Contacts of the helix formed by residues 434 - 442 (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 SER 434 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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406G LEU 4.9 1.7 + - - -
409G LEU 3.8 14.3 + - - -
410G THR* 2.9 19.0 + - - +
432G TYR* 3.4 22.9 - - - -
433G ALA* 1.3 74.4 - - - +
435G PRO* 1.3 73.9 - - - +
436G LYS* 4.0 12.0 + - - +
437G TYR* 3.2 29.1 + - - +
438G ILE* 3.3 11.8 + - - +
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Residues in contact with PRO 435 (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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432G TYR* 4.7 4.5 - - + +
433G ALA 3.7 3.1 - - - +
434G SER* 1.3 87.5 - - - +
436G LYS* 1.3 61.5 + - + +
438G ILE* 3.0 5.4 + - + +
439G GLN* 2.9 35.7 + - - +
452G GLN* 4.0 41.7 - - + +
453G GLY* 4.0 14.4 - - - +
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Residues in contact with LYS 436 (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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406G LEU* 3.3 42.2 + - + +
407G GLY* 4.1 14.5 + - - -
434G SER* 3.3 9.9 - - - +
435G PRO* 1.3 83.0 - - + +
437G TYR* 1.3 57.4 + - - +
439G GLN* 3.1 28.1 + - - +
440G ALA* 3.0 30.0 + - - +
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Residues in contact with TYR 437 (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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307G LEU* 6.2 2.2 - - + -
308G MET 5.1 0.5 + - - -
309G GLN* 3.2 36.9 - - - +
310G SER 4.7 0.5 + - - -
401G GLN* 4.2 5.3 + - - -
403G ASP* 6.3 0.2 - - + -
406G LEU* 4.2 17.0 - - + +
410G THR* 3.6 34.1 - - + +
411G LEU* 3.4 24.2 - - + +
433G ALA* 4.9 0.4 - - + -
434G SER* 3.2 22.2 + - - +
435G PRO 3.2 0.8 - - - -
436G LYS* 1.3 80.7 - - - +
438G ILE* 1.3 60.1 + - + +
440G ALA* 3.4 1.1 + - + +
441G ALA* 2.9 42.9 + - + +
107H PHE* 3.4 35.4 - + - -
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Residues in contact with ILE 438 (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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433G ALA* 4.3 4.0 - - + -
434G SER 3.6 10.5 - - - +
435G PRO* 3.0 7.9 + - + +
437G TYR* 1.3 76.4 - - + +
439G GLN* 1.3 63.3 + - - +
441G ALA* 4.8 0.7 - - - -
442G VAL* 2.9 50.8 + - + +
445G VAL* 5.0 9.4 - - + +
451G GLN* 5.6 6.7 - - + +
453G GLY* 3.6 32.1 - - - +
454G ILE* 4.3 0.4 - - + -
70H PHE* 3.8 27.1 - - + -
107H PHE* 3.7 35.0 - - + -
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Residues in contact with GLN 439 (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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406G LEU* 6.1 1.0 - - - +
435G PRO* 2.9 15.4 + - - +
436G LYS* 3.1 43.1 + - - +
438G ILE* 1.3 75.5 - - - +
440G ALA* 1.3 61.2 + - + +
442G VAL 4.2 3.6 - - - -
443G PRO* 4.0 17.1 - - - +
445G VAL 6.0 1.3 - - - -
446G TYR* 5.0 14.6 - - + -
452G GLN* 5.9 0.7 + - - -
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Residues in contact with ALA 440 (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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307G LEU* 4.0 14.0 - - + +
406G LEU* 4.0 26.9 - - + -
436G LYS 3.0 19.5 + - - +
437G TYR* 3.7 3.4 - - + +
439G GLN* 1.3 81.3 - - + +
441G ALA* 1.3 64.3 + - - +
443G PRO* 4.5 8.3 - - - +
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Residues in contact with ALA 441 (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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306G THR* 3.9 7.8 + - - -
307G LEU* 3.8 38.5 + - + +
308G MET 6.1 0.7 - - - +
309G GLN* 6.5 0.4 - - + -
437G TYR* 2.9 43.1 + - + +
438G ILE* 4.4 1.1 - - - +
440G ALA* 1.3 77.5 - - - +
442G VAL* 1.3 70.0 + - + +
443G PRO* 3.7 6.2 - - - +
107H PHE* 5.3 5.2 - - + -
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Residues in contact with VAL 442 (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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306G THR* 4.9 1.3 - - - +
438G ILE* 2.9 42.3 + - + +
439G GLN* 4.1 4.0 - - - +
441G ALA* 1.3 83.5 - - + +
443G PRO* 1.4 72.4 - - + +
445G VAL* 3.1 23.7 - - + +
70H PHE* 6.2 0.9 - - + -
107H PHE* 4.3 23.6 - - + -
108H ASP 4.4 2.9 - - - +
109H ASN* 3.9 20.4 - - + +
116H LYS* 3.7 28.3 - - - +
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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