Contacts of the helix formed by residues 480 - 489 (chain C) in PDB entry 1FSX
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 LEU 480 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465C ALA* 3.9 23.6 - - + +
468C LYS* 5.5 4.9 - - + +
469C ALA* 4.2 21.3 - - + +
476C LEU* 3.1 26.8 + - + +
477C PRO 4.0 3.4 - - - -
479C ALA* 1.3 84.5 - - + +
481C SER* 1.3 57.4 + - - +
482C GLU 3.4 2.5 - - - -
483C LEU* 3.3 27.3 + - + +
484C SER* 2.8 29.8 + - - -
532C VAL* 4.2 22.0 - - + -
535C VAL* 4.1 15.5 - - + -
536C LEU* 4.1 13.7 - - + -
543C HEM 6.0 2.0 - - + -
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Residues in contact with SER 481 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477C PRO 3.5 11.3 + - - -
478C GLY* 3.3 17.8 + - - -
479C ALA 3.5 1.7 + - - -
480C LEU* 1.3 76.8 - - - +
482C GLU* 1.3 59.3 + - - +
484C SER* 3.3 7.7 + - - -
485C ASP* 2.6 37.1 + - - +
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Residues in contact with GLU 482 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468C LYS* 5.9 1.4 + - - -
479C ALA 5.3 0.4 + - - -
480C LEU 3.4 0.4 - - - -
481C SER* 1.3 82.0 + - - +
483C LEU* 1.3 75.1 + - + +
485C ASP* 3.4 8.1 + - - +
486C LEU* 3.1 28.6 + - - +
543C HEM 3.3 24.0 - - - +
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Residues in contact with LEU 483 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465C ALA* 3.5 31.4 - - + -
468C LYS* 6.3 1.8 - - - +
480C LEU* 3.3 27.0 + - + +
481C SER 3.2 0.2 - - - -
482C GLU* 1.3 91.0 - - + +
484C SER* 1.3 65.0 + - - +
486C LEU* 3.9 4.0 - - + +
487C HIS* 2.8 39.6 + - + +
536C LEU* 3.7 14.0 - - + +
543C HEM 3.8 48.9 - - + -
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Residues in contact with SER 484 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477C PRO 5.9 0.2 - - - -
480C LEU 2.8 18.4 + - - -
481C SER* 3.3 11.2 - - - -
483C LEU* 1.3 77.0 - - - +
485C ASP* 1.3 59.3 + - - +
488C ALA* 2.9 35.3 + - - +
535C VAL* 3.0 26.6 + - - -
536C LEU* 3.5 14.3 - - - +
538C SER* 4.0 13.5 + - - -
539C LYS* 4.5 4.0 + - - +
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Residues in contact with ASP 485 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481C SER* 2.6 26.4 + - - +
482C GLU* 3.9 5.9 - - - +
483C LEU 3.3 0.2 - - - -
484C SER* 1.3 76.9 - - - +
486C LEU* 1.3 63.7 + - - +
488C ALA* 5.1 0.9 - - - -
489C HIS* 3.0 31.2 + - + +
490C LYS* 3.4 15.5 + - - +
539C LYS* 4.0 25.2 + - - +
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Residues in contact with LEU 486 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482C GLU* 3.1 22.0 + - - +
483C LEU* 3.9 6.3 - - + +
484C SER 3.3 0.2 - - - -
485C ASP* 1.3 80.2 - - - +
487C HIS* 1.3 65.6 + - + +
490C LYS* 3.3 22.5 + - + +
491C LEU* 2.9 52.7 + - + +
543C HEM 3.7 53.6 - - + +
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Residues in contact with HIS 487 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483C LEU* 2.8 38.5 + - + +
486C LEU* 1.3 81.4 - - + +
488C ALA* 1.3 57.3 + - - +
491C LEU* 3.7 8.7 - - + +
492C ARG 3.1 21.7 + - - -
493C VAL* 3.1 17.0 + - + -
498C PHE* 4.2 14.1 - + + -
536C LEU* 4.0 17.0 - - + +
540C TYR* 3.7 1.2 + - - -
543C HEM 2.1 98.0 + + + -
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Residues in contact with ALA 488 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484C SER 2.9 18.4 + - - +
487C HIS* 1.3 78.3 - - - +
489C HIS* 1.3 59.5 + - - +
492C ARG* 3.6 12.0 + - - -
536C LEU 3.6 12.3 + - - +
537C THR* 4.4 0.2 - - - -
539C LYS* 3.5 30.3 - - + +
540C TYR* 2.9 44.6 + - + -
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Residues in contact with HIS 489 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485C ASP* 3.0 21.1 + - + +
488C ALA* 1.3 77.2 - - - +
490C LYS* 1.3 74.5 + - + +
492C ARG* 3.7 40.6 + - - +
539C LYS* 3.3 40.7 - - + +
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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