Contacts of the helix formed by residues 466 - 476 (chain B) in PDB entry 4F1P
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 GLU 466 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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464B SER 4.3 0.4 - - - -
465B TRP* 1.3 76.0 - - - +
467B PRO* 1.3 80.0 - - - +
468B GLU* 3.5 30.6 - - + +
469B LEU* 3.0 23.4 + - + +
470B VAL* 3.2 10.6 + - - +
661B LYS* 4.2 29.3 + - + +
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Residues in contact with PRO 467 (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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465B TRP 3.7 4.0 - - - +
466B GLU* 1.3 92.6 - - + +
468B GLU* 1.3 65.8 + - - +
470B VAL* 3.2 10.9 + - + +
471B LYS* 3.0 28.7 + - + +
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Residues in contact with GLU 468 (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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466B GLU* 3.5 32.3 - - + +
467B PRO* 1.3 82.4 - - - +
469B LEU* 1.3 59.5 + - - +
471B LYS* 3.3 10.4 - - - +
472B LEU* 2.9 27.7 + - - +
620B LEU* 3.6 33.4 - - + +
621B LEU* 4.3 6.7 - - + +
624B GLU* 3.9 30.3 - - + +
658B LEU* 3.4 25.5 - - + +
661B LYS* 5.1 8.9 + - - +
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Residues in contact with LEU 469 (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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433B ILE* 3.9 42.4 - - + +
458B ARG* 5.9 0.7 - - + -
464B SER 5.7 1.8 - - - +
465B TRP* 3.7 24.7 - - + -
466B GLU* 3.0 25.3 + - + +
468B GLU* 1.3 78.7 - - - +
470B VAL* 1.3 64.2 + - - +
472B LEU* 3.3 20.7 + - + -
473B MET* 3.1 30.5 + - + +
624B GLU* 4.1 17.9 - - - +
628B GLN* 4.2 10.3 - - - +
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Residues in contact with VAL 470 (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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407B VAL* 4.4 16.8 - - + -
410B GLN* 3.8 33.2 - - + +
411B VAL* 4.1 16.4 - - + -
465B TRP* 3.6 30.3 - - + +
466B GLU 3.2 14.5 + - - +
467B PRO* 3.2 9.2 + - + +
469B LEU* 1.3 75.8 - - - +
471B LYS* 1.3 62.2 + - - +
473B MET* 3.3 9.1 + - - +
474B CYS* 3.2 26.9 + - - -
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Residues in contact with LYS 471 (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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410B GLN* 5.7 6.5 - - - +
467B PRO* 3.0 16.7 + - + +
468B GLU* 3.3 12.3 - - - +
470B VAL* 1.3 77.7 - - - +
472B LEU* 1.3 60.7 + - - +
474B CYS* 3.2 16.1 + - - +
475B GLU* 3.3 17.9 + - + +
621B LEU* 3.8 28.3 - - + +
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Residues in contact with LEU 472 (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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433B ILE 4.3 10.3 - - - +
436B GLY* 6.1 0.4 - - - -
468B GLU 2.9 16.1 + - - +
469B LEU* 3.6 18.4 - - + +
470B VAL 3.2 0.4 - - - -
471B LYS* 1.3 74.5 - - - +
473B MET* 1.3 66.4 + - + +
475B GLU* 3.2 11.9 + - - +
476B LEU* 3.3 19.8 + - + +
585B LEU* 3.8 18.6 - - + -
621B LEU* 3.8 18.1 - - + +
624B GLU* 3.8 16.6 - - + +
625B PHE* 3.6 56.3 - - + +
628B GLN* 4.6 0.9 - - + -
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Residues in contact with MET 473 (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 VAL* 4.1 30.7 - - + -
414B VAL* 4.3 5.7 - - - +
417B ASN* 4.5 4.0 + - - +
431B ALA* 3.8 18.2 - - + -
432B SER 3.9 6.3 - - - +
433B ILE* 4.3 11.4 - - - +
436B GLY* 3.7 20.5 - - - +
437B VAL 3.6 34.5 - - - +
438B THR* 4.7 0.7 - - + -
465B TRP* 3.8 21.8 - - + -
469B LEU* 3.1 19.2 + - + +
470B VAL 3.3 6.9 + - - +
472B LEU* 1.3 77.4 - - - +
474B CYS* 1.3 60.6 + - - +
476B LEU* 3.3 22.6 + - - -
477B GLY* 3.6 6.1 + - - -
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Residues in contact with CYS 474 (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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410B GLN* 3.9 38.6 - - - +
411B VAL* 4.8 3.4 - - - -
414B VAL* 3.6 37.4 - - + +
470B VAL* 3.2 17.8 + - - +
471B LYS* 3.6 10.8 - - + +
472B LEU 3.1 1.2 - - - -
473B MET* 1.3 76.7 - - - +
475B GLU* 1.3 67.3 + - - +
476B LEU 4.6 0.3 - - - +
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Residues in contact with GLU 475 (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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471B LYS* 3.3 6.9 + - + +
472B LEU 3.2 6.1 + - - +
474B CYS* 1.3 84.2 - - - +
476B LEU* 1.3 70.0 + - - +
480B ILE* 5.0 2.9 - - - +
585B LEU* 3.5 23.5 - - + +
586B PRO* 4.3 17.2 - - + +
621B LEU* 3.5 29.4 - - + -
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Residues in contact with LEU 476 (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 VAL* 4.1 9.7 - - - +
415B ASP* 5.2 0.9 - - - +
435B LEU 3.9 4.3 - - - +
436B GLY* 3.7 25.6 - - - +
472B LEU* 3.3 24.0 + - + +
473B MET 3.3 7.1 + - - +
474B CYS 4.6 0.3 - - - +
475B GLU* 1.3 87.3 - - - +
477B GLY* 1.3 66.0 + - - +
480B ILE* 4.0 21.2 - - + +
481B ILE* 4.1 18.8 - - + -
585B LEU* 3.8 32.8 - - + +
586B PRO 4.3 1.6 - - - -
589B ALA* 4.3 4.3 - - + -
625B PHE* 3.5 33.0 - - + -
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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