Contacts of the helix formed by residues 431 - 444 (chain E) in PDB entry 4E2I
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 GLY 431 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393E TRP* 5.2 3.4 - - - -
397E LEU* 3.9 11.7 - - - +
430E SER* 1.3 79.1 - - - +
432E LYS* 1.3 62.3 + - - +
433E THR 3.6 1.6 - - - -
434E THR* 3.2 20.6 + - - -
435E LEU* 2.9 26.2 + - - +
547E PHE* 3.3 17.0 - - - -
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Residues in contact with LYS 432 (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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418D LYS* 4.8 4.8 - - - +
540D ARG* 6.2 0.7 - - - +
424E PHE* 3.9 17.2 - - + +
426E GLY 3.1 28.5 - - - +
427E PRO 2.9 22.5 + - - -
428E ILE* 4.8 0.4 - - - +
429E ASP* 3.6 15.6 - - - +
430E SER* 3.0 22.2 + - - +
431E GLY* 1.3 73.2 - - - +
433E THR* 1.3 67.9 + - - +
434E THR 2.9 5.7 + - - -
435E LEU* 3.0 1.4 + - - +
436E ALA* 2.7 38.0 + - - +
474E ASP* 4.8 3.8 - - - -
527E THR* 4.9 7.2 - - + -
528E MET 3.9 3.8 - - - +
529E ASN* 3.3 20.9 - - - +
547E PHE* 3.4 27.1 - - + -
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Residues in contact with THR 433 (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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418D LYS* 5.5 6.4 + - - +
499D ASP* 6.0 0.2 - - - -
502D ASP* 4.4 18.9 + - + +
504D SER* 3.5 30.4 - - - +
505D VAL* 5.2 2.5 - - + -
540D ARG* 4.9 4.2 + - - -
431E GLY 3.6 0.2 - - - -
432E LYS* 1.3 87.8 + - - +
434E THR* 1.3 56.7 + - - +
436E ALA* 4.6 0.2 - - - -
437E ALA* 3.1 24.9 - - - +
473E GLU* 3.1 33.1 + - - +
474E ASP* 4.4 9.5 + - - -
527E THR* 5.8 1.1 - - - -
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Residues in contact with THR 434 (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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504D SER* 5.6 0.9 - - - -
393E TRP* 3.9 14.9 - - + -
394E LEU* 4.8 2.0 - - + -
397E LEU* 5.3 1.3 - - + -
431E GLY* 3.4 20.9 - - - -
432E LYS 2.9 0.4 - - - -
433E THR* 1.3 81.8 - - - +
435E LEU* 1.3 60.8 + - - +
437E ALA 4.1 0.2 - - - -
438E ALA* 3.5 7.8 + - - +
569E ILE* 3.2 51.4 - - + +
570E GLN* 3.5 24.6 - - + +
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Residues in contact with LEU 435 (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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394E LEU* 5.5 5.2 - - + -
397E LEU* 4.5 6.3 - - + -
398E LEU* 4.1 3.8 - - + -
401E MET* 3.8 33.4 - - + -
404E VAL* 6.4 1.3 - - + -
405E VAL* 5.5 1.1 - - + -
424E PHE* 3.5 29.2 - - + -
431E GLY 2.9 16.6 + - - +
434E THR* 1.3 75.3 - - - +
436E ALA* 1.3 63.1 + - - +
437E ALA 2.9 5.0 + - - -
438E ALA* 3.1 2.3 + - + +
439E LEU* 2.9 51.7 + - + +
545E ILE* 5.6 1.3 - - + -
547E PHE* 3.6 15.5 - - + -
569E ILE 5.4 0.2 - - - -
575E LEU* 4.3 20.2 - - + -
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Residues in contact with ALA 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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424E PHE* 3.8 13.4 - - + -
432E LYS 2.7 19.9 + - - +
433E THR* 4.6 0.4 - - - -
435E LEU* 1.3 73.8 - - - +
437E ALA* 1.3 57.8 + - - +
439E LEU* 4.3 6.6 - - - +
440E LEU* 3.7 14.4 + - - +
471E VAL* 3.7 23.1 - - + +
473E GLU* 3.7 13.0 - - - +
525E ILE* 4.6 6.9 - - + +
527E THR* 3.7 27.6 - - + -
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Residues in contact with ALA 437 (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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504D SER* 3.1 31.4 - - - +
505D VAL* 4.1 10.1 - - + +
433E THR 3.1 22.6 + - - +
434E THR 4.1 3.4 - - - +
435E LEU 2.9 0.6 - - - -
436E ALA* 1.3 78.5 - - - +
438E ALA* 1.3 67.4 + - - +
440E LEU* 3.0 21.3 + - - +
441E GLU* 3.4 5.9 + - - +
570E GLN* 4.3 10.5 - - + +
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Residues in contact with ALA 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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394E LEU* 5.8 0.4 - - + -
434E THR 3.5 12.1 + - - +
435E LEU* 3.1 5.3 + - + +
437E ALA* 1.3 79.8 - - - +
439E LEU* 1.3 57.7 + - - +
441E GLU* 3.1 3.8 + - - +
442E LEU* 2.9 24.1 + - - +
569E ILE 4.4 3.6 - - - +
570E GLN* 3.7 22.3 + - - -
571E SER 3.5 19.5 - - - +
572E GLY* 3.4 9.2 - - - +
575E LEU* 3.5 23.1 - - + -
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Residues in contact with LEU 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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405E VAL* 4.4 15.3 - - + -
408E PHE* 4.4 27.4 - - + -
424E PHE* 3.6 20.0 - - + -
435E LEU* 2.9 34.0 + - + +
436E ALA 4.4 3.4 - - - +
438E ALA* 1.3 76.6 - - - +
440E LEU* 1.3 63.5 + - - +
442E LEU* 3.6 12.6 - - + +
443E CYS* 3.0 29.1 + - - +
469E LEU* 4.7 2.1 - - - +
525E ILE* 3.5 28.0 - - + -
575E LEU* 3.5 20.4 - - + +
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Residues in contact with LEU 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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505D VAL* 4.7 11.9 - - + -
506D LYS* 5.0 10.8 - - + +
436E ALA 3.7 11.7 + - - +
437E ALA* 3.0 15.7 + - - +
439E LEU* 1.3 79.3 - - - +
441E GLU* 1.3 56.3 + - - +
444E GLY* 2.8 30.1 + - - -
445E GLY 3.4 32.9 + - - +
446E LYS* 3.5 8.3 - - - +
447E ALA* 3.8 28.7 - - + +
469E LEU* 3.5 25.1 - - + -
471E VAL* 3.5 13.7 - - + +
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Residues in contact with GLU 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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506D LYS* 5.4 8.7 + - - -
364E ARG* 2.8 49.1 + - - +
368E LEU* 3.7 7.2 - - + +
371E ARG* 3.4 25.0 + - - +
437E ALA 3.4 5.3 + - - +
438E ALA* 3.1 8.3 + - - +
440E LEU* 1.3 78.3 - - + +
442E LEU* 1.3 60.3 + - - +
443E CYS 3.3 0.4 - - - -
570E GLN 5.0 1.1 - - - +
571E SER* 3.6 12.0 + - - -
572E GLY* 2.8 30.3 + - - +
573E ILE* 4.1 3.1 + - - +
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Residues in contact with LEU 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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364E ARG* 3.5 6.8 - - - +
365E PHE* 3.9 13.6 - - + -
368E LEU* 3.5 26.4 - - + +
405E VAL* 3.7 23.8 - - + -
409E LEU* 4.4 11.4 - - + -
438E ALA 2.9 15.4 + - - +
439E LEU* 3.2 11.4 + - + +
441E GLU* 1.3 80.1 - - - +
443E CYS* 1.3 59.7 + - - +
572E GLY* 3.6 20.8 - - - +
575E LEU* 3.6 27.6 - - + -
576E LEU* 3.8 11.7 - - + +
579E LEU* 3.8 23.1 - - + -
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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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360E MET 5.4 0.5 - - - +
361E LEU* 3.7 26.3 - - + +
364E ARG* 3.2 20.6 - - - +
408E PHE* 3.9 14.6 - - - -
409E LEU* 3.5 31.2 - - - -
439E LEU 3.0 14.7 + - - +
442E LEU* 1.3 82.9 - - - +
444E GLY* 1.3 59.4 + - - +
468E PHE* 3.8 11.4 - - + +
469E LEU* 3.5 28.7 - - + -
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Residues in contact with GLY 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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364E ARG* 4.2 17.9 - - - -
440E LEU 2.8 21.3 + - - -
441E GLU 4.1 0.4 + - - -
442E LEU 3.8 0.4 - - - -
443E CYS* 1.3 75.0 - - - +
445E GLY* 1.3 59.6 + - - -
468E PHE* 3.4 23.7 - - - +
469E LEU* 3.4 13.4 - - - +
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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