Contacts of the helix formed by residues 434 - 442 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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406E LEU 4.7 1.1 + - - -
407E GLY 5.3 0.2 + - - -
409E LEU 3.6 19.0 + - - -
410E THR* 2.8 22.6 + - - -
432E TYR* 3.5 16.1 + - - -
433E ALA* 1.3 73.9 - - - +
435E PRO* 1.3 77.3 - - - +
436E LYS* 3.3 27.9 + - - +
437E TYR* 3.3 6.4 + - - +
438E ILE* 3.3 21.0 + - - +
453E GLY* 4.5 0.2 - - - -
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Residues in contact with PRO 435 (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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432E TYR* 4.3 8.1 - - + +
433E ALA 3.7 2.9 - - - +
434E SER* 1.3 90.2 - - - +
436E LYS* 1.3 64.6 + - + +
438E ILE* 3.1 4.9 + - - +
439E GLN* 2.9 31.3 + - - +
451E GLN* 4.5 18.2 - - + +
452E GLN* 3.3 37.3 - - - +
453E GLY* 4.1 2.9 - - - +
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Residues in contact with LYS 436 (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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406E LEU* 3.2 41.0 - - + +
407E GLY* 4.2 12.6 - - - -
434E SER* 3.3 15.0 + - - +
435E PRO* 1.3 88.8 - - + +
437E TYR* 1.3 57.7 + - - +
439E GLN* 3.1 26.6 + - - +
440E ALA* 2.9 30.2 + - - +
451E GLN* 5.6 2.2 - - - +
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Residues in contact with TYR 437 (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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307E LEU* 5.6 6.0 - - + +
308E MET 4.7 2.1 + - - -
309E GLN* 3.3 36.0 + - - +
310E SER 4.7 0.7 + - - -
401E GLN* 4.8 3.4 - - - -
406E LEU* 4.1 19.0 - - + +
410E THR* 3.9 37.9 - - + +
411E LEU* 3.5 21.9 - - + +
433E ALA* 5.1 0.2 - - + -
434E SER* 3.3 11.5 + - - +
435E PRO 3.2 0.6 - - - -
436E LYS* 1.3 80.1 - - - +
438E ILE* 1.3 60.2 + - + +
440E ALA* 3.3 4.0 + - - +
441E ALA* 2.9 44.1 + - + +
107F PHE* 3.4 38.2 - + - -
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Residues in contact with ILE 438 (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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433E ALA* 4.3 7.0 - - + -
434E SER 3.3 9.8 + - - +
435E PRO 3.1 7.4 + - - +
437E TYR* 1.3 76.3 - - + +
439E GLN* 1.3 55.3 + - - +
441E ALA* 4.9 0.7 - - - -
442E VAL* 2.7 59.6 + - + +
445E VAL* 5.0 12.1 - - + -
452E GLN 4.3 5.4 - - - +
453E GLY* 4.0 21.1 - - - -
454E ILE* 4.4 2.2 - - + -
70F PHE* 3.7 33.0 - - + -
107F PHE* 3.7 35.7 - - + -
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Residues in contact with GLN 439 (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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435E PRO 2.9 12.8 + - - +
436E LYS* 3.1 40.0 + - - +
438E ILE* 1.3 77.8 - - - +
440E ALA* 1.3 61.1 + - + +
442E VAL 3.9 4.9 - - - -
443E PRO* 3.3 28.7 - - - +
445E VAL* 6.0 1.8 - - + -
451E GLN* 3.0 35.7 + - + +
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Residues in contact with ALA 440 (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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307E LEU* 4.4 12.2 - - + +
406E LEU* 3.8 29.6 - - + -
436E LYS 2.9 17.8 + - - +
437E TYR* 3.6 4.7 - - + +
439E GLN* 1.3 81.6 - - + +
441E ALA* 1.3 64.9 + - - +
442E VAL 3.6 0.2 + - - -
443E PRO* 4.3 7.4 - - - +
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Residues in contact with ALA 441 (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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306E THR* 4.0 13.0 + - - -
307E LEU* 4.0 32.6 + - + +
437E TYR* 2.9 45.1 + - + +
438E ILE* 4.5 0.9 - - - +
440E ALA* 1.3 75.6 - - - +
442E VAL* 1.3 71.3 + - + +
443E PRO* 3.9 4.6 - - - +
107F PHE* 5.4 5.2 - - + -
116F LYS* 5.4 0.3 + - - -
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Residues in contact with VAL 442 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306E THR* 4.9 1.8 - - - +
438E ILE* 2.7 45.2 + - + +
439E GLN* 3.9 0.8 - - - -
441E ALA* 1.3 86.7 - - + +
443E PRO* 1.3 70.4 - - - +
444E LYS 3.8 1.3 - - - -
445E VAL* 3.8 12.5 + - - +
70F PHE* 6.2 0.7 - - + -
107F PHE* 4.7 15.5 - - + -
108F ASP 4.5 6.3 - - - +
109F ASN* 3.2 38.6 - - + +
116F LYS* 4.0 19.1 - - - +
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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