Contacts of the helix formed by residues 439 - 463 (chain C) in PDB entry 1G88
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
----------------------------------------------------------
396C ASP* 3.3 8.0 - - - +
413C TYR* 3.5 31.2 - - + +
436C LYS* 2.8 27.4 + - - -
438C PHE* 1.3 79.0 - - - +
440C LEU* 1.3 53.6 + - - +
441C ARG* 2.9 14.6 + - - +
442C GLN* 2.7 35.1 + - + +
443C CYS* 2.7 35.2 + - - +
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Residues in contact with LEU 440 (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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314C ILE* 3.3 25.1 - - + -
394C GLU* 3.5 29.6 - - + +
395C GLY* 3.9 20.2 - - - +
396C ASP* 3.1 13.9 + - - +
438C PHE* 3.8 16.9 - - + -
439C ASP* 1.3 70.3 - - - +
441C ARG* 1.3 54.0 + - - +
443C CYS* 2.9 4.7 + - + +
444C HIS* 2.5 38.3 + - - +
447C MET* 6.0 0.4 - - + -
531C ARG* 4.0 5.4 - - + -
532C ALA* 3.9 23.3 - - + +
535C LEU* 3.4 29.4 - - + -
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Residues in contact with ARG 441 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312C PRO* 2.7 55.6 + - - +
313C PRO 5.6 0.6 + - - -
314C ILE* 3.7 29.0 - - + +
394C GLU* 5.3 0.2 + - - -
396C ASP* 4.9 0.4 + - - -
439C ASP* 2.9 12.6 + - - +
440C LEU* 1.3 75.0 - - - +
442C GLN* 1.3 63.6 + - - +
444C HIS* 3.3 3.0 + - + +
445C ARG* 3.0 46.4 + - - +
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Residues in contact with GLN 442 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412C TYR 5.8 0.4 - - - -
413C TYR* 4.1 29.9 - - + +
416C ARG* 3.6 37.4 + - + +
417C GLU* 5.9 1.3 - - - +
438C PHE* 6.2 0.2 - - - -
439C ASP* 2.7 31.7 + - + +
441C ARG* 1.3 73.3 - - - +
443C CYS* 1.3 70.8 + - - +
445C ARG* 3.6 22.1 - - - +
446C GLN* 3.0 31.6 + - - +
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Residues in contact with CYS 443 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438C PHE* 3.4 31.4 - - + -
439C ASP 2.7 18.3 + - - +
440C LEU* 3.2 5.8 - - + +
442C GLN* 1.3 86.5 - - - +
444C HIS* 1.3 62.8 - - - +
446C GLN* 3.3 5.2 + - - +
447C MET* 2.9 41.7 + - - +
498C LEU* 3.6 22.4 - - - -
499C CYS* 4.3 11.9 - - - -
532C ALA* 4.6 3.1 - - - -
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Residues in contact with HIS 444 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314C ILE* 3.4 38.8 + - + +
440C LEU* 2.5 20.3 + - - +
441C ARG* 3.6 4.9 - - - +
443C CYS* 1.3 72.2 - - - +
445C ARG* 1.3 62.9 + - + +
447C MET* 3.1 43.8 + - + +
448C GLN* 3.2 45.6 + - - +
535C LEU* 4.2 14.9 - - + +
539C VAL* 4.2 10.1 - - + -
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Residues in contact with ARG 445 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441C ARG* 3.0 35.1 + - - +
442C GLN* 3.6 33.5 + - - +
444C HIS* 1.3 79.9 - - + +
446C GLN* 1.3 63.0 + - - +
447C MET 3.4 0.2 + - - -
448C GLN* 3.7 11.5 + - - +
449C GLN* 3.5 24.1 + - + +
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Residues in contact with GLN 446 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416C ARG* 5.2 13.3 - - - +
442C GLN* 3.0 30.3 + - - +
443C CYS* 3.7 5.4 - - - +
445C ARG* 1.3 78.6 - - - +
447C MET* 1.3 62.0 + - - +
449C GLN* 3.6 13.7 + - - +
450C GLN* 2.9 43.7 + - - +
498C LEU* 3.8 24.9 - - + -
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Residues in contact with MET 447 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443C CYS* 2.9 31.6 + - - +
444C HIS* 3.1 43.0 + - - +
446C GLN* 1.3 75.0 - - - +
448C GLN* 1.3 54.2 + - - +
450C GLN* 2.9 3.6 + - - +
451C ALA* 2.7 37.4 + - - +
495C LEU* 3.8 11.2 - - + +
498C LEU* 4.6 9.2 - - + -
499C CYS* 4.3 9.0 - - - -
532C ALA* 4.1 6.3 - - - +
535C LEU* 3.6 26.9 - - + +
536C LEU* 3.5 42.8 - - + -
539C VAL* 4.0 7.2 - - + -
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Residues in contact with GLN 448 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444C HIS* 3.2 49.0 + - + +
445C ARG* 4.1 9.3 - - - +
446C GLN 3.5 0.2 - - - -
447C MET* 1.3 73.8 - - - +
449C GLN* 1.3 59.1 + - - +
451C ALA* 3.3 1.7 + - - +
452C ALA* 2.9 30.8 + - - +
539C VAL* 3.9 28.5 - - + +
543C MET* 5.8 0.9 - - - +
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Residues in contact with GLN 449 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445C ARG* 3.5 18.0 + - + +
446C GLN* 4.0 14.9 - - - +
447C MET 3.3 0.4 - - - -
448C GLN* 1.3 78.2 - - - +
450C GLN* 1.3 57.2 + - - +
452C ALA* 3.7 6.9 + - + +
453C THR* 2.8 31.8 + - - -
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Residues in contact with GLN 450 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446C GLN* 2.9 38.7 + - - +
447C MET 2.9 3.6 + - - +
449C GLN* 1.3 76.7 - - - +
451C ALA* 1.3 65.6 + - - +
453C THR* 3.3 7.2 + - - -
454C ALA* 3.0 21.1 + - - +
491C GLY 4.9 0.8 + - - -
494C ASP* 3.7 33.7 + - - +
495C LEU* 3.4 23.7 - - + +
498C LEU* 3.2 18.6 - - - +
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Residues in contact with ALA 451 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447C MET 2.7 19.4 + - - +
448C GLN 3.8 3.6 - - - +
450C GLN* 1.3 72.6 - - - +
452C ALA* 1.3 57.4 + - - +
454C ALA* 2.9 25.3 - - - +
455C GLN* 3.0 13.0 + - - +
490C ILE* 4.6 1.2 - - + +
495C LEU* 4.0 22.8 - - + +
539C VAL* 3.9 22.0 - - + -
540C LEU* 5.3 2.7 - - + -
543C MET* 4.0 20.0 - - + +
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Residues in contact with ALA 452 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448C GLN 2.9 17.9 + - - +
449C GLN* 3.7 8.7 - - + +
451C ALA* 1.3 74.5 - - - +
453C THR* 1.3 64.3 + - - +
455C GLN* 3.1 12.3 + - - +
456C ALA* 3.1 23.1 + - - +
543C MET* 4.9 4.4 - - + +
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Residues in contact with THR 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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449C GLN* 2.8 21.6 + - - -
450C GLN* 3.3 8.2 + - - -
452C ALA* 1.3 74.4 - - - +
454C ALA* 1.3 66.1 + - - +
456C ALA* 3.9 6.6 - - + +
457C ALA* 3.0 26.2 + - + +
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Residues in contact with ALA 454 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450C GLN 3.0 13.0 + - - +
451C ALA* 2.9 18.3 + - - +
453C THR* 1.3 78.3 - - - +
455C GLN* 1.3 60.6 + - - +
457C ALA* 3.2 7.1 + - - +
458C ALA* 3.0 20.4 + - - +
490C ILE* 3.5 28.7 - - + +
491C GLY* 4.5 12.3 - - - -
495C LEU* 5.7 0.9 - - + -
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Residues in contact with GLN 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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451C ALA 3.0 6.4 + - - +
452C ALA* 3.3 11.0 - - - +
454C ALA* 1.3 78.7 - - - +
456C ALA* 1.3 66.2 + - - +
458C ALA* 2.7 22.7 + - - +
459C ALA* 3.0 15.2 + - - +
490C ILE* 4.1 16.4 - - + +
543C MET* 3.3 46.5 - - + +
544C PRO* 3.4 31.4 + - + +
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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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452C ALA 3.1 11.2 + - - +
453C THR* 3.9 7.4 - - + +
455C GLN* 1.3 78.9 - - - +
457C ALA* 1.3 65.0 + - - +
459C ALA* 3.2 6.4 + - - +
460C ALA* 2.8 26.2 + - - +
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Residues in contact with ALA 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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453C THR* 3.0 14.0 + - + +
454C ALA* 3.2 13.0 - - - +
456C ALA* 1.3 78.1 - - - +
458C ALA* 1.3 62.1 - - - +
460C ALA* 3.3 8.6 + - - +
461C GLN* 3.1 23.6 + - - +
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Residues in contact with ALA 458 (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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454C ALA 3.0 10.2 + - - +
455C GLN* 2.7 23.3 + - - +
457C ALA* 1.3 68.2 - - - +
459C ALA* 1.3 57.9 + - - +
461C GLN* 2.6 34.3 + - - +
462C ALA* 3.1 6.2 + - - +
486C ALA* 4.2 24.3 - - + +
490C ILE* 4.5 17.0 - - + -
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Residues in contact with ALA 459 (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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455C GLN* 3.0 12.9 + - - +
456C ALA* 3.8 8.5 - - - +
458C ALA* 1.3 76.8 - - - +
460C ALA* 1.3 57.4 + - - +
462C ALA* 3.0 24.3 + - - +
463C ALA* 3.3 12.1 + - - +
486C ALA* 5.6 0.2 - - - +
549C GLN* 5.8 0.9 - - - +
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Residues in contact with ALA 460 (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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456C ALA 2.8 19.1 + - - +
457C ALA* 3.4 10.5 - - - +
458C ALA 3.0 0.2 - - - -
459C ALA* 1.3 76.0 - - - +
461C GLN* 1.3 60.2 + - - +
462C ALA 3.4 0.2 - - - -
463C ALA* 4.2 7.4 - - - +
464C ALA* 3.7 17.7 + - - +
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Residues in contact with GLN 461 (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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457C ALA 3.1 11.5 + - - +
458C ALA* 2.6 25.1 + - - +
460C ALA* 1.3 74.3 + - - +
462C ALA* 1.3 62.0 + - - +
464C ALA* 3.5 19.5 - - - +
465C VAL* 3.5 12.0 - - + +
484C LEU* 4.7 0.7 - - - +
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Residues in contact with ALA 462 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458C ALA 3.1 6.1 + - - +
459C ALA* 3.0 13.8 + - - +
461C GLN* 1.3 74.6 - - - +
463C ALA* 1.3 66.5 + - - +
464C ALA 3.0 1.1 - - - -
465C VAL* 3.0 21.8 + - - +
484C LEU* 3.8 20.6 - - + +
486C ALA* 6.5 0.7 - - + -
549C GLN* 3.2 31.4 - - - +
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Residues in contact with ALA 463 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459C ALA 3.3 10.6 + - - +
460C ALA* 4.4 8.1 - - - +
461C GLN 3.5 0.2 - - - -
462C ALA* 1.3 78.3 - - - +
464C ALA* 1.3 53.6 + - - +
465C VAL 2.7 18.9 + - - +
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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