Contacts of the helix formed by residues 411 - 425 (chain A) in PDB entry 4CFE
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 LYS 411 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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410A SER* 1.3 78.1 - - - +
412A PRO* 1.3 78.1 - - + +
413A TYR* 4.3 5.2 - - + +
414A ASP* 3.0 39.3 + - - +
415A ILE* 3.0 13.3 + - - +
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Residues in contact with PRO 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410A SER 3.6 0.2 - - - -
411A LYS* 1.3 91.2 - - + +
413A TYR* 1.3 60.9 + - - +
415A ILE* 3.4 7.1 + - + +
416A MET* 3.2 27.7 + - - +
436A TYR* 3.6 29.2 - - + +
457A LEU* 4.1 13.5 - - + +
465A TYR* 3.4 37.7 - - + +
203B PRO* 4.8 7.0 - - + -
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Residues in contact with TYR 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411A LYS* 3.2 4.2 - - + +
412A PRO* 1.3 78.7 - - - +
414A ASP* 1.3 75.0 + - - +
416A MET* 3.5 6.2 + - + +
417A ALA* 2.9 42.0 + - + +
436A TYR* 4.9 3.5 + - - +
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Residues in contact with ASP 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410A SER* 4.5 9.4 - - - +
411A LYS* 3.0 39.0 + - + +
413A TYR* 1.3 94.1 - - - +
415A ILE* 1.3 56.3 + - - +
417A ALA* 3.5 6.2 + - - +
418A GLU* 2.9 29.3 + - - +
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Residues in contact with ILE 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408A SER* 3.8 26.0 - - - +
410A SER* 3.6 15.0 - - - +
411A LYS 3.0 13.8 + - - +
412A PRO* 3.6 6.7 - - + +
413A TYR 3.2 0.2 - - - -
414A ASP* 1.3 77.6 - - - +
416A MET* 1.3 74.6 + - + +
418A GLU* 3.1 7.1 + - - +
419A VAL* 2.9 35.9 + - + +
457A LEU* 4.2 18.8 - - + -
465A TYR* 3.9 32.8 - - + -
467A LEU* 5.5 6.7 - - + -
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Residues in contact with MET 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412A PRO 3.2 15.6 + - - +
413A TYR* 4.0 7.2 - - + +
415A ILE* 1.3 87.6 - - + +
417A ALA* 1.3 59.5 + - - +
419A VAL* 3.2 17.9 - - + +
420A TYR* 3.0 44.7 + - + +
435A ALA 3.6 23.1 - - - +
436A TYR* 4.0 13.9 - - + -
438A LEU* 3.8 28.5 - - + -
455A LEU* 6.3 0.7 - - + -
457A LEU* 3.9 28.9 - - + +
467A LEU* 4.3 13.5 - - + -
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Residues in contact with ALA 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A TYR* 2.9 37.2 + - + +
414A ASP* 3.8 8.1 - - - +
416A MET* 1.3 76.5 - - - +
418A GLU* 1.3 61.5 + - - +
420A TYR* 3.6 11.2 + - - +
421A ARG* 3.5 22.8 + - - +
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Residues in contact with GLU 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414A ASP 2.9 18.9 + - - +
415A ILE* 3.1 8.3 + - - +
417A ALA* 1.3 75.1 - - - +
419A VAL* 1.3 63.9 + - + +
420A TYR 3.1 1.6 - - - -
421A ARG* 3.2 31.7 + - - +
422A ALA* 3.2 21.3 + - - +
549A THR 4.7 2.8 - - - +
550A LEU* 3.6 24.9 - - + +
551A ALA* 4.3 19.0 + - + +
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Residues in contact with VAL 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A ILE* 2.9 27.7 + - + +
416A MET* 3.2 37.9 - - + +
418A GLU* 1.3 74.4 - - + +
420A TYR* 1.3 67.2 - - + +
422A ALA* 3.8 9.8 - - + +
423A MET* 3.1 42.6 + - + +
438A LEU* 5.2 2.0 - - + -
455A LEU* 5.5 4.0 - - + -
467A LEU* 4.1 25.8 - - + -
546A LEU* 4.9 3.8 - - + +
550A LEU* 4.0 18.2 - - + -
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Residues in contact with TYR 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416A MET* 3.0 37.8 + - + +
417A ALA* 3.8 10.3 - - - +
418A GLU 3.1 0.4 - - - -
419A VAL* 1.3 82.2 - - + +
421A ARG* 1.3 59.3 + - - +
422A ALA 3.1 4.2 + - - -
423A MET* 3.5 14.8 + - + +
424A LYS* 3.6 25.4 + - - +
430A TRP* 3.5 38.1 - + + -
432A VAL* 5.1 4.7 - - - +
434A ASN 5.2 1.0 + - - -
435A ALA* 4.9 6.1 + - - -
438A LEU* 3.9 35.7 - - + +
192B TYR* 3.2 44.3 + - + -
193B VAL 4.7 4.4 + - - -
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Residues in contact with ARG 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417A ALA 3.5 12.0 + - - +
418A GLU* 3.2 38.3 + - - +
420A TYR* 1.3 77.8 - - - +
422A ALA* 1.3 60.9 + - - +
423A MET 3.3 0.4 - - - -
424A LYS* 3.6 29.4 + - + +
425A GLN* 3.8 26.0 + - - +
85D THR 4.3 1.2 + - - -
86D GLY 3.9 1.8 - - - -
87D GLY* 3.4 31.8 - - - +
88D GLY 5.3 0.6 - - - +
110D ASN* 2.9 39.3 + - - +
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Residues in contact with ALA 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418A GLU* 3.2 18.0 + - - +
419A VAL 3.8 4.5 - - - +
420A TYR 3.1 0.6 - - - -
421A ARG* 1.3 79.5 - - - +
423A MET* 1.3 62.3 + - - +
424A LYS 3.3 0.7 - - - -
425A GLN* 3.8 10.1 + - - +
426A LEU* 3.6 23.7 - - - +
546A LEU* 3.7 19.7 - - + -
549A THR* 3.7 25.5 + - - +
550A LEU* 3.8 10.1 - - + -
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Residues in contact with MET 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419A VAL* 3.1 35.1 + - + +
420A TYR* 3.5 6.9 + - + +
421A ARG 3.3 0.2 - - - -
422A ALA* 1.3 76.1 - - - +
424A LYS* 1.3 60.1 + - - +
425A GLN 3.4 0.2 - - - -
426A LEU 3.7 1.3 - - - +
427A ASP* 2.9 23.2 + - - -
428A PHE* 2.9 44.4 + - + +
430A TRP* 3.4 40.8 - - - +
438A LEU* 4.7 9.6 - - + -
440A VAL* 3.6 17.3 - - + -
455A LEU* 3.6 30.7 - - + -
546A LEU* 4.4 6.3 - - + -
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Residues in contact with LYS 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420A TYR* 3.6 24.8 + - - +
421A ARG* 3.6 19.5 - - + +
422A ALA 3.3 0.4 - - - -
423A MET* 1.3 79.2 - - - +
425A GLN* 1.3 62.6 + - + +
426A LEU 3.1 1.1 + - - -
427A ASP* 3.3 20.3 + - - +
430A TRP* 5.5 4.6 - - + -
190B GLU* 4.9 17.2 + - - +
192B TYR* 5.9 4.2 - - - +
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Residues in contact with GLN 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421A ARG* 3.8 30.1 + - - +
422A ALA* 3.8 9.7 + - - +
423A MET 3.4 0.4 - - - -
424A LYS* 1.3 76.8 - - + +
426A LEU* 1.3 68.1 + - + +
427A ASP* 3.5 2.0 - - - -
549A THR* 4.6 17.6 - - + +
85D THR* 3.3 46.1 + - + +
86D GLY* 4.1 8.9 - - - -
87D GLY 5.0 0.2 - - - +
110D ASN* 4.7 4.9 - - - +
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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