Contacts of the strand formed by residues 227 - 235 (chain A) in PDB entry 5JSJ
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 LYS 227 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A GLU* 2.8 48.2 + - + +
220A TYR 3.4 17.7 - - - +
221A ALA* 4.0 13.0 - - + -
222A LYS* 4.3 1.1 - - - +
226A SER* 1.3 83.6 - - - +
228A ARG* 1.3 69.7 + - - +
229A THR* 4.7 8.6 - - + +
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Residues in contact with ARG 228 (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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219A GLU* 3.2 3.6 - - - +
220A TYR* 2.8 55.0 + - - +
222A LYS* 5.1 10.1 - - + +
227A LYS* 1.3 78.3 - - - +
229A THR* 1.3 64.0 + - - +
247A PHE* 3.8 32.6 - - + +
248A ASP 5.8 2.0 - - - +
250A ASP* 3.7 9.5 + - - +
254A TYR* 2.6 39.6 + - - -
256A TYR* 4.0 19.0 + - - -
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Residues in contact with THR 229 (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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217A GLN* 5.8 1.8 - - - -
218A VAL 3.5 6.7 - - - +
219A GLU* 3.8 26.7 - - + +
227A LYS* 4.7 11.2 - - + +
228A ARG* 1.3 77.2 - - - +
230A GLY* 1.3 59.2 - - - +
247A PHE* 3.3 10.1 - - - +
248A ASP* 3.1 40.5 + - - +
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Residues in contact with GLY 230 (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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217A GLN* 3.5 14.3 + - - +
218A VAL* 2.9 36.3 + - - -
229A THR* 1.3 76.5 - - - +
231A MET* 1.3 61.2 + - - -
245A ILE* 4.9 0.2 - - - -
246A LYS 3.1 12.8 - - - -
247A PHE* 4.0 7.3 - - - -
248A ASP* 4.3 9.2 + - - -
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Residues in contact with MET 231 (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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82A VAL* 3.9 18.8 - - + +
83A ASN* 3.6 37.7 - - + +
86A LEU* 5.5 1.3 - - + -
215A GLY* 3.9 17.3 - - - +
216A LYS 3.6 11.4 - - - +
217A GLN* 3.8 19.3 - - - +
218A VAL* 4.3 0.4 - - - +
230A GLY* 1.3 73.7 - - - -
232A VAL* 1.3 75.9 + - - +
233A ILE* 3.6 20.4 + - + +
245A ILE* 3.4 4.9 - - - +
246A LYS* 2.8 36.0 + - + +
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Residues in contact with VAL 232 (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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82A VAL* 4.0 0.3 - - - +
213A LEU* 3.6 26.2 - - + +
214A VAL* 4.0 4.7 - - - -
215A GLY* 2.8 27.2 + - - -
216A LYS* 3.2 10.3 + - + +
218A VAL* 3.9 23.1 - - + -
231A MET* 1.3 78.0 - - - +
233A ILE* 1.3 61.3 + - - +
234A HIS 4.3 1.8 - - - +
243A TYR* 3.5 41.3 - - + -
244A PHE 3.5 4.5 - - - +
245A ILE* 4.1 10.3 - - + -
258A LEU* 4.5 14.6 - - + -
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Residues in contact with ILE 233 (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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80A VAL* 3.8 39.1 - - + +
81A PRO* 5.1 5.7 - - - +
82A VAL* 4.0 9.5 - - - +
86A LEU* 4.3 6.5 - - + -
88A LEU* 4.4 8.7 - - + -
214A VAL* 3.3 15.8 - - - +
231A MET* 3.7 33.9 - - + +
232A VAL* 1.3 76.3 - - - +
234A HIS* 1.3 69.0 + - + +
244A PHE* 3.0 29.0 + - + +
245A ILE 4.4 0.7 - - - +
246A LYS* 4.1 12.8 - - + +
253A ILE* 4.3 25.4 - - + -
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Residues in contact with HIS 234 (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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78A ASP* 5.8 3.1 + - - -
81A PRO* 6.2 1.6 - - - +
167A TYR* 6.1 1.0 - - - -
214A VAL* 3.9 6.0 - - - +
232A VAL 3.8 0.8 - - - -
233A ILE* 1.3 85.0 + - + +
235A GLN* 1.3 86.3 + - - +
236A VAL* 4.0 7.1 - - - +
237A GLU* 5.0 4.1 + - + +
243A TYR* 3.2 12.7 - - - -
244A PHE* 2.9 69.2 + + + -
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Residues in contact with GLN 235 (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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212A SER 3.8 13.3 + - - +
214A VAL* 3.7 11.6 - - + +
234A HIS* 1.3 91.2 + - - +
236A VAL* 1.3 70.8 + - - +
237A GLU* 3.3 13.5 + - - +
240A PRO* 3.3 36.7 - - - +
242A VAL 4.1 0.2 - - - +
243A TYR* 2.9 38.9 + - + -
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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