Contacts of the helix formed by residues 450 - 458 (chain E) in PDB entry 5I4V
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 PRO 450 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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272E THR* 3.1 36.3 - - + -
276E ILE* 3.7 24.5 - - + -
448E LYS 4.7 0.7 - - - +
449E LEU* 1.3 89.7 - - + +
451E PRO* 1.3 79.6 - - + +
452E LEU 4.6 2.2 - - - +
453E LEU* 3.1 16.6 + - + +
454E SER* 3.0 17.4 + - - -
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Residues in contact with PRO 451 (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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449E LEU 3.8 0.6 - - - +
450E PRO* 1.3 87.6 - - + +
452E LEU* 1.3 55.4 + - - +
454E SER* 2.9 10.1 + - - -
455E GLU* 2.7 36.4 + - - +
470E ILE* 4.7 18.4 - - + -
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Residues in contact with LEU 452 (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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276E ILE* 4.4 27.1 - - + +
279E VAL* 3.8 37.9 - - + -
280E GLN* 5.0 4.3 - - + +
450E PRO* 3.2 1.2 + - - +
451E PRO* 1.3 79.5 - - - +
453E LEU* 1.3 66.2 + - + +
455E GLU* 3.4 7.0 + - - +
456E ILE* 3.1 29.1 + - + +
470E ILE* 3.9 32.4 - - + +
471E LEU* 4.6 11.4 - - + +
474E LEU* 4.1 19.1 - - + -
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Residues in contact with LEU 453 (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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272E THR* 3.8 21.1 - - + +
275E ALA* 4.1 10.5 - - + -
276E ILE* 3.6 35.4 - - + +
279E VAL* 4.3 15.5 - - + -
449E LEU* 4.4 7.1 - - + +
450E PRO* 3.1 30.0 + - + +
452E LEU* 1.3 80.9 - - + +
454E SER* 1.3 61.0 + - - +
456E ILE* 3.2 8.9 - - - +
457E TRP* 3.0 57.9 + - + +
501E 67S 4.2 12.8 - - - -
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Residues in contact with SER 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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449E LEU* 3.5 28.5 + - - +
450E PRO 3.0 6.6 + - - -
451E PRO* 2.9 12.7 + - - -
453E LEU* 1.3 75.3 - - - +
455E GLU* 1.3 59.3 + - - +
458E ASP* 2.8 26.7 + - - -
459E VAL* 3.0 39.8 + - - +
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Residues in contact with GLU 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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305E LYS* 3.4 12.1 + - + +
451E PRO 2.7 15.4 + - - +
452E LEU* 3.4 12.6 - - - +
454E SER* 1.3 76.1 - - - +
456E ILE* 1.3 64.9 + - + +
458E ASP* 3.3 14.9 - - - +
469E LYS* 3.5 20.1 + - - +
470E ILE* 3.0 32.1 + - - +
471E LEU* 2.8 40.4 + - + +
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Residues in contact with ILE 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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279E VAL* 4.3 18.8 - - + -
304E LEU* 4.2 3.8 - - + +
305E LYS* 3.8 47.2 - - + +
308E THR* 3.1 42.8 - - + +
452E LEU* 3.1 17.5 + - + +
453E LEU* 3.2 20.0 - - + +
455E GLU* 1.3 82.3 - - + +
457E TRP* 1.3 83.1 + - + +
458E ASP* 4.3 0.9 - - - +
471E LEU* 4.9 11.7 - - + -
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Residues in contact with TRP 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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275E ALA* 5.0 2.5 - - + -
279E VAL* 5.7 1.1 - - + -
305E LYS 4.6 6.7 + - - -
308E THR* 4.4 11.3 - - + +
309E ILE* 4.1 16.2 - - + +
312E MET* 3.7 38.6 - - + -
435E HIS* 3.5 40.0 - + + -
439E VAL* 4.9 9.1 - - + +
449E LEU* 4.3 10.8 - - + -
453E LEU* 3.0 49.9 + - + +
454E SER 3.7 0.2 - - - -
456E ILE* 1.3 94.3 - - + +
458E ASP* 1.3 75.9 + - - +
459E VAL* 3.8 9.6 - - + +
501E 67S 4.0 20.9 - + - -
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Residues in contact with ASP 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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305E LYS* 3.0 32.2 + - - -
439E VAL* 5.6 0.7 - - - +
443E ARG* 5.3 3.8 + - - -
454E SER 2.8 11.2 + - - -
455E GLU 3.3 3.6 - - - +
456E ILE 4.8 0.4 - - - -
457E TRP* 1.3 84.6 - - - +
459E VAL* 1.3 59.8 + - - +
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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