Contacts of the helix formed by residues 412 - 423 (chain B) in PDB entry 4EGA
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 412 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353B ASP* 3.7 32.1 - - - -
407B PHE* 3.7 15.9 - + - -
408B ARG 3.3 23.8 - - - -
409B LEU* 3.0 12.6 + - - +
411B ALA* 1.3 84.3 - - + +
413B ARG* 1.3 57.4 + - - +
414B GLU 3.3 2.2 - - - -
415B ARG* 3.3 34.8 + - - +
416B LEU* 2.7 45.3 + - + +
529B ALA* 3.8 17.9 - - + -
532B LEU* 3.8 20.6 - - + -
533B SER* 3.7 28.9 - - - -
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Residues in contact with ARG 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409B LEU 4.0 3.4 + - - -
410B SER 3.7 12.4 + - - +
411B ALA 3.6 0.8 - - - -
412B PHE* 1.3 76.5 - - - +
414B GLU* 1.3 86.6 + - + +
416B LEU* 3.3 1.8 + - - +
417B LEU* 2.9 41.5 + - + +
440B VAL* 3.3 31.8 + - + +
441B GLU* 3.2 26.0 + - - +
443B GLY* 3.9 16.7 - - - -
444B LEU* 4.2 19.5 - - + +
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Residues in contact with GLU 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411B ALA 5.2 1.8 + - - +
412B PHE 3.3 0.4 - - - -
413B ARG* 1.3 99.4 + - + +
415B ARG* 1.3 65.1 + - + +
417B LEU* 3.2 10.4 + - + +
418B GLU* 3.0 33.8 + - + +
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Residues in contact with ARG 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B ASP* 5.7 0.6 + - - -
411B ALA* 3.0 28.7 + - - +
412B PHE* 3.3 34.4 + - - +
414B GLU* 1.3 77.3 - - + +
416B LEU* 1.3 62.4 + - - +
418B GLU* 3.3 18.9 + - - +
419B TRP* 3.1 22.3 + - - +
532B LEU* 3.7 34.5 + - + +
533B SER* 5.7 0.4 - - - +
804B GOL 4.4 16.2 - - - -
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Residues in contact with LEU 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B PHE* 2.7 33.5 + - + +
413B ARG 3.6 3.4 - - - +
415B ARG* 1.3 71.9 - - - +
417B LEU* 1.3 65.7 + - - +
419B TRP* 2.9 20.8 + - + +
420B TYR* 2.9 41.5 + - + +
440B VAL* 4.4 3.4 - - + -
444B LEU* 3.8 26.7 - - + -
524B ALA 4.3 0.2 - - - +
525B ILE* 3.8 27.1 - - + +
528B PRO* 3.8 30.3 - - + -
529B ALA* 4.1 7.9 - - + +
532B LEU* 4.3 8.5 - - + -
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Residues in contact with LEU 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413B ARG* 2.9 49.3 + - + +
414B GLU* 3.6 7.4 - - + +
416B LEU* 1.3 76.1 - - - +
418B GLU* 1.3 63.4 + - + +
420B TYR* 3.4 15.0 + - + +
421B HIS* 3.1 39.9 + - + +
437B ILE* 4.2 12.6 - - + -
440B VAL* 3.8 21.1 - - + -
441B GLU* 4.0 32.8 - - + +
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Residues in contact with GLU 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414B GLU* 3.0 21.5 + - + +
415B ARG* 3.6 26.6 + - - +
417B LEU* 1.3 75.0 - - + +
419B TRP* 1.3 57.6 + - - +
421B HIS* 3.4 5.3 + - - +
422B ALA* 2.9 32.7 + - - +
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Residues in contact with TRP 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415B ARG 3.1 11.8 + - - +
416B LEU* 2.9 11.8 + - + +
418B GLU* 1.3 77.6 - - - +
420B TYR* 1.3 96.4 + + - +
422B ALA* 4.6 0.7 - - - -
423B ASN* 2.7 64.7 + - - +
426B CYS* 4.0 25.1 - - + -
427B ILE* 5.4 0.9 - - + -
524B ALA* 4.1 2.7 - - - -
528B PRO* 3.7 33.0 - - + -
532B LEU* 6.0 1.1 - - + -
538B LEU* 3.6 36.7 - - + +
539B PRO* 3.4 33.3 + - + -
542B ILE* 4.4 12.1 - - + -
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Residues in contact with TYR 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416B LEU* 2.9 34.0 + - + +
417B LEU* 3.4 15.0 + - + +
419B TRP* 1.3 100.9 - + - +
421B HIS* 1.3 62.3 + - + +
423B ASN 3.5 15.2 - - - +
424B PRO* 3.6 0.3 - - - +
426B CYS* 4.4 8.3 - - - -
427B ILE* 4.2 14.8 - - + -
433B ARG* 3.1 22.4 + - + +
436B VAL* 3.5 17.6 - - + +
437B ILE* 3.7 33.4 - - + -
440B VAL* 3.4 38.0 - - + +
524B ALA 2.8 30.3 + - - -
525B ILE* 3.8 3.5 - - - +
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Residues in contact with HIS 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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690A THR* 4.6 13.4 + - + -
691A ASP* 3.2 38.1 + - + +
693A GLU* 5.3 4.3 - - - +
417B LEU* 3.1 34.5 + - + +
418B GLU* 4.0 4.3 - - - +
420B TYR* 1.3 77.5 - - + +
422B ALA* 1.3 61.9 + - - +
423B ASN 3.3 0.6 + - - -
424B PRO* 3.8 11.3 - - - +
433B ARG* 4.2 6.1 + - - +
437B ILE* 4.2 34.0 - - + +
441B GLU* 4.6 6.4 + - - -
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Residues in contact with ALA 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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633A ALA* 5.7 4.0 - - - +
418B GLU 2.9 19.5 + - - +
419B TRP* 4.6 0.4 - - - -
421B HIS* 1.3 77.9 - - - +
423B ASN* 1.3 71.6 + - - +
424B PRO* 3.4 7.7 - - - +
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Residues in contact with ASN 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419B TRP* 2.7 49.5 + - - +
420B TYR 3.5 3.4 - - - +
422B ALA* 1.3 94.1 - - - +
424B PRO* 1.3 59.3 - - - +
425B GLY 3.1 4.7 - - - -
426B CYS* 2.9 41.8 + - + +
540B LYS 5.7 1.1 - - - +
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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