Contacts of the helix formed by residues 478 - 488 (chain U) 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 U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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473U TYR* 4.1 28.0 + + - -
474U LEU* 2.9 27.8 + - + +
477U ASN* 1.3 79.1 - - + +
479U ASN* 1.3 60.4 + - - +
480U GLU* 3.3 2.5 - - - +
481U LEU* 3.6 33.9 + - + +
482U LEU* 3.3 21.5 + - - +
498U SER* 4.8 4.0 + - - -
502U ALA* 3.5 36.0 - - + +
505U SER* 5.8 1.0 - - - -
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Residues in contact with ASN 479 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474U LEU 3.0 3.3 + - - +
475U LYS* 3.0 40.8 + - - +
476U SER 5.5 0.2 - - - -
477U ASN 2.7 10.5 + - - +
478U HIS* 1.3 72.8 - - - +
480U GLU* 1.3 67.9 + - + +
481U LEU 3.2 0.7 - - - -
482U LEU* 3.2 18.9 + - - +
483U THR* 3.2 19.6 + - - -
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Residues in contact with GLU 480 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477U ASN 5.1 5.2 - - - +
478U HIS* 5.2 0.4 - - - -
479U ASN* 1.3 81.4 - - + +
481U LEU* 1.3 69.8 + - + +
483U THR* 3.6 9.2 + - - -
484U GLU* 3.5 22.8 + - - +
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Residues in contact with LEU 481 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474U LEU* 6.3 0.4 - - + -
478U HIS* 3.6 42.2 - - + +
479U ASN 3.2 0.4 - - - -
480U GLU* 1.3 86.3 - - + +
482U LEU* 1.3 65.8 + - + +
484U GLU* 3.2 21.7 + - + +
485U ILE* 3.5 12.8 + - - +
495U LEU* 4.6 21.3 - - + +
498U SER* 3.8 32.1 - - - +
499U LEU* 5.6 8.5 - - + +
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Residues in contact with LEU 482 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441U GLU* 3.3 51.1 - - + +
442U GLU* 6.1 3.4 - - + -
445U PRO* 4.3 6.5 - - + -
471U LEU* 6.4 0.4 - - + -
474U LEU* 3.9 51.6 - - + +
475U LYS* 4.0 20.6 - - + -
478U HIS 3.3 12.8 - - - +
479U ASN* 3.2 15.4 + - - +
481U LEU* 1.3 79.4 - - + +
483U THR* 1.3 60.1 + - - +
485U ILE* 3.4 12.4 + - + +
486U ARG* 3.5 4.2 + - - +
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Residues in contact with THR 483 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479U ASN* 3.2 20.0 + - - -
480U GLU* 3.8 12.4 + - - -
481U LEU 3.2 0.4 - - - -
482U LEU* 1.3 75.2 - - - +
484U GLU* 1.3 61.9 + - - +
486U ARG* 3.0 37.5 + - - +
487U GLU* 2.8 53.5 + - - +
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Residues in contact with GLU 484 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480U GLU 3.5 15.6 + - - +
481U LEU* 3.2 15.9 + - + +
483U THR* 1.3 77.9 - - - +
485U ILE* 1.3 58.6 + - + +
487U GLU* 5.2 3.9 - - - +
488U LYS* 2.9 52.7 + - - +
495U LEU* 3.3 42.0 - - + +
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Residues in contact with ILE 485 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382U VAL* 5.6 0.2 - - - +
384U ALA* 4.2 20.4 - - + -
440U THR* 4.2 9.5 - - + +
441U GLU* 3.9 25.0 - - + +
444U VAL* 4.2 17.3 - - + -
445U PRO* 5.8 3.1 - - + -
481U LEU 3.5 15.9 - - - +
482U LEU* 3.6 12.6 - - + +
483U THR 3.2 0.2 - - - -
484U GLU* 1.3 79.4 - - + +
486U ARG* 1.3 59.6 + - - +
489U GLY* 2.9 30.9 + - - +
490U GLU 5.1 4.5 - - - +
491U LEU* 3.4 38.4 - - + -
495U LEU* 5.3 1.3 - - + -
499U LEU* 6.2 2.5 - - + -
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Residues in contact with ARG 486 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441U GLU* 3.3 37.1 + - - +
482U LEU 3.5 3.5 + - - +
483U THR* 3.0 43.1 + - - +
485U ILE* 1.3 79.6 - - - +
487U GLU* 1.3 82.3 + - - +
488U LYS 3.3 5.0 + - - +
489U GLY* 4.1 1.2 + - - -
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Residues in contact with GLU 487 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483U THR* 2.8 36.1 + - + +
484U GLU* 4.7 3.6 - - - +
486U ARG* 1.3 97.8 + - - +
488U LYS* 1.3 65.1 + - + +
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Residues in contact with LYS 488 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484U GLU* 2.9 37.7 + - + +
486U ARG 4.0 2.0 - - - +
487U GLU* 1.3 84.9 - - + +
489U GLY* 1.3 61.1 + - - +
490U GLU* 4.1 15.0 - - + +
495U LEU* 5.5 2.7 - - + -
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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