Contacts of the strand formed by residues 228 - 234 (chain A) in PDB entry 5TK5
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 VAL 228 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A GLN* 3.5 24.9 - - - +
226A VAL 4.5 3.4 - - - +
227A ASP* 1.3 79.9 - - - +
229A TRP* 1.3 61.8 + - - +
230A LEU* 3.8 24.2 + - + -
254A LEU 3.9 0.5 - - - +
255A LEU* 3.6 3.9 - - - +
256A VAL* 2.7 46.3 + - + +
262A TYR* 4.4 15.0 - - + +
274A SER* 4.1 9.6 - - - -
275A VAL 3.6 4.9 - - - +
276A THR* 3.7 24.0 - - + +
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Residues in contact with TRP 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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7A VAL* 4.0 10.1 - - + -
27A MET* 4.0 11.0 - - - -
28A HIS* 3.6 33.1 + + - -
32A LEU* 3.8 19.2 - - + +
34A VAL* 4.0 24.7 - - + -
36A PHE* 4.6 3.6 - + - -
102A LEU* 3.9 22.9 - - + -
104A VAL* 4.9 2.9 - - + -
228A VAL* 1.3 74.5 - - - +
230A LEU* 1.3 60.7 + - - +
231A TRP* 3.7 38.4 - + + -
253A SER* 3.6 32.9 + - - -
254A LEU 3.7 17.0 - - - +
255A LEU* 4.0 4.7 - - + -
273A LEU 3.8 0.3 - - - +
274A SER* 3.1 5.0 - - - -
275A VAL* 2.8 61.3 + - + +
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Residues in contact with LEU 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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228A VAL* 3.8 14.4 - - + -
229A TRP* 1.3 73.9 + - - +
231A TRP* 1.3 62.2 + - - +
232A GLN 4.2 0.4 - - - -
239A VAL* 4.0 27.1 - - + -
248A LEU* 4.6 7.0 - - + -
253A SER* 3.0 7.3 - - - -
254A LEU* 2.8 43.9 + - + +
256A VAL* 4.1 23.1 - - + -
262A TYR* 4.3 17.5 - - + +
264A TRP* 3.8 31.0 - - + -
273A LEU 3.3 3.8 - - - +
274A SER* 3.6 26.5 - - - -
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Residues in contact with TRP 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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7A VAL* 3.3 36.7 - - + +
8A ARG* 5.1 6.3 - - - -
56A TYR* 3.9 31.6 - + - -
58A LEU* 4.6 8.7 - - + -
102A LEU* 4.0 20.6 - - + -
183A LEU* 5.4 2.5 - - + -
229A TRP* 3.7 28.7 + + + +
230A LEU* 1.3 76.8 - - - +
232A GLN* 1.3 72.6 + - - +
233A LEU* 3.4 27.2 + - + +
248A LEU* 5.5 0.2 - - - -
251A ASP* 3.0 30.7 + - - +
252A ASP 3.6 11.2 - - - -
272A ALA* 3.3 4.3 - - - -
273A LEU* 2.8 57.1 + - + +
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Residues in contact with GLN 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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230A LEU 4.2 0.4 - - - -
231A TRP* 1.3 70.4 - - - +
233A LEU* 1.3 54.5 + - - +
234A GLU 3.0 20.6 + - - -
235A GLY 3.3 21.3 + - - +
236A SER 4.0 1.7 - - - -
237A SER* 2.6 33.1 + - - -
248A LEU* 3.8 20.4 - - + +
249A ALA 3.7 14.1 - - - +
251A ASP* 2.8 35.5 + - - -
252A ASP 2.9 15.2 + - - +
264A TRP* 4.2 0.3 - - - -
266A ARG* 5.7 0.4 - - - +
270A SER* 3.7 18.2 + - - -
271A VAL 3.3 15.4 + - - -
272A ALA* 3.6 14.1 - - - +
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Residues in contact with LEU 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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183A LEU* 3.9 15.7 - - + -
184A ASP* 5.4 4.0 - - - +
187A LEU* 3.6 29.2 - - + -
231A TRP* 3.6 55.0 - - + +
232A GLN* 1.3 73.9 - - - +
234A GLU* 1.3 70.3 + - + +
250A PRO* 4.2 6.9 - - - +
251A ASP* 4.1 10.4 + - - +
271A VAL* 2.8 19.3 + - + +
272A ALA* 4.8 0.4 - - - -
273A LEU* 3.9 20.2 - - + +
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Residues in contact with GLU 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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184A ASP* 4.9 9.7 - - - +
187A LEU* 6.1 2.3 - - + +
188A ASP* 4.8 8.7 - - - +
232A GLN* 3.0 6.8 + - - -
233A LEU* 1.3 84.6 - - + +
235A GLY* 1.3 68.1 + - - +
250A PRO* 4.9 1.8 - - - -
269A GLY 4.6 6.1 - - - +
270A SER* 3.3 1.2 - - - -
271A VAL* 2.9 50.3 + - + +
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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