Contacts of the helix formed by residues 369 - 381 (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 THR 369 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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366C LEU* 3.9 24.7 - - + +
578C LYS* 3.7 14.6 - - - +
589C LEU* 3.0 44.8 + - + +
368E LEU* 1.3 74.2 - - - +
370E GLU* 1.3 65.6 + - - +
371E ASP* 3.5 4.8 + - - +
372E MET* 2.9 29.9 + - - +
373E GLU* 3.0 10.8 + - - +
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Residues in contact with GLU 370 (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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558C TYR* 6.2 0.2 - - - -
561C ARG* 4.9 14.3 + - - +
563C LYS* 4.0 26.7 - - - +
566C THR* 5.7 0.9 + - - -
368E LEU 3.8 1.6 + - - -
369E THR* 1.3 72.4 - - - +
371E ASP* 1.3 57.4 + - - +
373E GLU* 3.5 9.1 + - + +
374E LYS* 3.0 29.0 + - + +
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Residues in contact with ASP 371 (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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426C ARG* 4.4 5.2 + - - -
430C GLN* 3.5 21.6 + - - +
432C TYR* 2.5 28.6 + - - -
561C ARG* 3.6 31.3 + - - +
589C LEU 4.0 11.9 - - - +
369E THR* 3.0 9.5 + - - +
370E GLU* 1.3 77.4 - - - +
372E MET* 1.3 64.4 + - - +
374E LYS* 3.5 6.1 + - - +
375E GLU* 3.1 24.7 + - - +
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Residues in contact with MET 372 (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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366C LEU* 5.0 6.5 - - + -
589C LEU* 4.0 22.4 - - + +
368E LEU* 4.2 25.6 - - + -
369E THR* 2.9 36.6 + - - +
371E ASP* 1.3 76.4 - - - +
373E GLU* 1.3 55.0 + - - +
375E GLU* 3.0 7.1 + - - +
376E ILE* 2.7 41.2 + - + +
581E TRP* 3.3 59.9 - - + +
589E LEU* 3.8 19.5 - - + -
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Residues in contact with GLU 373 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368E LEU* 3.9 24.8 + - + +
369E THR 3.0 11.6 + - - +
370E GLU* 3.5 15.5 - - + +
372E MET* 1.3 77.6 - - - +
374E LYS* 1.3 56.6 + - - +
376E ILE* 3.4 8.6 + - - +
377E SER* 2.9 31.9 + - - -
577E LYS* 3.2 32.1 + - - +
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Residues in contact with LYS 374 (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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370E GLU* 3.0 17.2 + - + +
371E ASP* 3.7 8.1 - - - +
373E GLU* 1.3 72.7 - - - +
375E GLU* 1.3 60.6 + - - +
377E SER* 2.8 24.7 + - - +
378E ASN* 2.8 52.3 + - - +
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Residues in contact with GLU 375 (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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430C GLN* 4.0 16.6 + - - -
371E ASP 3.1 11.3 + - - +
372E MET* 3.0 9.3 + - - +
374E LYS* 1.3 79.5 - - - +
376E ILE* 1.3 62.8 + - - +
378E ASN* 3.4 9.2 + - - +
379E ALA* 3.2 22.5 + - - +
581E TRP* 3.9 9.6 + - + -
584E LEU* 3.9 20.0 - - + +
585E HIS* 2.7 41.2 + - - -
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Residues in contact with ILE 376 (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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368E LEU* 3.3 31.2 - - + -
372E MET* 2.7 26.6 + - + +
373E GLU* 3.5 8.5 - - - +
375E GLU* 1.3 72.5 - - - +
377E SER* 1.3 58.9 + - - +
379E ALA* 3.2 5.5 + - - +
380E LEU* 3.1 34.1 + - + +
577E LYS* 3.2 44.2 - - + +
580E VAL* 3.9 28.2 - - + +
581E TRP* 4.1 20.0 - - + -
584E LEU* 4.9 0.4 - - - -
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Residues in contact with SER 377 (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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373E GLU* 2.9 18.5 + - - -
374E LYS* 2.8 30.5 + - - +
376E ILE* 1.3 78.7 - - - +
378E ASN* 1.3 56.4 + - - +
380E LEU* 4.0 6.9 - - - +
381E GLY* 2.6 34.5 + - - -
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Residues in contact with ASN 378 (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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374E LYS* 2.8 61.1 + - - +
375E GLU* 3.9 7.9 - - - +
377E SER* 1.3 78.9 + - - +
379E ALA* 1.3 62.5 + - - +
381E GLY* 3.4 10.0 + - - +
382E HIS 4.6 1.2 - - - +
399E ARG* 3.0 21.2 + - - +
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Residues in contact with ALA 379 (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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375E GLU 3.2 13.6 + - - +
376E ILE 3.4 9.0 - - - +
377E SER 3.1 0.4 - - - -
378E ASN* 1.3 78.2 - - - +
380E LEU* 1.3 58.1 + - - +
389E LEU* 4.0 22.7 - - + +
399E ARG* 3.3 30.4 + - - +
402E ILE* 3.8 12.9 - - + +
580E VAL* 4.0 17.9 - - + -
584E LEU* 4.1 11.4 - - + -
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Residues in contact with LEU 380 (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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376E ILE* 3.1 33.2 + - + +
377E SER* 4.0 5.8 - - - +
379E ALA* 1.3 70.8 - - - +
381E GLY* 1.3 69.1 + - - +
402E ILE* 3.8 27.8 - - + +
403E GLN* 3.7 10.9 + - - -
405E LEU* 4.7 6.7 - - + +
406E LYS* 3.2 61.8 + - + +
577E LYS* 5.1 7.4 - - + -
580E VAL* 4.8 12.1 - - + -
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Residues in contact with GLY 381 (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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377E SER 2.6 22.4 + - - -
378E ASN* 3.4 4.4 + - - -
379E ALA 3.3 1.6 - - - -
380E LEU* 1.3 78.7 - - - +
382E HIS* 1.3 68.5 + - - +
399E ARG* 3.2 18.2 + - - -
403E GLN* 3.5 2.8 + - - -
406E LYS* 5.3 2.5 - - - -
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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