Contacts of the strand formed by residues 255 - 263 (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 THR 255 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177J THR* 4.4 12.1 - - - -
178J ASP 3.4 15.9 - - - +
179J THR* 4.2 18.2 + - - +
253J GLY 4.4 0.9 + - - -
254J GLN* 1.3 74.6 + - - +
256J LEU* 1.3 70.9 + - - +
273J VAL* 3.3 7.0 - - - -
274J GLN* 2.9 49.9 + - + +
275J GLU* 2.6 24.3 + - - -
171K PRO* 4.7 9.6 - - + +
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Residues in contact with LEU 256 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176J LEU 4.8 0.2 - - - -
177J THR* 3.4 4.9 - - - -
178J ASP* 2.9 38.2 + - + +
180J THR* 4.0 15.3 - - - +
214J LEU* 5.3 2.2 - - + -
219J THR* 3.7 31.2 - - + +
222J PHE* 3.6 44.9 - - + -
223J SER 5.5 0.2 - - - +
250J VAL* 3.9 29.4 - - + -
254J GLN 5.5 0.2 - - - +
255J THR* 1.3 81.0 - - - +
257J GLN* 1.3 60.5 + - - +
258J THR* 4.1 4.3 - - - +
271J THR* 4.4 8.7 - - + -
272J LYS 3.3 9.0 - - - +
273J VAL* 4.5 1.8 - - + -
280J VAL* 4.7 0.2 - - + -
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Residues in contact with GLN 257 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175J VAL* 4.0 20.8 - - + +
176J LEU 3.9 2.2 - - - -
177J THR* 4.1 15.0 - - + +
256J LEU* 1.3 74.2 - - - +
258J THR* 1.3 61.3 + - - +
259J GLU* 3.6 8.7 + - + +
270J GLN 3.6 1.0 - - - +
271J THR* 3.2 5.1 - - - +
272J LYS* 2.7 63.2 + - + +
274J GLN* 2.9 42.8 - - + +
277J GLY* 5.7 1.2 - - - -
171K PRO* 5.3 1.4 - - - +
172K PRO* 6.1 1.4 - - - +
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Residues in contact with THR 258 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175J VAL* 3.1 23.2 - - - +
176J LEU 3.0 20.0 + - - -
178J ASP* 5.2 1.7 + - - -
222J PHE* 5.0 0.5 - - - +
223J SER* 2.8 50.8 + - - +
226J ARG* 4.6 7.6 - - + +
227J VAL* 4.8 0.2 - - + -
256J LEU* 5.1 3.8 - - - +
257J GLN* 1.3 72.7 + - - +
259J GLU* 1.3 60.0 + - - +
260J MET* 3.8 27.6 - - + +
269J PHE* 4.2 9.4 - - + -
270J GLN 3.5 7.2 - - - +
271J THR* 4.0 3.1 - - - +
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Residues in contact with GLU 259 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172J PRO* 4.1 16.0 - - + +
174J ALA 3.8 4.7 - - - -
175J VAL* 4.0 15.0 - - + +
257J GLN* 4.3 13.4 - - + +
258J THR* 1.3 73.3 - - - +
260J MET* 1.3 60.8 + - - +
261J TRP* 3.4 19.6 - - + -
269J PHE* 3.0 8.3 - - - +
270J GLN* 2.7 66.7 + - - +
272J LYS* 3.0 35.4 + - + +
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Residues in contact with MET 260 (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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172J PRO* 3.5 2.1 - - - +
173J ASP* 2.7 33.5 + - - +
174J ALA 2.8 22.8 + - - +
176J LEU* 3.5 42.0 - - + +
226J ARG* 4.4 5.2 - - + -
227J VAL* 3.8 27.1 - - + -
230J GLN* 4.1 7.2 - - + -
231J PHE* 3.5 32.1 - - + -
258J THR* 3.8 25.8 - - + +
259J GLU* 1.3 79.0 - - - +
261J TRP* 1.3 57.4 + - - +
262J LYS 4.3 0.7 - - - -
267J ILE* 4.1 2.2 - - + -
268J HIS 3.2 6.5 - - - +
269J PHE* 4.2 7.2 - - + -
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Residues in contact with TRP 261 (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* 3.4 37.5 - - + -
168J PRO* 3.6 45.7 + - + -
170J ARG* 2.6 45.0 + - + +
172J PRO* 3.4 31.2 - - + -
173J ASP* 3.4 4.9 - - - -
259J GLU* 3.4 42.2 - - + -
260J MET* 1.3 76.9 - - - +
262J LYS* 1.3 61.9 + - - +
263J GLU 3.6 1.4 + - - -
267J ILE* 3.4 5.9 - - - -
268J HIS* 2.8 50.7 + - + +
269J PHE* 4.1 0.2 - - - -
270J GLN* 3.7 14.6 - - + -
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Residues in contact with LYS 262 (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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170J ARG* 3.4 14.0 + - - -
173J ASP* 2.7 17.1 + - - +
231J PHE* 3.7 31.6 - - + -
260J MET 4.3 0.2 - - - -
261J TRP* 1.3 72.1 - - - +
263J GLU* 1.3 63.4 + - - +
264J GLY* 3.0 27.5 + - - +
265J ASN* 5.9 0.7 - - - +
267J ILE* 3.5 19.7 - - + -
39K LYS* 4.6 29.3 + - - +
40K ASP* 5.6 1.2 - - - +
41K PRO* 5.0 9.1 - - - +
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Residues in contact with GLU 263 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168J PRO* 3.8 15.3 - - + +
170J ARG* 2.9 35.7 + - - +
261J TRP 4.6 0.4 - - - +
262J LYS* 1.3 72.7 - - - +
264J GLY* 1.3 63.5 + - - +
265J ASN 3.2 0.9 + - - -
266J ARG* 3.0 28.4 + - + +
268J HIS* 3.5 29.4 - - + +
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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