Contacts of the helix formed by residues 435 - 451 (chain E) in PDB entry 2I2X
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 ASP 435 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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390E TYR* 3.6 9.2 - - - -
433E PRO* 3.5 6.0 - - + +
434E ASP* 1.3 79.8 - - - +
436E MET* 1.3 64.8 + - - +
437E ASP* 3.4 17.0 + - - +
438E LYS* 2.9 39.6 + - + +
439E PHE* 3.7 12.5 + - - +
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Residues in contact with MET 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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194E ILE* 6.3 0.2 - - + -
388E ASN* 3.8 28.1 - - - +
389E ILE* 4.0 23.6 - - + -
390E TYR* 3.6 42.6 - - + -
434E ASP 3.7 2.4 + - - -
435E ASP* 1.3 75.1 + - - +
437E ASP* 1.3 68.7 + - - +
438E LYS 3.3 0.4 - - - -
439E PHE* 3.4 3.8 + - - +
440E MET* 2.9 56.6 + - + +
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Residues in contact with ASP 437 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435E ASP* 3.4 16.8 + - - +
436E MET* 1.3 83.9 - - - +
438E LYS* 1.3 57.0 + - - +
440E MET* 3.7 6.8 - - - +
441E ASP* 3.0 32.6 + - - +
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Residues in contact with LYS 438 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433E PRO* 4.4 19.3 - - + -
435E ASP* 2.9 29.5 + - + +
437E ASP* 1.3 75.4 - - - +
439E PHE* 1.3 52.3 + - - +
441E ASP* 3.6 4.0 - - - +
442E ASP* 2.7 71.7 + - - +
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Residues in contact with PHE 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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182E PRO* 3.8 21.8 - - + -
185E LEU* 3.8 15.7 - - + -
186E TYR* 3.9 23.3 - + - -
190E CYS* 4.2 8.1 - - - -
390E TYR* 3.4 48.0 - + + +
432E LEU* 3.8 31.4 - - + -
433E PRO* 4.5 9.1 - - + +
435E ASP 3.7 4.0 + - - +
436E MET 3.4 7.5 + - - +
438E LYS* 1.3 76.0 - - - +
440E MET* 1.3 63.3 + - - +
442E ASP* 4.1 7.2 - - + -
443E CYS* 2.8 61.8 + - - +
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Residues in contact with MET 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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186E TYR* 3.9 17.5 + - + -
190E CYS* 3.7 35.7 - - + -
191E LEU* 5.8 0.2 - - + -
194E ILE* 3.8 18.4 - - + -
389E ILE* 5.5 0.7 - - + -
436E MET* 2.9 51.7 + - + +
437E ASP* 3.7 7.2 - - - +
439E PHE* 1.3 78.2 - - + +
441E ASP* 1.3 57.4 + - - +
443E CYS* 3.8 2.3 - - - +
444E LEU* 2.9 32.0 + - - +
461E PHE* 3.5 39.2 - - + -
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Residues in contact with ASP 441 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437E ASP 3.0 18.0 + - - +
438E LYS* 3.6 4.0 - - - +
440E MET* 1.3 75.0 - - - +
442E ASP* 1.3 70.3 + - - +
444E LEU* 2.9 26.6 + - - +
445E THR* 3.3 22.2 + - - +
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Residues in contact with ASP 442 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433E PRO* 5.2 4.7 - - - +
438E LYS* 2.7 60.5 + - - +
439E PHE* 3.7 9.1 - - + +
441E ASP* 1.3 75.4 - - - +
443E CYS* 1.3 62.1 + - - +
445E THR* 4.0 5.4 + - - -
446E LYS* 3.4 21.4 + - - +
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Residues in contact with CYS 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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182E PRO* 4.8 3.4 - - - -
186E TYR* 3.5 35.7 - - + -
439E PHE* 2.8 61.6 + - - +
442E ASP* 1.3 72.9 - - - +
444E LEU* 1.3 67.1 + - - +
446E LYS* 3.0 5.4 + - - -
447E TYR* 2.9 42.3 + - + +
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Residues in contact with LEU 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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186E TYR* 4.1 16.8 + - - +
440E MET 2.9 23.8 + - - +
441E ASP* 2.9 15.9 + - - +
443E CYS* 1.3 72.0 - - - +
445E THR* 1.3 62.5 + - + +
448E LYS* 2.8 72.5 + - + +
454E PHE* 4.3 8.1 - - + -
456E PRO* 4.2 15.0 - - + -
461E PHE* 4.6 28.5 - - + -
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Residues in contact with THR 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 ASP* 3.3 20.0 + - - +
442E ASP* 4.1 4.3 + - - -
443E CYS 3.3 0.4 - - - -
444E LEU* 1.3 82.6 - - + +
446E LYS* 1.3 64.5 + - - +
448E LYS* 3.9 16.3 - - + +
449E SER* 3.3 24.1 + - - -
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Residues in contact with LYS 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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180E ASP* 3.1 24.0 + - - -
182E PRO* 5.6 4.5 - - - -
442E ASP 3.4 20.1 + - - +
443E CYS* 3.0 7.2 + - - +
445E THR* 1.3 78.7 + - - +
447E TYR* 1.3 88.5 + - + +
449E SER* 3.5 3.1 + - - -
450E GLU* 2.8 65.4 + - - +
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Residues in contact with TYR 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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171E VAL* 3.8 20.6 - - + -
174E TYR* 4.5 13.7 - + - -
175E ALA* 5.4 0.7 - - + -
180E ASP* 2.7 30.6 + - - -
182E PRO* 3.7 2.6 - - - +
183E GLY* 2.8 30.8 + - - -
186E TYR* 3.6 20.9 - + + -
443E CYS* 2.9 46.4 + - + +
446E LYS* 1.3 100.0 - - + +
448E LYS* 1.3 60.2 + - - +
449E SER 3.2 0.7 - - - -
450E GLU* 3.7 2.7 - - + +
451E VAL* 2.7 48.6 + - + +
454E PHE* 3.6 19.9 - - + -
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Residues in contact with LYS 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 LEU* 2.8 46.2 + - + +
445E THR* 4.0 14.8 - - + +
446E LYS 3.3 0.2 - - - -
447E TYR* 1.3 78.4 - - - +
449E SER* 1.3 59.9 + - - +
451E VAL 4.0 8.1 - - - +
452E LYS* 4.3 13.5 - - - +
454E PHE* 3.9 12.3 - - + +
456E PRO* 3.6 31.7 - - + +
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Residues in contact with SER 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 THR 3.3 18.6 + - - -
446E LYS* 3.9 3.0 + - - -
447E TYR 3.2 0.2 - - - -
448E LYS* 1.3 79.9 - - - +
450E GLU* 1.3 63.1 + - - +
451E VAL 5.2 0.2 - - - -
452E LYS* 5.0 11.9 + - - +
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Residues in contact with GLU 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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174E TYR* 2.9 50.7 + - + +
446E LYS* 2.8 54.2 + - - +
447E TYR* 4.3 3.3 - - + -
449E SER* 1.3 83.4 - - - +
451E VAL* 1.3 62.0 + - - +
452E LYS* 3.9 2.8 + - - +
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Residues in contact with VAL 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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170E GLU* 4.3 15.5 - - + +
171E VAL* 4.8 5.2 - - + -
174E TYR* 3.5 44.2 - - + -
447E TYR* 2.7 35.1 + - + +
448E LYS 4.0 5.7 - - - +
450E GLU* 1.3 71.4 - - - +
452E LYS* 1.3 59.0 + - - +
453E VAL* 3.6 25.6 - - + -
454E PHE* 3.1 36.2 + - + +
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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