Contacts of the strand formed by residues 425 - 433 (chain G) in PDB entry 5IXM
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 MET 425 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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417G GLU* 4.2 6.1 - - - +
418G TYR 3.4 14.8 - - - +
419G ARG* 4.3 11.9 - - + +
423G ASP 5.3 0.7 - - - +
424G ARG* 1.3 76.6 - - - +
426G ILE* 1.3 76.8 + - - +
427G GLN* 3.7 7.2 - - + +
460G THR* 3.2 45.5 - - + +
461G ALA* 3.2 9.0 - - - +
462G SER* 2.9 40.0 + - - +
463G TRP* 3.8 4.9 - - - -
545G LEU* 4.8 9.0 - - - -
552G TYR* 3.4 43.5 - - + +
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Residues in contact with ILE 426 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416G MET* 4.8 6.1 - - + -
417G GLU* 3.3 3.8 - - - +
418G TYR* 2.8 45.6 + - + +
425G MET* 1.3 81.1 - - - +
427G GLN* 1.3 65.8 + - - +
428G LEU* 3.9 22.2 - - + -
459G THR* 5.2 3.8 - - + -
460G THR 3.5 8.7 - - - +
461G ALA* 4.7 8.1 - - + -
463G TRP* 3.5 31.6 - - + -
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Residues in contact with GLN 427 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415G ILE* 3.1 32.0 - - + +
416G MET 3.3 11.4 - - - +
417G GLU* 3.6 14.5 + - + +
425G MET* 3.9 8.9 - - + +
426G ILE* 1.3 78.4 - - - +
428G LEU* 1.3 65.6 + - - +
429G ASN* 4.9 7.8 + - - +
458G GLY 3.7 0.7 - - - +
459G THR* 3.3 6.8 - - - +
460G THR* 2.9 44.9 + - - +
476G TYR* 5.3 3.6 + - - -
552G TYR* 3.0 35.6 - - - -
553G GLN 3.5 17.4 + - - +
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Residues in contact with LEU 428 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415G ILE* 3.4 3.2 - - - +
416G MET* 2.9 62.5 + - + +
426G ILE* 3.9 16.2 - - + -
427G GLN* 1.3 79.6 - - - +
429G ASN* 1.3 65.6 + - - +
458G GLY 3.4 6.7 - - - +
459G THR* 4.3 15.3 - - + +
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Residues in contact with ASN 429 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414G ALA 3.2 13.0 - - - +
415G ILE* 3.9 17.0 - - + +
427G GLN* 4.9 8.9 + - - +
428G LEU* 1.3 78.4 - - - +
430G TYR* 1.3 65.3 + - - +
431G ARG* 3.8 21.5 - - + +
456G GLN* 4.4 2.8 + - - +
457G VAL* 3.6 5.4 - - - +
458G GLY* 2.9 43.6 + - - +
460G THR* 5.4 0.2 + - - -
476G TYR* 3.4 38.8 + - - -
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Residues in contact with TYR 430 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412G GLY 5.4 0.9 - - - -
413G ASN* 3.1 11.2 - - - +
414G ALA* 2.9 40.0 + - + +
429G ASN* 1.3 75.0 - - - +
431G ARG* 1.3 71.4 + - - +
432G TYR* 3.6 35.2 - - + +
455G SER* 2.9 28.1 + - - -
456G GLN 3.3 18.4 - - - -
457G VAL* 3.6 22.7 - - + -
479G THR* 5.0 1.8 - - + -
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Residues in contact with ARG 431 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411G LEU* 6.0 0.2 - - - +
412G GLY 3.8 3.8 - - - +
413G ASN* 4.0 28.4 + - + +
429G ASN* 3.8 16.8 - - + +
430G TYR* 1.3 84.0 - - - +
432G TYR* 1.3 60.5 + - - +
454G ILE* 3.7 10.4 - - + +
455G SER* 3.3 4.0 - - - -
456G GLN* 2.9 40.0 + - + +
67H VAL* 3.6 40.0 - - - +
68H SER* 4.4 2.2 - - - -
77H GLU* 2.5 45.9 + - - +
79H GLN* 5.2 5.3 + - - -
105H THR* 3.2 30.1 + - - +
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Residues in contact with TYR 432 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409G LEU* 3.9 35.9 + - + +
410G THR 4.1 6.5 - - - -
411G LEU* 3.5 6.6 - - - +
412G GLY* 2.8 43.7 + - - +
430G TYR* 3.6 28.9 - + + +
431G ARG* 1.3 75.6 - - - +
433G ALA* 1.3 65.9 + - - +
434G SER* 3.4 36.0 - - - -
435G PRO* 4.7 3.8 - - + +
454G ILE* 3.1 23.3 - - - -
455G SER* 4.4 5.6 - - - -
480G LYS* 5.1 11.0 - - - -
77H GLU* 4.7 2.6 + - - +
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Residues in contact with ALA 433 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410G THR 3.3 7.0 - - - +
411G LEU* 3.6 7.6 - - + -
432G TYR* 1.3 80.5 - - - +
434G SER* 1.3 65.9 + - - +
435G PRO* 4.1 0.5 - - - +
437G TYR* 4.9 1.1 - - + -
438G ILE* 4.3 6.5 - - + -
453G GLY* 3.0 4.2 - - - -
454G ILE* 2.9 46.5 + - + +
77H GLU* 4.4 1.1 - - - +
107H PHE* 3.5 32.1 - - + -
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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