Contacts of the strand formed by residues 453 - 460 (chain E) in PDB entry 1M1J
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 LYS 453 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260E ARG* 3.4 13.0 - - - +
261E GLN* 4.2 15.9 - - + +
317E GLU 5.3 0.2 - - - -
318E MET* 3.1 7.1 - - - +
319E GLU* 2.9 67.9 + - + +
325E LYS* 5.9 0.4 - - - +
451E MET* 3.5 5.3 - - - +
452E LYS* 1.3 102.0 - - + +
454E MET* 1.3 62.4 + - - +
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Residues in contact with MET 454 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258E GLN* 3.5 10.7 + - - +
259E ASN* 3.4 1.4 - - - -
260E ARG* 2.7 46.0 + - + +
316E ILE* 3.9 19.7 - - - -
317E GLU 3.3 19.1 - - - +
318E MET* 3.7 30.5 - - + -
416E PRO* 3.9 29.2 - - + +
439E ILE* 3.8 32.5 - - + -
440E VAL 5.0 2.9 - - - +
441E TRP* 4.2 11.7 - - + -
451E MET* 4.4 8.5 - - + -
453E LYS* 1.3 75.8 - - - +
455E SER* 1.3 62.9 + - - +
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Residues in contact with SER 455 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256E LEU* 4.0 11.0 - - - -
258E GLN* 3.2 13.7 - - - +
259E ASN* 3.6 15.3 - - - -
315E LEU 4.3 0.2 - - - -
316E ILE* 3.2 6.9 - - - +
317E GLU* 2.8 54.7 + - - +
454E MET* 1.3 78.1 - - - +
456E MET* 1.3 67.0 + - - +
457E LYS* 4.2 10.5 + - - -
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Residues in contact with MET 456 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256E LEU* 3.7 1.6 - - - -
257E ILE* 2.8 49.4 + - + +
258E GLN* 2.9 40.6 + - + +
297E TRP* 4.5 3.6 - - + -
314E VAL* 4.3 14.8 - - + -
315E LEU 3.6 4.9 - - - -
316E ILE* 3.8 28.9 - - + -
333E PHE* 4.7 10.1 - - + -
357E LEU* 6.0 1.1 - - + -
406E TRP* 4.1 33.7 - - + -
407E TRP* 4.6 10.5 - - + -
416E PRO* 4.7 4.5 - - + -
454E MET* 5.6 0.2 - - - -
455E SER* 1.3 80.5 - - - +
457E LYS* 1.3 58.8 + - - +
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Residues in contact with LYS 457 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246E ASP* 2.7 34.4 + - + +
249E THR* 4.0 2.6 + - - -
254E TRP* 3.5 34.0 - - + -
255E THR 3.6 5.8 - - - +
256E LEU* 3.6 31.6 - - + +
314E VAL* 3.2 3.1 - - - +
315E LEU* 2.6 43.3 + - + +
317E GLU* 2.8 36.3 + - - +
455E SER* 4.2 9.4 + - - +
456E MET* 1.3 73.6 - - - +
458E ILE* 1.3 63.4 + - - +
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Residues in contact with ILE 458 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254E TRP* 3.5 2.7 - - - -
255E THR* 2.9 45.5 + - - +
257E ILE* 3.7 29.4 - - + -
303E ILE* 5.0 2.2 - - + +
306E LEU* 3.4 42.4 - - + -
307E THR* 4.7 5.6 - - + -
312E THR* 3.8 15.9 - - + -
313E LYS 3.2 10.1 - - - +
314E VAL* 3.8 13.9 - - + -
333E PHE* 4.0 10.1 - - + -
457E LYS* 1.3 79.1 - - - +
459E LYS* 1.3 64.8 + - - +
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Residues in contact with LYS 459 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217E GLU* 3.6 20.2 - - + -
221E ARG* 5.5 2.0 - - - +
250E ASP* 3.0 23.0 + - - -
251E ASN* 3.6 12.1 + - - +
252E GLY 2.6 29.8 + - - +
253E GLY 3.7 8.7 - - - +
254E TRP* 3.4 34.5 - - + +
312E THR* 3.6 4.5 - - - -
313E LYS* 3.0 40.5 + - - +
458E ILE* 1.3 79.4 - - - +
460E PRO* 1.3 89.4 - - + +
462E PHE* 6.4 2.0 - - - -
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Residues in contact with PRO 460 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215E GLU* 3.7 31.4 - - + +
217E GLU* 3.5 32.8 - - + +
253E GLY 4.6 0.7 - - - +
255E THR* 5.9 0.7 - - - +
309E ILE* 6.0 6.3 - - + -
310E GLY* 6.1 0.9 - - - -
311E PRO 3.5 8.7 - - - +
312E THR* 4.5 3.6 - - + +
313E LYS* 4.4 3.8 + - - -
459E LYS* 1.3 96.0 - - + +
461E TYR* 1.3 61.1 + - - +
462E PHE* 3.6 11.5 + - + +
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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
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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