Contacts of the helix formed by residues 437 - 446 (chain E) in PDB entry 1IAS
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 437 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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376E LYS* 4.4 4.9 - - - +
435E ASP 4.7 0.4 - - - -
436E PRO* 1.3 76.4 - - - +
438E VAL* 1.3 64.7 + - - +
439E GLU* 3.4 8.0 + - - +
440E GLU* 2.8 44.9 + - - +
441E MET* 3.1 22.7 + - - +
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Residues in contact with VAL 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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372E ARG* 3.3 46.4 - - - +
376E LYS* 3.5 36.4 - - + +
379E MET* 5.1 1.1 - - - -
384E LEU* 3.8 22.0 - - + +
437E SER* 1.3 73.4 - - - +
439E GLU* 1.3 57.5 + - - +
441E MET* 3.6 2.3 + - - +
442E ARG* 3.0 27.9 + - + +
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Residues in contact with GLU 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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437E SER* 3.0 6.8 - - - +
438E VAL* 1.3 79.6 - - - +
440E GLU* 1.3 66.3 + - + +
442E ARG* 3.3 10.3 + - + +
443E LYS* 3.2 23.3 + - + +
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Residues in contact with GLU 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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432E VAL* 3.6 16.7 - - + +
433E PRO* 3.5 30.5 - - + +
435E ASP 4.2 2.6 - - - +
436E PRO* 3.3 10.4 - - - +
437E SER* 2.8 47.8 + - - +
439E GLU* 1.3 78.4 - - + +
441E MET* 1.3 62.6 + - - +
443E LYS* 3.6 4.7 + - - +
444E VAL* 3.3 26.2 + - - +
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Residues in contact with MET 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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376E LYS* 3.9 16.6 - - + +
377E ARG* 3.3 34.1 - - - +
379E MET 5.3 1.1 - - - +
384E LEU* 3.8 21.3 - - + -
428E TYR* 3.4 25.8 - - + -
432E VAL* 3.9 19.5 - - - -
436E PRO* 3.5 25.6 - - + -
437E SER 3.1 19.4 + - - +
440E GLU* 1.3 75.8 - - - +
442E ARG* 1.3 59.7 + - - +
444E VAL* 3.2 5.6 + - + +
445E VAL* 2.9 43.6 + - + +
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Residues in contact with ARG 442 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372E ARG* 5.7 2.4 - - - +
384E LEU* 3.8 29.7 + - + +
385E ASP* 3.6 38.2 + - - +
386E ASP* 5.6 0.4 - - - +
438E VAL* 3.0 19.9 + - - +
439E GLU* 3.3 10.7 + - + +
441E MET* 1.3 76.4 - - - +
443E LYS* 1.3 57.3 + - - +
446E CYS* 2.8 48.9 + - + +
447E GLU* 3.2 10.9 + - + +
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Residues in contact with LYS 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 GLU* 3.2 15.5 + - + +
440E GLU* 3.8 7.2 - - - +
441E MET 3.2 0.2 - - - -
442E ARG* 1.3 77.4 - - - +
444E VAL* 1.3 55.3 + - + +
447E GLU* 3.1 35.8 + - - +
448E GLN* 2.8 57.4 + - + +
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Residues in contact with VAL 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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428E TYR* 5.1 8.1 - - + -
431E LEU* 3.4 57.4 - - + +
432E VAL* 5.0 3.4 - - + -
440E GLU 3.3 16.8 - - - +
441E MET* 3.2 7.3 + - - +
443E LYS* 1.3 77.7 - - + +
445E VAL* 1.3 62.1 + - + +
448E GLN* 3.8 17.1 - - - +
449E LYS 3.5 3.8 + - - -
450E LEU* 2.8 40.1 + - + +
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Residues in contact with VAL 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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381E PRO* 3.5 25.2 - - + +
384E LEU* 3.7 21.8 - - + -
402E TYR* 4.0 9.4 - - - +
428E TYR* 3.7 35.7 - - + -
441E MET* 2.9 24.0 + - + +
444E VAL* 1.3 81.3 - - + +
446E CYS* 1.3 63.6 + - - +
449E LYS* 3.4 10.6 - - - +
450E LEU 4.0 1.1 - - - +
451E ARG* 2.9 36.8 + - - +
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Residues in contact with CYS 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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381E PRO* 3.5 35.4 - - - -
384E LEU* 3.8 18.6 - - - -
385E ASP* 3.7 23.1 - - + +
442E ARG* 2.8 30.2 + - + +
445E VAL* 1.3 74.6 - - - +
447E GLU* 1.3 65.9 + - + +
449E LYS* 3.4 17.0 - - - +
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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