Contacts of the helix formed by residues 441 - 450 (chain E) in PDB entry 2IO1
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 PHE 441 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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413E ASP* 3.0 29.6 - - - -
417E ASN* 4.1 1.6 - - - -
439E SER* 2.9 15.5 + - - +
440E THR* 1.3 82.6 - - - +
442E PHE* 1.3 62.4 + - - +
443E TYR 3.7 0.4 - - - -
444E PRO* 3.7 7.0 - - + +
445E LYS* 3.4 23.2 + - - +
457E TRP* 3.7 8.9 - - + -
24F GLN* 5.9 0.4 - - - -
58F ARG* 3.6 17.9 - - + -
60F ARG* 3.8 32.8 - - + -
86F PHE* 3.3 50.5 - + + -
87F GLN 3.4 16.2 - - - -
89F GLN* 3.2 24.7 - - + +
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Residues in contact with PHE 442 (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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438E PHE* 3.5 50.0 - + + -
439E SER 3.0 17.2 + - - +
441E PHE* 1.3 76.4 - - - +
443E TYR* 1.3 70.2 + - - +
445E LYS* 3.2 4.3 + - - +
446E LEU* 3.0 27.4 + - + +
454E VAL* 3.6 27.8 - - + +
457E TRP* 3.6 31.4 - + + -
471E VAL* 4.1 9.9 - - + -
508E LEU* 4.0 22.2 - - + -
511E TYR* 3.6 36.1 - + - -
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Residues in contact with TYR 443 (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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439E SER 4.6 0.8 + - - -
440E THR 4.4 0.8 + - - -
442E PHE* 1.3 80.8 - - - +
444E PRO* 1.3 70.9 - - + +
446E LEU* 3.1 7.4 + - + +
447E LYS* 2.8 68.0 + - + +
471E VAL* 4.7 3.5 - - + +
472E PRO 4.5 5.6 - - - +
473E ILE* 3.7 38.8 - - + -
474E HIS 5.6 2.9 - - - -
503E ARG 4.5 0.2 - - - -
504E ILE* 3.2 57.2 - - + +
507E ILE* 3.7 24.8 - - + +
508E LEU* 4.1 20.0 - - + -
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Residues in contact with PRO 444 (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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440E THR 3.5 19.7 - - - +
441E PHE* 3.7 8.1 - - + +
442E PHE 3.5 2.9 - - - -
443E TYR* 1.3 100.3 - - + +
445E LYS* 1.3 58.8 + - - +
447E LYS* 4.0 8.2 - - + +
448E SER* 3.4 22.9 + - - -
474E HIS* 4.8 15.7 - - + +
24F GLN* 5.4 8.5 - - - +
86F PHE* 5.1 7.0 - - + -
89F GLN* 4.1 14.4 - - - +
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Residues in contact with LYS 445 (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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441E PHE 3.4 17.4 + - - +
442E PHE 3.2 4.2 + - - +
443E TYR 3.1 0.6 - - - -
444E PRO* 1.3 78.4 - - - +
446E LEU* 1.3 61.2 + - - +
448E SER* 4.4 5.6 - - - +
449E GLY* 2.9 28.8 + - - -
450E GLY 4.0 0.3 + - - -
453E ALA* 4.0 25.6 - - + +
454E VAL* 3.6 20.4 - - + -
457E TRP* 4.0 10.8 - - + -
22F ALA* 5.8 4.2 - - - +
84F ASP* 2.9 34.7 + - - +
86F PHE* 3.7 16.3 - - + -
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Residues in contact with LEU 446 (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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442E PHE* 3.0 23.8 + - + +
443E TYR* 3.1 6.9 + - + +
445E LYS* 1.3 77.1 - - - +
447E LYS* 1.3 62.7 + - - +
450E GLY* 3.1 19.9 + - - +
451E TYR* 3.8 23.3 - - + +
454E VAL* 3.9 22.2 - - + -
507E ILE* 4.2 21.8 - - + +
508E LEU* 4.1 21.8 - - + -
511E TYR* 3.9 35.4 - - + -
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Residues in contact with LYS 447 (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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443E TYR* 2.8 58.3 + - + +
444E PRO* 4.4 7.4 - - - +
446E LEU* 1.3 78.2 - - - +
448E SER* 1.3 59.1 + - - +
450E GLY 4.9 0.7 + - - -
503E ARG* 6.3 0.7 - - - -
504E ILE* 5.7 1.4 - - - +
507E ILE* 4.2 21.8 - - + -
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Residues in contact with SER 448 (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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444E PRO 3.4 17.6 + - - -
445E LYS* 3.9 7.3 + - - +
447E LYS* 1.3 80.6 - - - +
449E GLY* 1.3 58.8 + - - +
450E GLY 3.8 0.4 - - - -
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Residues in contact with GLY 449 (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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445E LYS* 2.9 16.2 + - - -
448E SER* 1.3 82.0 - - - +
450E GLY* 1.3 66.7 + - - +
452E GLN* 4.6 3.5 + - - +
453E ALA* 3.5 18.4 + - - +
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Residues in contact with GLY 450 (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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445E LYS 4.7 0.3 - - - +
446E LEU* 3.1 24.9 + - - +
447E LYS 4.9 0.6 + - - -
448E SER 3.8 0.4 - - - -
449E GLY* 1.3 74.1 - - - +
451E TYR* 1.3 55.4 + - - -
452E GLN 3.1 3.1 - - - -
453E ALA* 2.6 32.9 + - - +
454E VAL* 3.6 2.9 + - - +
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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