Contacts of the strand formed by residues 309 - 315 (chain M) in PDB entry 1L0V
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 GLY 309 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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305M SER* 3.9 3.8 + - - -
306M THR* 2.8 35.1 + - - +
307M PRO 3.2 1.4 - - - -
308M ARG* 1.3 82.4 - - - +
310M ASP* 1.3 67.5 + - - +
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Residues in contact with ASP 310 (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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237M PRO* 4.9 2.4 - - - +
294M PHE* 4.8 7.2 - - + -
298M TRP* 3.5 32.1 + - + +
303M THR* 3.9 21.5 + - + -
304M ILE 3.3 6.9 - - - +
305M SER* 3.8 16.6 + - - -
309M GLY* 1.3 76.4 - - - +
311M VAL* 1.3 72.6 + - - +
351M ARG* 4.1 20.7 + - - +
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Residues in contact with VAL 311 (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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237M PRO* 4.9 7.2 - - + -
294M PHE* 4.1 7.1 - - - -
303M THR* 4.5 2.7 - - - -
304M ILE* 3.1 47.9 + - + +
306M THR* 3.7 29.8 - - + +
310M ASP* 1.3 84.4 - - - +
312M VAL* 1.3 77.0 + - - +
313M TYR* 4.9 2.0 - - + +
349M PRO* 3.3 17.9 - - + -
350M VAL 2.7 37.5 - - - +
351M ARG* 4.9 0.2 - - + -
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Residues in contact with VAL 312 (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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254M LEU* 4.8 0.7 - - + -
255M VAL 3.9 8.1 - - - +
256M ASN* 4.9 6.3 - - - +
262M TYR* 3.4 37.9 - - + +
294M PHE* 3.6 33.0 - - + -
297M GLU* 4.8 10.8 - - + -
302M ASN 5.3 4.3 - - - +
303M THR* 5.6 3.4 - - + +
304M ILE* 5.3 1.1 - - - +
311M VAL* 1.3 92.9 - - - +
313M TYR* 1.3 70.9 + - - +
350M VAL* 3.1 31.0 + - + +
351M ARG* 4.4 1.1 - - - +
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Residues in contact with TYR 313 (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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253M ILE 3.4 2.8 - - - +
254M LEU* 3.2 10.3 - - - -
255M VAL* 3.0 47.2 + - + +
256M ASN 4.4 11.7 - - - -
304M ILE* 3.2 54.1 - - + +
306M THR* 5.0 5.2 - - - +
311M VAL* 4.9 1.3 - - + -
312M VAL* 1.3 84.9 - - - +
314M LEU* 1.3 59.8 + - - +
315M ASP 3.4 1.3 + - - +
347M PRO* 4.0 34.3 - - + -
348M ILE 3.5 13.9 - - - -
349M PRO* 3.9 24.1 - - + +
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Residues in contact with LEU 314 (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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234M THR* 4.2 19.3 - - + +
243M MET* 4.5 7.2 - - + -
247M CYS* 3.6 32.3 - - + -
248M ARG* 3.9 24.0 - - + -
252M GLY* 4.3 3.8 - - - -
253M ILE 3.7 22.7 - - - +
254M LEU* 3.9 10.5 - - + -
313M TYR* 1.3 70.1 - - - +
315M ASP* 1.3 62.1 + - - +
316M LEU* 4.5 5.4 - - + -
348M ILE* 2.9 50.2 + - + +
350M VAL* 3.6 19.8 - - + +
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Residues in contact with ASP 315 (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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252M GLY* 3.8 0.2 - - - -
253M ILE* 3.1 33.8 + - + +
255M VAL* 5.1 9.2 - - + -
313M TYR 3.4 2.6 + - - +
314M LEU* 1.3 74.5 - - - +
316M LEU* 1.3 67.9 + - - +
317M ARG* 3.1 44.1 + - - +
318M HIS* 3.1 37.3 + - + -
347M PRO* 3.2 25.0 - - + +
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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