Contacts of the strand formed by residues 241 - 249 (chain J) in PDB entry 1S7X
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 241 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207J GLY 3.2 15.4 + - - -
208J PHE* 3.0 53.3 + - + -
209J TYR* 3.9 16.8 - + - -
210J PRO 4.3 0.4 - - - -
211J ALA* 3.8 35.4 - - + -
233J THR* 3.9 7.4 - - + -
234J ARG* 3.3 19.7 - - - +
235J PRO* 3.5 28.9 - - + -
236J ALA 4.2 0.2 - - - +
239J GLY 3.9 15.3 - - - -
240J THR* 1.3 75.9 - - - +
242J GLN* 1.3 64.2 + - - +
26K TYR* 5.7 1.8 - - - -
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Residues in contact with GLN 242 (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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204J TRP* 4.9 2.7 - - + -
205J ALA 3.4 6.5 - - - -
206J LEU* 3.5 28.8 - - + +
207J GLY 5.2 0.9 - - - +
208J PHE* 3.8 2.7 - - - -
233J THR* 3.6 2.8 - - - +
234J ARG* 2.9 73.5 + - - +
236J ALA* 3.9 17.0 - - + +
241J PHE* 1.3 77.2 - - - +
243J LYS* 1.3 64.0 + - - +
10K TYR* 3.3 11.6 - - - -
11K SER 3.7 6.2 + - - +
12K ARG* 2.8 36.4 + - - +
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Residues in contact with LYS 243 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204J TRP* 3.7 3.8 - - - +
205J ALA* 2.9 35.3 + - + +
208J PHE* 4.4 10.1 - - + -
213J ILE* 3.9 20.9 - - + +
214J THR* 6.0 0.7 - - - +
215J LEU* 3.7 23.2 - - + +
230J LEU* 4.4 16.5 - - - +
231J VAL* 2.8 37.5 + - - +
232J GLU* 3.9 7.3 + - - +
233J THR* 3.2 30.6 + - - +
234J ARG* 5.2 1.1 - - - +
242J GLN* 1.3 77.4 - - - +
244J TRP* 1.3 71.2 + - - +
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Residues in contact with TRP 244 (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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202J ARG* 3.6 35.9 - - + -
203J CYS 3.3 11.9 - - - +
204J TRP* 4.1 34.5 - + + -
215J LEU* 3.9 3.4 - - - -
229J GLU* 3.7 31.6 - - + -
230J LEU* 3.5 8.8 - - - +
231J VAL* 3.4 58.4 + - + +
234J ARG* 4.5 6.4 - - - +
243J LYS* 1.3 80.3 - - - +
245J ALA* 1.3 62.6 + - - +
246J SER* 3.3 38.4 - - - -
99K MET* 3.6 26.7 - - + +
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Residues in contact with ALA 245 (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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203J CYS* 3.1 23.2 + - + +
215J LEU* 3.8 26.0 - - + +
217J TRP* 3.0 20.6 + - + +
228J MET* 4.0 20.0 - - - -
229J GLU 3.3 11.9 - - - +
230J LEU* 4.5 5.6 - - + -
243J LYS* 6.2 0.9 - - - -
244J TRP* 1.3 78.5 - - - +
246J SER* 1.3 60.7 + - - +
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Residues in contact with SER 246 (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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200J THR* 4.7 13.1 - - - +
201J LEU 3.2 16.6 - - - -
202J ARG* 3.8 23.7 + - - -
217J TRP* 4.3 0.7 - - - -
228J MET* 3.4 7.1 - - - +
229J GLU* 3.0 38.9 + - - +
244J TRP* 3.3 24.1 - - - -
245J ALA* 1.3 74.3 - - - +
247J VAL* 1.3 65.3 + - - +
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Residues in contact with VAL 247 (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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199J VAL 3.7 0.3 - - - +
200J THR* 3.3 9.1 - - - -
201J LEU* 3.2 30.0 + - + +
217J TRP* 3.8 39.3 - - + +
224J LEU* 5.0 17.0 - - + -
226J GLN* 4.3 17.5 - - + +
227J ASP 4.4 6.3 - - - +
228J MET* 4.5 12.1 - - + -
229J GLU* 5.9 0.2 - - - -
246J SER* 1.3 80.3 + - - +
248J VAL* 1.3 77.0 + - + +
249J VAL* 4.0 18.5 - - + +
257J TYR* 4.8 3.4 - - + -
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Residues in contact with VAL 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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194J ARG* 4.6 13.2 - - - +
198J GLU* 4.8 13.2 - - - +
199J VAL 3.8 5.2 - - - +
200J THR* 4.2 15.3 - - + -
226J GLN* 4.7 13.9 - - - +
227J ASP* 4.8 16.5 + - + +
247J VAL* 1.3 84.7 - - - +
249J VAL* 1.3 67.4 + - - +
250J PRO* 4.8 0.5 - - - +
257J TYR* 4.5 5.7 + - - -
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Residues in contact with VAL 249 (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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198J GLU* 4.2 6.8 + - - -
199J VAL* 3.2 34.4 + - + +
201J LEU* 3.7 19.7 - - + -
247J VAL* 4.0 11.4 - - + +
248J VAL* 1.3 81.6 - - - +
250J PRO* 1.3 71.6 - - - +
253J LYS 3.4 11.2 - - - +
254J GLU* 3.6 22.0 - - + -
257J TYR* 3.4 50.9 - - + -
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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