Contacts of the helix formed by residues 478 - 489 (chain L) in PDB entry 3FKS
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 HIS 478 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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473L TYR* 3.7 33.4 + + - -
474L LEU* 2.8 26.4 + - + +
477L ASN* 1.3 82.4 - - + +
479L ASN* 1.3 61.6 + - - +
480L GLU 3.4 2.2 - - - +
481L LEU* 3.7 36.7 + - + +
482L LEU* 4.1 6.8 + - - +
498L SER* 4.9 3.0 + - - -
502L ALA* 3.4 41.6 - - + +
505L SER* 4.8 1.8 + - - -
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Residues in contact with ASN 479 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474L LEU 3.0 6.2 + - - -
475L LYS* 2.9 35.6 + - - +
476L SER 4.8 3.1 - - - +
477L ASN 3.1 8.1 + - - +
478L HIS* 1.3 73.0 - - - +
480L GLU* 1.3 66.7 + - + +
481L LEU 3.1 3.3 + - - -
482L LEU* 3.4 14.5 + - - +
483L THR* 3.2 17.2 + - - -
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Residues in contact with GLU 480 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478L HIS* 3.4 0.6 - - - -
479L ASN* 1.3 78.7 + - + +
481L LEU* 1.3 69.5 + - + +
483L THR* 3.4 16.7 + - - +
484L GLU* 3.3 23.2 + - + +
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Residues in contact with LEU 481 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474L LEU* 6.4 0.7 - - + -
478L HIS* 3.9 41.1 - - + +
479L ASN 3.1 0.6 - - - -
480L GLU* 1.3 82.4 - - + +
482L LEU* 1.3 68.9 + - + +
484L GLU* 2.8 17.8 + - + +
485L ILE* 3.0 18.9 + - + +
495L LEU* 3.8 27.1 - - + +
498L SER* 3.7 33.7 - - - +
499L LEU* 5.1 4.9 - - + +
502L ALA* 5.7 1.8 - - + -
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Residues in contact with LEU 482 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441L GLU* 3.3 42.5 - - + +
442L GLU* 5.3 5.2 - - + -
445L PRO* 4.0 5.4 - - + -
471L LEU* 6.4 0.4 - - + -
474L LEU* 3.8 48.0 - - + +
475L LYS* 3.9 27.8 - - + -
478L HIS 4.1 8.7 - - - +
479L ASN* 3.4 8.5 + - - +
481L LEU* 1.3 76.6 - - + +
483L THR* 1.3 62.8 + - - +
485L ILE* 3.2 12.9 + - + +
486L ARG* 3.0 20.4 + - - +
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Residues in contact with THR 483 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479L ASN* 3.2 21.5 + - - -
480L GLU* 3.4 18.3 + - - +
481L LEU 3.0 0.4 - - - -
482L LEU* 1.3 79.3 - - - +
484L GLU* 1.3 60.7 + - - +
486L ARG* 3.2 35.2 + - - +
487L GLU* 3.0 37.5 + - - +
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Residues in contact with GLU 484 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480L GLU 3.3 11.4 + - - +
481L LEU* 2.8 11.3 + - + +
483L THR* 1.3 79.3 - - - +
485L ILE* 1.3 56.4 + - - +
487L GLU* 5.2 4.5 - - - +
488L LYS* 2.7 73.0 + - - +
495L LEU* 3.8 36.8 - - + +
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Residues in contact with ILE 485 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382L VAL* 5.5 0.5 - - - +
384L ALA* 4.2 11.2 - - + +
440L THR* 4.6 4.0 - - + +
441L GLU* 3.7 37.0 - - + +
444L VAL* 4.1 34.1 - - + -
445L PRO* 4.4 9.2 - - + -
481L LEU* 3.0 13.4 + - + +
482L LEU* 3.4 18.6 - - + +
484L GLU* 1.3 75.7 - - + +
486L ARG* 1.3 59.6 + - - +
488L LYS* 5.2 0.4 - - - -
489L GLY* 2.9 30.0 + - - +
490L GLU 5.3 2.9 - - - +
491L LEU* 4.2 19.7 - - + -
495L LEU* 4.9 4.0 - - + +
499L LEU* 5.8 5.2 - - + -
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Residues in contact with ARG 486 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440L THR* 6.4 0.4 - - - -
441L GLU* 3.3 39.1 + - - +
482L LEU 3.0 11.1 + - - +
483L THR* 3.2 36.1 + - - +
485L ILE* 1.3 80.5 - - - +
487L GLU* 1.3 93.1 + - - +
489L GLY* 4.0 4.5 + - - -
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Residues in contact with GLU 487 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483L THR* 3.0 26.9 + - - +
484L GLU* 4.5 4.2 - - - +
486L ARG* 1.3 106.6 + - - +
488L LYS* 1.3 68.9 + - + +
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Residues in contact with LYS 488 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484L GLU* 2.7 56.0 + - - +
487L GLU* 1.3 76.9 - - + +
489L GLY* 1.3 60.9 + - - +
490L GLU* 3.2 19.9 + - + +
495L LEU* 5.0 3.4 - - + -
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Residues in contact with GLY 489 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382L VAL* 3.5 18.1 - - - +
383L LYS* 3.4 9.2 + - - +
384L ALA* 3.1 21.2 + - - -
485L ILE 2.9 21.1 + - - -
486L ARG 4.4 4.0 - - - -
487L GLU 3.4 1.0 - - - -
488L LYS* 1.3 77.6 - - - +
490L GLU* 1.3 60.5 + - - +
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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