Contacts of the helix formed by residues 283 - 296 (chain A) in PDB entry 3S5O
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 PHE 283 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A EDO 4.9 1.3 - - - -
278A ALA* 3.0 24.5 + - - +
282A ARG* 1.3 115.4 - - + +
284A GLY* 1.3 66.9 + - - +
286A PRO* 3.3 13.0 - - - +
287A GLY* 3.0 23.6 + - - -
309A LEU* 3.9 12.0 - - + +
313A GLU* 3.6 41.5 - - + -
316A ALA* 3.6 22.7 - - + -
317A LEU* 3.7 35.7 - - + -
320A ASP* 4.5 1.3 - - - -
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Residues in contact with GLY 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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3A EDO 3.5 17.7 - - - -
6A EDO 4.0 4.7 - - - -
278A ALA 3.9 3.0 + - - -
279A VAL 3.4 16.3 - - - +
280A THR 2.9 22.7 + - - -
282A ARG 3.7 0.4 - - - -
283A PHE* 1.3 77.6 - - - +
285A ILE* 1.3 58.1 + - - -
287A GLY* 3.0 4.0 + - - -
288A LEU 2.9 22.9 + - - -
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Residues in contact with ILE 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A EDO 3.2 12.6 + - - +
6A EDO 3.8 17.3 - - - -
43A THR* 4.9 3.6 - - + -
77A SER 3.3 26.7 - - - +
78A ASN* 3.8 24.9 - - - +
80A GLU* 3.7 38.6 - - + +
284A GLY* 1.3 68.0 - - - -
286A PRO* 1.3 69.6 - - + +
288A LEU* 3.1 8.1 + - + -
289A LYS* 2.8 42.9 + - + +
302A CYS* 3.8 9.9 - - - -
306A LEU* 4.3 4.3 - - + -
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Residues in contact with PRO 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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3A EDO 3.7 11.9 - - - +
283A PHE 3.3 11.4 - - - +
285A ILE* 1.3 92.5 - - + +
287A GLY* 1.3 60.4 + - - +
289A LYS* 4.0 2.2 - - + +
290A LYS* 3.1 24.1 + - - +
302A CYS* 3.9 19.5 - - - -
306A LEU* 4.4 13.2 - - + -
307A GLN 3.4 26.9 - - - +
308A GLU* 5.0 0.9 - - - -
309A LEU* 3.9 20.6 - - + +
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Residues in contact with GLY 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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278A ALA 4.6 1.1 - - - -
279A VAL* 4.2 6.7 - - - -
283A PHE* 3.0 30.7 + - - +
284A GLY 3.0 4.5 + - - -
286A PRO* 1.3 73.6 - - - +
288A LEU* 1.3 65.3 + - - +
290A LYS 3.3 0.9 + - - -
291A ILE* 3.0 23.9 + - - +
309A LEU* 4.1 11.6 - - - +
317A LEU* 3.6 12.5 - - - +
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Residues in contact with LEU 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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43A THR* 3.7 24.7 - - + -
78A ASN* 3.6 23.8 - - + +
241A ALA* 3.4 23.6 - - + +
244A ASN* 3.9 23.6 - - + +
245A VAL* 4.7 5.6 - - + -
279A VAL* 3.9 26.7 - - + +
284A GLY 2.9 12.7 + - - +
285A ILE* 3.5 10.8 - - + +
287A GLY* 1.3 76.4 - - - +
289A LYS* 1.3 57.4 + - - +
291A ILE* 3.0 14.7 - - + +
292A MET* 2.9 38.5 + - + +
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Residues in contact with LYS 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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43A THR* 3.8 28.0 - - + -
44A THR 2.8 26.4 + - - -
45A PRO* 4.5 0.2 - - - +
46A PHE* 3.6 2.4 - - - -
80A GLU* 2.7 27.5 + - - -
285A ILE* 2.8 25.2 + - + +
286A PRO* 4.2 4.0 - - + +
288A LEU* 1.3 73.4 - - - +
290A LYS* 1.3 57.6 + - - +
292A MET* 3.4 2.6 + - - -
293A ASP* 3.0 27.9 + - - -
299A GLY* 3.2 37.1 + - - +
300A GLY 3.5 20.4 - - - +
301A PRO 2.9 21.2 + - - +
302A CYS* 3.9 13.7 - - - -
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Residues in contact with LYS 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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286A PRO 3.1 19.2 + - - +
287A GLY 3.6 4.5 - - - +
288A LEU 3.3 0.2 - - - -
289A LYS* 1.3 73.6 - - - +
291A ILE* 1.3 65.3 + - - +
293A ASP* 3.2 20.4 + - + +
294A TRP* 3.0 56.1 + - + +
308A GLU* 5.8 3.3 + - - -
309A LEU* 4.4 8.3 - - + +
314A GLU* 3.2 29.8 + - + -
317A LEU* 3.7 19.7 - - + -
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Residues in contact with ILE 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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245A VAL* 3.7 17.7 - - + -
279A VAL* 3.7 17.9 - - + -
287A GLY 3.0 16.1 + - - +
288A LEU* 3.0 23.8 - - + +
290A LYS* 1.3 73.9 - - - +
292A MET* 1.3 65.5 + - - +
294A TRP* 3.1 28.3 + - + -
295A PHE* 2.9 45.1 + - + -
317A LEU* 4.3 5.8 - - + +
321A PHE* 3.7 45.8 - - + -
327A LEU* 4.2 4.5 - - + -
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Residues in contact with MET 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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4A EDO 3.6 22.0 - - - +
43A THR* 3.8 27.1 - - - +
60A ASN* 3.7 12.3 - - - +
64A LEU* 5.8 0.2 - - + -
244A ASN* 4.2 13.2 - - + +
245A VAL* 3.5 21.8 - - + -
288A LEU* 2.9 27.6 + - + +
289A LYS* 3.4 13.2 - - - +
291A ILE* 1.3 74.4 - - - +
293A ASP* 1.3 62.1 + - - +
295A PHE* 3.2 3.1 + - - -
296A GLY 3.1 4.9 + - - -
297A TYR* 2.9 42.8 + - + +
298A TYR 3.6 19.1 - - - +
299A GLY* 3.7 7.9 - - - +
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Residues in contact with ASP 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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289A LYS 3.0 16.6 + - - +
290A LYS* 3.2 26.8 + - + +
292A MET* 1.3 74.4 - - - +
294A TRP* 1.3 67.7 + - + +
296A GLY* 3.1 14.9 + - - -
297A TYR 3.6 8.2 - - - +
298A TYR* 4.4 1.9 - - - -
299A GLY 2.9 22.7 + - - -
300A GLY* 2.9 17.5 + - - +
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Residues in contact with TRP 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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5A EDO 3.8 13.2 + - - -
290A LYS* 3.0 38.2 + - + +
291A ILE* 3.1 25.5 + - + +
293A ASP* 1.3 84.6 - - + +
295A PHE* 1.3 65.9 + - + +
296A GLY 3.3 0.4 + - - -
314A GLU* 3.4 43.9 + - - -
317A LEU* 4.0 11.2 - - + -
318A ARG* 3.6 57.3 - - + +
327A LEU* 3.9 19.6 - - + +
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Residues in contact with PHE 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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2A EDO 3.1 21.6 - - - -
5A EDO 3.9 28.3 + - - -
245A VAL* 3.4 32.5 - - + -
246A LEU* 3.6 20.2 - - + -
291A ILE* 2.9 42.2 + - + +
292A MET 3.2 4.4 + - - +
294A TRP* 1.3 81.2 - - + +
296A GLY* 1.3 58.1 + - - +
297A TYR* 3.5 15.5 - + + -
321A PHE* 4.1 12.6 - + - -
326A TRP 3.5 21.1 - - - -
327A LEU* 4.1 16.6 - - + -
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Residues in contact with GLY 296 (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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1A EDO 4.4 3.8 + - - -
2A EDO 3.6 7.6 - - - -
59A GLU* 5.3 0.3 - - - +
63A LYS* 2.8 22.7 + - - -
293A ASP 3.1 13.0 + - - -
294A TRP 3.3 1.6 + - - -
295A PHE* 1.3 78.1 - - - +
297A TYR* 1.3 63.0 + - - +
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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