 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A THR* 4.7 9.0 - - + -
268A LYS* 4.6 20.0 - - + +
269A ARG 3.5 26.0 - - - +
270A ILE* 3.7 13.0 - - + +
287A PHE* 4.1 0.8 - - - -
289A GLY* 1.3 71.6 - - - -
291A TYR* 1.3 65.1 + - - +
306A ARG* 3.8 1.4 - - - -
307A VAL* 3.0 15.7 + - + +
308A LYS* 2.9 69.0 + - + +
311A VAL* 3.6 22.7 - - + -
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Residues in contact with TYR 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A ILE* 4.0 6.8 - - - +
242A GLY* 2.5 24.8 + - - -
243A LEU 3.4 18.8 - - - -
245A ILE* 3.5 26.7 - - + -
268A LYS* 3.5 5.5 - - - +
269A ARG* 2.9 38.6 + - + +
271A VAL* 3.5 20.2 - - + -
288A MET* 3.4 44.8 + - + +
289A GLY* 3.6 5.6 - - - -
290A LEU* 1.3 79.0 - - - +
292A GLU* 1.3 61.4 + - - +
304A TRP* 3.5 34.6 - - + -
305A LYS 3.2 3.8 - - - +
306A ARG* 3.5 15.6 + - + -
307A VAL* 4.6 1.3 - - - -
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Residues in contact with GLU 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A GLN* 3.7 15.6 - - + +
268A LYS* 2.8 33.0 + - + +
290A LEU 4.4 0.2 + - - -
291A TYR* 1.3 75.6 - - - +
293A PHE* 1.3 70.7 + - - +
294A GLN* 3.5 13.1 + - - +
304A TRP* 3.3 4.2 - - - -
305A LYS* 2.5 42.5 + - - +
307A VAL* 3.6 27.2 - - + +
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Residues in contact with PHE 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262A TRP* 3.8 40.4 - + + -
263A LYS* 4.4 12.1 - - + -
266A PRO 5.3 0.2 - - - +
267A GLN* 3.1 43.1 + - - +
292A GLU* 1.3 76.9 - - - +
294A GLN* 1.3 63.1 + - - +
295A LYS* 3.0 42.0 - - - -
296A ALA* 3.8 9.0 - - + -
302A ALA* 4.8 2.5 - - + -
303A VAL 3.5 10.1 - - - -
304A TRP* 3.5 34.6 - + + -
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Residues in contact with GLN 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292A GLU* 3.9 12.8 + - - +
293A PHE* 1.3 81.0 + - - +
295A LYS* 1.3 64.1 + - + +
303A VAL* 2.8 24.5 + - + +
305A LYS* 3.5 50.3 - - + +
307A VAL* 5.6 1.8 - - - +
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Residues in contact with LYS 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293A PHE* 3.0 28.5 - - - -
294A GLN* 1.3 84.7 - - - +
296A ALA* 1.3 76.5 + - - +
297A ASP* 4.3 13.2 - - + +
301A GLY 4.1 6.3 - - - +
302A ALA* 3.5 17.2 - - - -
303A VAL* 3.5 26.9 + - + -
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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