Contacts of the strand formed by residues 235 - 243 (chain M) in PDB entry 6VDK
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 TRP 235 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160A LYS* 5.9 1.8 - - - +
44C GLN* 4.7 19.5 - - + -
45C LEU* 3.2 29.4 - - + -
46C LYS* 3.4 7.2 - - - -
47C GLY* 3.3 22.7 - - - -
226M TYR* 4.4 8.1 - - + -
227M TYR* 3.3 26.5 - - - -
228M ARG* 3.1 62.4 - - + +
233M PRO 3.2 15.7 + - - -
234M VAL* 1.3 91.1 - - - +
236M LYS* 1.3 68.0 + - - +
264M LYS 5.1 0.2 - - - -
265M ALA* 4.3 15.0 - - - -
266M LYS* 4.3 7.9 - - + -
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Residues in contact with LYS 236 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226M TYR* 3.3 14.3 - - - +
227M TYR* 3.0 54.3 + - + +
229M ASP* 3.0 28.3 + - - +
232M ASP* 6.0 2.2 + - - -
234M VAL* 5.2 7.6 - - + +
235M TRP* 1.3 79.3 - - - +
237M GLY* 1.3 61.8 + - - +
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Residues in contact with GLY 237 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225M VAL 4.0 1.6 - - - -
226M TYR* 3.5 9.5 - - - -
227M TYR* 3.8 13.5 + - - -
236M LYS* 1.3 82.0 - - - +
238M PRO* 1.3 75.3 - - - +
253M ASP* 4.3 6.9 + - - -
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Residues in contact with PRO 238 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C ASP* 5.6 2.2 - - - +
224M ARG* 3.7 25.6 - - + -
225M VAL 2.9 16.4 - - - +
226M TYR* 3.5 29.4 - - + +
237M GLY* 1.3 79.4 - - - +
239M ALA* 1.3 61.4 + - - +
240M LYS* 5.5 1.5 + - - -
253M ASP* 2.9 21.8 - - - +
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Residues in contact with ALA 239 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223M PHE 3.6 0.2 - - - +
224M ARG* 3.4 9.1 - - - -
225M VAL* 2.9 44.9 + - + +
227M TYR* 4.9 4.0 - - + -
238M PRO* 1.3 75.8 - - - +
240M LYS* 1.3 65.8 + - - +
251M ILE* 3.7 17.3 - - + -
252M GLN 3.3 18.2 - - - +
253M ASP* 3.6 14.4 - - + +
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Residues in contact with LYS 240 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222M ASN* 6.5 1.1 - - - -
223M PHE 4.0 8.7 - - - +
224M ARG* 5.9 5.6 - - + -
238M PRO 5.5 1.2 + - - -
239M ALA* 1.3 77.7 - - - +
241M LEU* 1.3 68.5 + - - +
242M LEU* 3.9 4.1 - - + +
251M ILE* 3.2 4.6 - - - -
252M GLN* 2.9 55.1 + - + +
253M ASP 3.9 17.4 + - - -
254M ASN* 5.1 2.4 + - - -
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Residues in contact with LEU 241 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222M ASN* 6.1 1.1 - - - +
223M PHE* 3.3 41.0 + - + +
224M ARG 4.2 2.2 - - - +
225M VAL* 4.4 11.2 - - + -
240M LYS* 1.3 75.9 - - - +
242M LEU* 1.3 69.2 + - - +
243M TRP 5.0 0.2 - - - +
244M LYS* 4.3 20.9 - - + +
249M VAL* 4.2 21.5 - - + -
251M ILE* 3.7 7.4 - - + -
267M ILE* 3.7 39.7 - - + -
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Residues in contact with LEU 242 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E A 5.2 8.3 + - + +
240M LYS* 4.0 7.9 - - + +
241M LEU* 1.3 85.1 - - - +
243M TRP* 1.3 67.4 + - - +
250M VAL* 3.0 16.1 + - + +
251M ILE* 3.6 31.6 - - - +
252M GLN* 4.2 9.9 - - + -
257M ILE* 3.8 34.5 - - + -
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Residues in contact with TRP 243 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E A 3.3 79.7 + + + +
16E C 4.3 25.4 - + - -
242M LEU* 1.3 83.4 - - - +
244M LYS* 1.3 80.7 + - - +
245M GLY* 3.7 4.4 + - - -
248M ALA 4.5 0.2 - - - +
249M VAL* 3.6 4.5 - - - -
250M VAL* 3.1 36.2 + - + +
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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