Contacts of the strand formed by residues 266 - 273 (chain J) in PDB entry 1S9C
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 ARG 266 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165J VAL* 3.8 26.1 - - - +
263J GLU* 3.0 34.2 + - + +
264J GLY 3.3 0.4 - - - -
265J ASN* 1.3 80.6 - - - +
267J ILE* 1.3 63.5 + - - +
268J HIS* 3.6 33.2 + - + +
285J TYR* 3.2 37.5 + - + -
286J VAL 3.7 3.6 - - - -
287J ASP* 2.7 40.6 + - - +
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Residues in contact with ILE 267 (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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227J VAL* 3.9 22.2 - - + -
231J PHE* 3.6 45.1 - - + -
260J MET* 4.1 5.8 - - + -
261J TRP 3.4 7.0 - - - +
262J LYS* 3.5 34.3 - - + -
264J GLY 4.8 3.1 - - - +
266J ARG* 1.3 76.3 - - - +
268J HIS* 1.3 67.4 + - - +
269J PHE* 4.1 0.5 - - - -
285J TYR* 3.2 3.4 - - - -
286J VAL* 3.0 35.4 + - + +
288J LEU* 3.8 26.5 - - + -
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Residues in contact with HIS 268 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165J VAL* 3.7 26.3 - - + +
166J ALA 3.5 17.3 + - - -
167J ILE* 4.4 3.5 - - - -
168J PRO* 3.6 24.6 - - + +
260J MET* 3.2 4.7 - - - +
261J TRP* 2.8 38.2 + - + +
263J GLU* 3.5 37.0 - - + +
266J ARG* 3.6 30.9 - - + +
267J ILE* 1.3 73.9 - - - +
269J PHE* 1.3 60.8 + - - +
284J ALA 3.5 11.5 + - - +
285J TYR* 4.1 1.7 - - - +
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Residues in contact with PHE 269 (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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167J ILE* 4.3 4.5 - - - +
220J PHE* 5.2 8.7 - + - -
223J SER* 3.6 27.6 - - - -
224J ALA* 4.9 9.2 - - + -
227J VAL* 4.2 14.8 - - + -
242J VAL* 5.3 3.4 - - + -
244J ALA* 4.4 9.4 - - + -
258J THR* 4.2 2.9 - - + -
259J GLU 3.0 14.8 - - - +
260J MET* 4.2 11.9 - - + -
261J TRP* 4.1 4.0 - - - -
267J ILE 4.1 3.8 - - - -
268J HIS* 1.3 76.6 - - - +
270J GLN* 1.3 63.2 + - - +
271J THR* 3.8 15.0 - - - -
281J ILE* 4.0 9.9 - - + -
283J ASN 4.4 0.5 + - - -
284J ALA* 3.0 57.6 + - + +
285J TYR* 3.6 29.6 - - - -
286J VAL* 4.3 6.3 - - + -
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Residues in contact with GLN 270 (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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167J ILE* 3.5 33.1 - - + +
257J GLN 3.6 0.3 - - - +
258J THR* 3.5 1.9 - - - +
259J GLU* 2.7 57.0 + - - +
261J TRP* 3.7 10.3 - - + -
269J PHE* 1.3 76.8 - - - +
271J THR* 1.3 64.8 + - - +
272J LYS* 3.9 8.8 - - - +
279J ILE* 3.2 32.6 - - + +
281J ILE 3.4 16.6 - - - +
282J SER* 4.4 9.5 - - - -
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Residues in contact with THR 271 (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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219J THR* 4.1 10.5 - - + -
223J SER* 2.7 33.8 + - - +
256J LEU* 4.4 6.1 - - + -
257J GLN 3.2 14.1 - - - +
258J THR* 4.0 4.7 - - - +
269J PHE* 3.8 3.5 - - - -
270J GLN* 1.3 76.5 + - - +
272J LYS* 1.3 64.4 + - - +
279J ILE* 3.5 4.2 - - - +
280J VAL* 2.7 42.8 + - + +
281J ILE* 2.9 34.5 + - - +
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Residues in contact with LYS 272 (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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256J LEU* 3.3 5.7 - - - +
257J GLN* 2.7 49.7 + - + +
259J GLU* 3.0 41.5 + - - +
270J GLN* 3.9 11.6 - - - +
271J THR* 1.3 82.5 - - - +
273J VAL* 1.3 64.8 + - - +
274J GLN 3.8 0.2 - - - -
277J GLY* 4.0 16.1 + - - +
278J ASP 3.1 15.0 - - - +
279J ILE* 3.8 19.3 - - + -
280J VAL* 4.3 1.6 - - - +
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Residues in contact with VAL 273 (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 PRO 4.5 2.2 - - - +
250J VAL* 3.8 17.9 - - + -
254J GLN* 3.8 34.8 - - + +
255J THR 3.3 6.1 - - - +
256J LEU* 4.5 3.1 - - + -
272J LYS* 1.3 78.0 - - - +
274J GLN* 1.3 49.5 + - - +
275J GLU* 2.7 30.7 + - + +
276J THR* 3.0 16.6 + - - +
277J GLY* 2.7 31.6 + - - -
278J ASP* 3.0 7.8 + - + +
280J VAL* 3.5 27.4 - - + -
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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