Contacts of the strand formed by residues 247 - 254 (chain J) in PDB entry 1O1F
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 GLY 247 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246J PHE* 1.3 82.5 - - - +
248J MLY 1.3 66.7 + - - +
267J THR* 3.6 1.9 - - - -
268J TYR* 3.0 36.6 + - - -
269J LEU* 4.4 0.6 + - - +
463J ASP 3.3 10.8 - - - -
464J ILE* 4.2 15.9 - - - -
465J ALA 5.7 0.2 - - - -
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Residues in contact with MLY 248 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186J THR* 3.3 33.4 - - - -
189J THR* 4.8 13.5 - - - -
190J MLY 4.8 9.4 - - - -
193J ILE* 5.6 1.6 - - - -
226J ASN* 2.8 43.2 - - - -
229J LEU* 5.4 9.7 - - + +
230J GLU* 5.0 5.4 - - - -
234J ASN* 5.9 0.2 - - - -
244J SER* 4.6 7.0 - - - -
246J PHE* 4.0 26.5 - - + -
247J GLY* 1.3 78.1 - - - +
249J PHE* 1.3 65.1 + - - +
250J ILE* 3.8 31.6 - - + -
265J ILE* 4.5 15.3 - - + -
266J GLU 3.3 11.2 - - - +
267J THR* 4.9 0.2 - - - -
268J TYR* 4.1 6.2 - - - -
461J VAL 3.7 0.8 - - - +
462J LEU* 3.5 3.2 - - - +
463J ASP* 2.4 64.9 + - + +
464J ILE* 4.2 0.4 - - - +
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Residues in contact with PHE 249 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174J SER* 5.5 1.1 - - - -
248J MLY 1.3 77.0 - - - +
250J ILE* 1.3 60.5 + - - +
251J ARG* 4.0 27.8 - - + -
264J ASP 3.0 13.2 - - - +
265J ILE* 3.6 0.4 - - - -
266J GLU* 3.1 24.6 + - + +
268J TYR* 3.8 23.1 - - + +
458J PHE* 4.7 5.4 - + - -
460J GLY* 3.9 28.5 - - - -
461J VAL 3.5 6.3 - - - -
462J LEU* 3.6 28.9 - - + -
660J LEU* 3.9 19.3 - - + -
663J ASN* 4.2 21.1 - - + -
664J LEU* 4.0 24.5 - - + -
667J THR* 6.0 0.2 - - - -
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Residues in contact with ILE 250 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189J THR* 5.0 3.4 - - + -
193J ILE* 3.1 35.9 - - + -
222J ILE* 6.0 0.7 - - + -
226J ASN* 5.4 0.7 - - - +
248J MLY 3.8 38.8 - - + -
249J PHE* 1.3 76.8 - - - +
251J ARG* 1.3 70.2 + - - +
252J ILE* 3.6 13.6 + - + -
263J ALA* 4.3 6.3 - - + -
264J ASP 3.2 18.6 - - - +
265J ILE* 4.3 17.3 - - + -
459J ILE 3.5 2.8 - - - +
460J GLY* 3.3 4.3 - - - -
461J VAL* 3.1 37.5 + - + +
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Residues in contact with ARG 251 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249J PHE* 4.0 21.3 - - + -
250J ILE* 1.3 77.3 - - - +
252J ILE* 1.3 62.2 - - - +
253J HIS* 3.1 47.3 + - + -
263J ALA* 3.0 22.7 - - - -
264J ASP* 3.0 42.9 + - + -
458J PHE* 3.7 35.5 - - + -
459J ILE 4.0 2.2 - - - -
663J ASN* 3.6 34.2 + - - +
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Residues in contact with ILE 252 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193J ILE* 3.9 33.9 - - + -
196J PHE* 4.6 19.5 - - + -
222J ILE* 5.0 6.7 - - + -
250J ILE* 3.6 12.3 + - + -
251J ARG* 1.3 71.6 - - - +
253J HIS* 1.3 62.4 + - - +
254J PHE* 3.3 24.5 - - + -
260J LEU* 3.2 34.8 - - + -
262J SER 3.4 4.5 - - - +
263J ALA* 4.6 7.4 - - + -
458J PHE* 3.0 3.1 - - - -
459J ILE 2.7 43.8 + - - +
461J VAL* 4.6 9.6 - - + -
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Residues in contact with HIS 253 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251J ARG* 3.1 66.4 + - + -
252J ILE* 1.3 71.2 - - - +
254J PHE* 1.3 64.7 + - - +
260J LEU* 4.4 0.2 - - - -
261J ALA* 2.9 25.2 + - - +
262J SER* 2.4 39.5 + - - +
263J ALA 4.3 0.2 + - - -
264J ASP* 3.6 10.1 + - - -
455J ARG* 4.2 32.6 + - + -
457J TYR 3.5 6.5 - - - +
458J PHE* 3.6 20.0 - + + +
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Residues in contact with PHE 254 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163J TYR* 4.1 11.4 - + - -
166J MET* 3.0 39.5 - - + -
196J PHE* 3.6 31.2 - + + -
200J ALA* 4.3 8.3 - - + -
252J ILE* 3.3 28.3 - - + -
253J HIS* 1.3 76.6 - - - +
255J GLY* 1.3 69.3 + - - +
258J GLY* 3.9 20.0 - - - +
259J LYS 4.2 0.9 - - - -
260J LEU* 3.7 30.7 - - + -
261J ALA* 4.2 0.9 - - - +
455J ARG* 3.8 3.1 - - - -
456J GLN 3.4 11.8 + - - -
457J TYR 2.7 18.1 + - - +
459J ILE* 3.3 25.8 - - + -
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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