Contacts of the helix formed by residues 439 - 458 (chain C) in PDB entry 3F7F
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 ASP 439 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404C VAL* 4.5 3.5 - - - +
433C ILE 4.0 4.2 - - - +
434C MET* 3.9 6.1 - - + +
435C ALA* 2.9 34.5 + - - +
436C HIS* 3.2 31.1 + - - +
437C ASN 3.5 1.2 + - - -
438C GLU* 1.3 73.0 - - - +
440C GLU* 1.3 55.6 + - - +
441C GLU* 3.1 27.7 - - - +
442C TYR* 2.8 41.5 + - + +
443C LEU* 3.4 4.0 + - - +
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Residues in contact with GLU 440 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404C VAL* 5.0 11.9 - - + -
438C GLU* 2.6 24.8 + - + +
439C ASP* 1.3 71.4 - - - +
441C GLU* 1.3 62.4 + - - +
443C LEU* 3.3 12.8 + - + +
444C ALA* 3.0 24.3 + - - +
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Residues in contact with GLU 441 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439C ASP* 3.1 14.8 - - - +
440C GLU* 1.3 78.2 - - - +
442C TYR* 1.3 59.5 + - - +
444C ALA* 3.5 14.3 - - - +
445C ASN* 3.3 17.8 + - - +
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Residues in contact with TYR 442 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408C PHE* 4.3 11.0 - + - -
424C GLN* 3.6 19.0 + - - +
427C LEU* 3.1 45.1 - - + +
432C ILE* 4.0 24.4 + - + -
433C ILE* 4.9 0.8 - - - +
434C MET* 3.2 64.9 + - + +
439C ASP* 2.8 29.2 + - - +
441C GLU* 1.3 72.8 - - - +
443C LEU* 1.3 57.6 + - - +
444C ALA 2.9 1.1 - - - -
445C ASN* 2.3 42.3 + - - +
446C LEU* 3.2 7.4 + - + -
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Residues in contact with LEU 443 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403C ASP 5.3 0.2 - - - +
404C VAL* 3.5 38.4 - - + +
407C GLY* 4.1 19.5 - - - +
408C PHE* 5.3 7.2 - - + -
411C LEU* 4.3 12.6 - - + -
434C MET* 5.8 0.7 - - + -
439C ASP 3.4 4.8 + - - +
440C GLU* 3.3 12.5 + - + +
442C TYR* 1.3 83.0 - - + +
444C ALA* 1.3 66.6 + - - +
445C ASN 3.1 0.9 + - - -
446C LEU* 3.1 12.3 + - - +
447C GLU* 3.1 44.4 + - + +
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Residues in contact with ALA 444 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440C GLU 3.0 12.4 + - - +
441C GLU* 3.5 15.3 - - - +
442C TYR 2.7 4.0 + - - -
443C LEU* 1.3 82.5 - - + +
445C ASN* 1.3 61.3 + - - +
447C GLU* 3.5 17.0 - - - +
448C THR* 3.6 9.7 + - - -
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Residues in contact with ASN 445 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427C LEU* 4.0 17.0 - - + -
432C ILE* 3.8 31.1 - - + +
441C GLU* 3.3 22.0 + - - +
442C TYR* 2.3 29.9 + - - +
444C ALA* 1.3 67.0 - - - +
446C LEU* 1.3 65.2 + - - +
447C GLU 3.1 1.6 - - - -
448C THR* 2.9 18.7 + - - -
449C ILE* 3.0 17.6 + - + +
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Residues in contact with LEU 446 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408C PHE* 3.4 39.0 - - + -
411C LEU* 4.5 7.4 - - + -
420C PHE* 3.9 16.2 - - + -
423C ALA* 4.0 14.8 - - + -
424C GLN* 4.3 9.4 - - + +
427C LEU* 3.7 29.7 - - + +
442C TYR* 3.2 9.7 + - + -
443C LEU* 3.1 15.2 + - - +
445C ASN* 1.3 77.8 - - - +
447C GLU* 1.3 64.8 + - - +
449C ILE* 4.6 2.5 - - - +
450C LEU* 2.8 51.0 + - + +
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Residues in contact with GLU 447 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391C SER* 5.3 2.4 + - - -
411C LEU* 3.8 24.5 - - + +
414C ARG* 5.3 5.5 + - - -
415C TYR* 4.5 4.4 + - - -
443C LEU* 3.2 33.0 - - + +
444C ALA* 3.5 12.8 - - - +
445C ASN 3.1 0.2 - - - -
446C LEU* 1.3 79.5 - - - +
448C THR* 1.3 58.9 + - - +
450C LEU* 3.7 8.2 - - - +
451C ARG* 3.0 30.4 + - - +
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Residues in contact with THR 448 (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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444C ALA 3.6 9.7 + - - -
445C ASN* 2.9 10.1 + - - -
447C GLU* 1.3 76.3 - - - +
449C ILE* 1.3 65.5 + - + +
451C ARG* 3.4 29.0 + - - +
452C ASP* 2.9 48.0 + - - +
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Residues in contact with ILE 449 (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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423C ALA* 3.4 36.8 - - + +
426C ILE* 4.3 22.4 - - + -
427C LEU* 4.5 16.2 - - + -
432C ILE* 6.2 1.8 - - + -
445C ASN* 3.0 15.8 + - + +
446C LEU* 3.9 6.7 - - - +
448C THR* 1.3 79.4 - - + +
450C LEU* 1.3 57.6 + - - +
452C ASP* 2.8 12.6 + - + +
453C VAL* 2.6 44.1 + - + +
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Residues in contact with LEU 450 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411C LEU* 3.7 37.7 - - + -
415C TYR* 3.7 29.0 - - + -
419C ILE* 4.1 12.2 - - + +
420C PHE* 3.6 33.2 - - + +
423C ALA* 3.5 21.8 - - + -
446C LEU* 2.8 43.7 + - + +
447C GLU* 3.7 3.1 - - - +
449C ILE* 1.3 71.2 - - - +
451C ARG* 1.3 65.0 + - - +
453C VAL* 3.7 1.1 - - - +
454C LYS* 2.8 26.2 + - - +
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Residues in contact with ARG 451 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392C GLU* 5.2 15.0 - - + -
414C ARG* 6.0 1.6 - - - +
415C TYR* 3.8 16.8 + - - +
447C GLU 3.0 17.6 + - - +
448C THR* 3.5 34.5 + - - +
450C LEU* 1.3 76.9 - - - +
452C ASP* 1.3 75.9 + - - +
454C LYS* 3.5 4.1 + - - +
455C THR* 2.9 35.4 + - - +
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Residues in contact with ASP 452 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448C THR* 2.9 33.5 + - - +
449C ILE* 2.8 20.6 + - + +
451C ARG* 1.3 87.8 + - - +
453C VAL* 1.3 54.8 + - + +
455C THR* 3.1 10.1 + - - +
456C ALA* 2.7 36.7 + - - +
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Residues in contact with VAL 453 (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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419C ILE* 3.9 17.5 - - + -
422C ARG* 3.7 24.0 - - + +
423C ALA* 4.2 5.4 - - - -
426C ILE* 4.1 13.2 - - + -
449C ILE* 2.6 41.5 + - + +
450C LEU 3.8 2.9 - - - +
452C ASP* 1.3 71.2 - - + +
454C LYS* 1.3 53.7 + - - +
456C ALA* 3.0 6.6 + - - +
457C PHE* 2.7 68.8 + - + -
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Residues in contact with LYS 454 (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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6C ARG* 5.0 1.2 - - - +
8C ASP* 3.1 28.6 + - - -
385C SER* 4.8 0.4 + - - -
388C ASP* 3.0 36.8 + - - +
415C TYR* 4.1 20.0 - - + -
419C ILE* 3.8 27.7 - - + +
450C LEU 2.8 16.6 + - - +
451C ARG* 3.5 5.2 - - - +
453C VAL* 1.3 78.3 - - - +
455C THR* 1.3 54.4 + - - +
457C PHE* 3.0 1.3 + - - -
458C ASN* 2.7 57.9 + - - +
480C ASN* 5.8 0.2 - - - +
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Residues in contact with THR 455 (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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359C THR* 3.1 42.6 - - + +
384C LYS* 5.6 6.7 - - - -
451C ARG* 2.9 21.2 + - - +
452C ASP* 3.4 14.7 + - - +
454C LYS* 1.3 79.2 - - - +
456C ALA* 1.3 64.0 + - - +
458C ASN* 3.4 12.6 + - - +
459C GLU 3.4 7.8 + - - -
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Residues in contact with ALA 456 (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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359C THR* 4.5 12.1 - - + -
422C ARG* 6.1 2.2 - - - +
452C ASP 2.7 16.5 + - - +
453C VAL* 3.4 11.4 - - - +
455C THR* 1.3 69.3 - - - +
457C PHE* 1.3 71.8 + - + +
458C ASN 2.9 1.6 - - - -
459C GLU* 2.8 23.7 + - - +
476C PHE* 4.3 5.7 - - - +
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Residues in contact with PHE 457 (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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418C GLN* 3.4 33.4 - - + -
419C ILE* 3.6 28.7 - - + -
422C ARG* 3.9 36.1 - - + -
453C VAL* 2.7 41.9 + - + +
454C LYS* 3.4 5.4 - - - +
456C ALA* 1.3 76.5 - - + +
458C ASN* 1.3 63.2 + - - +
459C GLU 3.5 0.3 + - - -
475C CYS* 3.2 11.8 - - - +
476C PHE* 5.4 0.2 - - - -
477C GLN* 3.1 64.7 + - + +
480C ASN* 3.7 9.3 - - - +
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Residues in contact with ASN 458 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C ARG* 3.0 31.3 + - - +
8C ASP* 3.6 16.5 - - - +
359C THR 5.0 3.3 - - - +
361C SER* 6.1 0.5 - - - -
454C LYS* 2.7 56.6 + - - +
455C THR* 3.6 8.7 - - - +
456C ALA 2.9 0.6 + - - -
457C PHE* 1.3 78.9 - - - +
459C GLU* 1.3 65.8 + - - +
460C ALA* 3.1 4.5 + - - +
475C CYS* 3.9 17.6 - - - -
480C ASN* 4.3 9.9 + - - +
481C HIS 5.0 1.0 - - - +
482C SER* 3.7 5.7 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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