Contacts of the strand formed by residues 281 - 286 (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 SER 281 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246M ALA* 4.0 2.3 - - - +
247M THR* 3.3 21.5 - - - +
249M LEU* 4.9 2.9 - - - -
275M ALA* 3.1 40.1 + - - +
278M LYS 4.8 0.4 - - - -
280M PRO* 1.3 80.8 - - - +
282M ILE* 1.3 60.7 + - - +
283M ILE* 4.5 0.3 - - - +
325M GLN 3.8 3.7 + - - -
326M VAL* 3.4 14.0 - - - +
327M LYS* 2.7 36.4 + - - +
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Residues in contact with ILE 282 (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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202M ILE* 3.0 42.2 - - + -
240M CYS* 4.6 5.8 - - + -
244M THR* 3.3 35.7 - - + +
246M ALA* 5.1 5.5 - - + +
247M THR 3.4 5.3 + - - -
248M PHE* 3.6 22.7 - - + -
249M LEU* 2.4 35.3 + - - +
281M SER* 1.3 75.1 - - - +
283M ILE* 1.3 57.9 + - - +
284M PHE* 3.6 1.0 + - - +
327M LYS* 3.2 10.5 - - + +
329M ILE* 3.3 29.6 - - + -
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Residues in contact with ILE 283 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249M LEU* 2.5 50.9 - - + +
251M LEU* 4.8 10.3 - - + -
271M ALA* 4.2 4.9 - - + +
272M PHE* 3.9 27.6 - - + -
275M ALA* 4.0 6.5 - - + -
281M SER* 4.5 0.4 - - - +
282M ILE* 1.3 71.9 - - - +
284M PHE* 1.3 61.6 + - - +
285M ILE* 3.8 22.6 + - + +
326M VAL* 3.4 28.5 - - + -
327M LYS 2.6 11.6 + - - +
328M VAL* 3.5 6.9 - - + -
329M ILE 2.9 25.8 + - - -
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Residues in contact with PHE 284 (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* 4.0 14.1 - + + -
225M MET* 6.2 2.0 - - + -
233M LYS 4.9 1.8 - - - -
234M THR* 4.4 14.6 - - + -
237M ALA* 2.5 41.3 - - + -
248M PHE* 3.8 18.2 - + + -
249M LEU 2.3 20.3 + - - +
250M LYS* 3.7 14.4 - - + -
251M LEU* 2.6 35.6 + - - +
282M ILE* 3.6 2.5 + - + -
283M ILE 1.3 67.6 - - - +
285M ILE* 1.3 98.7 + - - +
286M ASP* 3.7 26.2 - - + -
329M ILE* 3.2 20.0 - - + +
330M ALA 4.8 0.2 - - - -
331M ALA* 4.1 17.3 - - + -
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Residues in contact with ILE 285 (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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251M LEU* 3.2 20.0 - - + +
253M GLY* 4.6 5.6 - - - -
256M LEU* 5.4 0.9 - - + -
272M PHE* 6.3 1.3 - - + -
283M ILE* 4.2 19.5 - - + +
284M PHE* 1.3 85.4 - - - +
286M ASP* 1.3 69.1 + - - +
287M GLU 3.4 0.3 + - - -
288M LEU* 4.1 25.7 + - + -
291M ILE* 4.5 10.5 - - + -
313M LEU* 4.6 25.6 - - + -
328M VAL* 4.5 18.4 - - + -
329M ILE 2.7 6.2 + - - +
330M ALA* 3.3 13.7 - - + +
331M ALA 3.2 20.1 + - - +
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Residues in contact with ASP 286 (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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304H ASN* 3.3 20.1 + - - +
308H GLY* 4.0 11.4 - - - +
309H PHE* 4.9 3.3 - - - +
234M THR* 4.0 15.0 + - - -
251M LEU 3.1 13.4 + - - +
252M ALA* 4.8 2.0 - - - -
253M GLY* 3.2 13.0 + - - -
284M PHE* 3.7 24.1 - - + -
285M ILE* 1.3 71.8 - - - +
287M GLU* 1.3 108.3 + - - +
331M ALA* 4.2 9.0 - - - +
501M ADP 4.6 6.2 + - - -
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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