Contacts of the strand formed by residues 247 - 252 (chain M) in PDB entry 5GJQ
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 THR 247 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176M GLU* 5.2 10.3 - - + +
177M VAL 6.2 0.2 - - - +
180M ARG* 4.3 0.4 - - - +
245M LYS 3.8 0.8 + - - -
246M ALA* 1.3 66.5 - - - +
248M PHE* 1.3 72.5 + - - +
249M LEU* 3.4 2.5 + - + +
274M LEU* 5.1 10.1 - - + -
275M ALA* 6.1 0.4 - - - -
278M LYS* 3.8 45.2 + - + +
280M PRO* 3.1 16.6 + - - +
281M SER* 3.3 27.0 - - - -
282M ILE 4.4 0.2 - - - -
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Residues in contact with PHE 248 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309H PHE* 2.9 42.2 - + - -
175M MET 3.9 3.6 - - - +
176M GLU* 4.4 1.4 - - - -
177M VAL* 2.8 51.5 + - + +
180M ARG* 3.2 23.5 - - - +
237M ALA* 4.7 5.4 - - + -
240M CYS* 6.0 0.4 - - + -
241M ALA* 3.7 19.7 - - + -
244M THR* 5.2 2.5 - - - +
246M ALA 3.0 6.4 + - - -
247M THR* 1.3 79.0 - - - +
249M LEU* 1.3 63.5 + - - +
250M LYS* 3.0 32.1 - - + -
282M ILE* 3.6 25.4 - - + +
284M PHE* 3.8 22.9 - + + -
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Residues in contact with LEU 249 (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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172M VAL* 6.4 0.2 - - + -
175M MET* 3.5 40.2 - - + +
176M GLU* 5.6 0.4 - - - -
247M THR* 3.4 6.5 + - + +
248M PHE* 1.3 71.3 - - - +
250M LYS* 1.3 53.4 + - - +
251M LEU* 5.1 0.4 - - + -
271M ALA* 3.6 20.9 - - + +
274M LEU* 5.1 13.0 - - + -
275M ALA* 3.8 10.8 - - + -
281M SER* 4.9 2.0 - - - -
282M ILE 2.4 25.6 + - - +
283M ILE* 2.5 59.6 - - + +
284M PHE 2.3 30.5 + - - -
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Residues in contact with LYS 250 (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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309H PHE* 3.9 23.6 + - + -
310H ASP* 3.4 39.8 + - - +
174M ALA 5.1 6.5 - - - -
175M MET* 3.5 23.4 + - - +
176M GLU 4.1 15.0 - - - -
177M VAL* 3.7 10.1 - - + +
248M PHE* 3.0 33.1 - - + -
249M LEU* 1.3 71.8 - - - +
251M LEU* 1.3 62.1 + - - +
284M PHE* 3.6 12.3 - - + -
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Residues in contact with LEU 251 (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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175M MET* 3.1 43.7 - - + -
249M LEU* 5.1 0.9 - - + -
250M LYS* 1.3 76.5 - - - +
252M ALA* 1.3 66.2 + - - +
255M GLN* 3.1 20.4 - - + +
256M LEU* 3.3 42.4 - - + -
268M VAL* 6.0 1.1 - - + -
271M ALA* 5.3 6.3 - - + -
283M ILE* 4.8 11.7 - - + -
284M PHE* 2.6 23.9 + - - +
285M ILE* 3.2 21.0 - - + -
286M ASP* 3.1 17.0 + - - +
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Residues in contact with ALA 252 (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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301H GLU* 4.8 1.3 - - - +
304H ASN* 3.0 28.9 - - - +
251M LEU* 1.3 89.7 - - - +
253M GLY* 1.3 65.1 + - - +
254M PRO* 3.4 7.8 - - + -
255M GLN* 3.2 41.7 + - + +
256M LEU* 3.7 3.5 - - - +
285M ILE* 5.1 0.2 - - - -
286M ASP* 4.4 6.5 - - + +
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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
------------------------------------------------------------
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