Contacts of the helix formed by residues 441 - 456 (chain C) in PDB entry 3OS8
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 GLN 441 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393C TRP* 3.7 2.9 - - - -
439C ASN* 2.7 32.3 + - - +
440C LEU* 1.3 77.1 + - - +
442C GLY* 1.3 55.1 + - - +
443C GLU* 3.9 15.4 - - + +
444C GLU* 3.0 31.5 + - + +
445C PHE* 2.8 34.8 + - - +
503C ARG* 4.8 1.1 - - - +
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Residues in contact with GLY 442 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320C LEU* 4.6 7.9 - - - -
393C TRP* 3.4 28.0 - - - -
441C GLN* 1.3 72.1 - - - +
443C GLU* 1.3 66.0 + - - +
445C PHE* 3.2 4.2 + - - +
446C VAL* 3.1 29.3 + - - +
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Residues in contact with GLU 443 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316C VAL* 3.6 25.2 - - + +
320C LEU* 4.3 14.3 - - + +
441C GLN* 3.2 17.5 - - + +
442C GLY* 1.3 78.9 + - - +
444C GLU* 1.3 61.4 + - + +
446C VAL* 3.1 23.3 - - - +
447C CYS* 3.4 14.0 - - - -
489C LEU* 3.8 29.2 - - + -
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Residues in contact with GLU 444 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440C LEU* 3.4 14.5 - - + +
441C GLN* 3.0 34.4 + - + +
443C GLU* 1.3 73.8 - - + +
445C PHE* 1.3 66.5 + - - +
447C CYS* 3.1 5.5 + - - +
448C LEU* 3.0 24.8 + - - +
486C LEU* 4.0 23.0 - - + +
489C LEU* 4.6 13.7 - - + +
490C MET* 4.1 14.2 - - + +
503C ARG* 2.7 50.3 + - - -
507C LEU* 4.4 5.8 - - + -
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Residues in contact with PHE 445 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323C GLU* 3.6 21.3 - - - -
389C ILE* 3.6 32.8 - - + -
390C GLY* 4.1 11.2 - - - -
393C TRP* 3.5 63.3 - + + -
435C PHE* 4.7 0.4 - + - -
440C LEU* 4.1 13.6 - - + +
441C GLN 2.8 13.2 + - - +
442C GLY* 3.4 7.9 - - - +
444C GLU* 1.3 78.2 - - - +
446C VAL* 1.3 72.0 + - + +
448C LEU* 3.1 5.7 + - - +
449C LYS* 3.0 46.1 + - + +
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Residues in contact with VAL 446 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316C VAL* 4.8 4.0 - - + +
319C LEU* 3.7 30.7 - - + +
320C LEU* 4.0 17.7 - - + +
323C GLU* 3.7 37.7 - - + +
360C TRP* 5.2 2.0 + - - +
442C GLY 3.1 13.3 + - - +
443C GLU* 3.1 23.6 - - - +
445C PHE* 1.3 83.1 - - + +
447C CYS* 1.3 60.7 + - - +
449C LYS* 3.5 7.6 + - - +
450C SER* 3.0 28.4 + - - -
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Residues in contact with CYS 447 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315C MET* 5.4 0.2 - - - -
316C VAL* 4.8 2.5 - - - -
319C LEU* 4.1 16.4 - - - -
443C GLU 3.4 14.8 - - - -
444C GLU 3.1 8.9 + - - +
446C VAL* 1.3 81.0 - - - +
448C LEU* 1.3 60.9 + - - +
450C SER* 3.3 3.1 + - - -
451C ILE* 2.9 33.7 + - - +
482C ILE* 3.8 19.1 - - + +
485C THR* 3.9 27.6 - - - -
486C LEU* 3.8 22.9 - - + -
489C LEU* 4.3 3.8 - - - -
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Residues in contact with LEU 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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389C ILE* 4.1 19.3 - - + -
435C PHE* 4.7 8.1 - - + -
440C LEU* 4.4 17.5 - - + -
444C GLU 3.0 16.3 + - - +
445C PHE* 3.1 8.3 + - - +
447C CYS* 1.3 76.6 - - + +
449C LYS* 1.3 63.1 + - - +
451C ILE* 3.0 11.0 + - + +
452C ILE* 3.0 27.6 + - - +
486C LEU* 4.8 5.8 - - + -
507C LEU* 4.1 55.0 - - + +
508C LEU* 4.4 9.4 - - + -
510C ILE* 6.0 0.7 - - + -
511C LEU* 4.2 19.8 - - + +
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Residues in contact with LYS 449 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323C GLU* 2.6 37.3 + - - -
324C PRO* 3.7 17.8 - - - +
360C TRP* 3.8 33.0 - - + +
386C ILE* 4.0 21.6 - - + +
389C ILE* 3.8 21.6 - - + +
390C GLY* 5.2 2.4 - - - +
445C PHE* 3.0 37.3 + - + +
446C VAL* 3.7 7.4 - - - +
447C CYS 3.3 0.2 - - - -
448C LEU* 1.3 76.9 - - - +
450C SER* 1.3 60.8 + - - +
452C ILE* 3.2 12.8 + - - +
453C LEU* 3.1 17.2 + - - +
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Residues in contact with SER 450 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319C LEU* 3.3 27.9 - - - +
360C TRP* 4.1 9.6 - - - -
364C VAL* 4.1 17.0 - - - +
446C VAL 3.0 15.9 + - - -
447C CYS 3.5 7.6 - - - -
449C LYS* 1.3 72.9 - - - +
451C ILE* 1.3 65.3 + - - +
453C LEU* 3.2 7.0 + - - +
454C LEU* 3.1 26.9 + - - +
482C ILE* 3.9 18.4 - - - -
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Residues in contact with ILE 451 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509A LEU* 3.7 21.5 - - + -
447C CYS 2.9 21.4 + - - +
448C LEU* 3.4 12.1 - - + +
450C SER* 1.3 75.7 - - - +
452C ILE* 1.3 58.5 + - - +
454C LEU 3.3 0.7 + - - -
455C ASN* 2.8 36.6 + - + +
479C LEU* 4.0 25.0 - - + +
482C ILE* 3.7 25.1 - - + -
483C THR* 5.5 4.0 - - - +
486C LEU* 3.9 21.5 - - + -
508C LEU* 3.9 16.6 - - + -
511C LEU* 3.6 20.6 - - + -
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Residues in contact with ILE 452 (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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382C ALA* 3.8 4.1 - - + +
385C GLU* 3.6 29.2 - - + +
386C ILE* 4.0 13.7 - - + -
389C ILE* 3.9 40.2 - - + -
448C LEU 3.0 14.5 + - - +
449C LYS* 3.4 7.2 - - - +
451C ILE* 1.3 75.7 - - - +
453C LEU* 1.3 64.3 + - - +
455C ASN* 4.8 1.6 - - - -
456C SER* 3.0 41.0 + - - +
511C LEU* 4.0 23.1 - - + -
514C ILE* 4.2 17.9 - - + -
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Residues in contact with LEU 453 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360C TRP* 3.9 10.5 - - + -
361C ALA* 3.9 13.9 - - + -
364C VAL* 3.8 32.3 - - + -
367C PHE* 3.8 36.1 - - + -
378C LEU* 3.5 31.9 - - + +
379C LEU* 4.0 29.2 - - + +
382C ALA* 4.0 6.1 - - + -
386C ILE* 4.2 11.0 - - + +
449C LYS 3.1 9.7 + - - +
450C SER 3.4 7.9 - - - +
451C ILE 3.2 0.4 - - - -
452C ILE* 1.3 82.2 - - - +
454C LEU* 1.3 61.0 + - + +
456C SER 4.3 1.2 + - - -
457C GLY 4.8 0.2 + - - -
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Residues in contact with LEU 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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364C VAL* 4.7 10.8 - - + -
366C GLY 5.4 1.3 - - - -
367C PHE* 4.3 23.8 - - + +
370C LEU* 4.8 3.1 - - + -
378C LEU* 3.9 24.1 - - + +
450C SER 3.1 10.6 + - - +
453C LEU* 1.3 82.9 - - + +
455C ASN* 1.3 60.8 + - - +
458C VAL* 3.6 9.0 - - - +
475C ILE* 3.3 37.1 - - + +
478C VAL* 3.4 36.3 - - + -
479C LEU* 4.0 16.8 - - + -
482C ILE* 3.9 20.0 - - + -
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Residues in contact with ASN 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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509A LEU* 3.5 32.3 - - - +
512A SER* 3.2 23.9 + - - -
513A HIS* 2.7 53.3 + - - -
451C ILE* 2.8 27.9 + - + +
452C ILE* 4.5 1.3 - - - +
454C LEU* 1.3 77.3 - - - +
456C SER* 1.3 58.4 + - - +
457C GLY 3.3 2.2 - - - -
458C VAL* 3.2 10.4 - - - +
459C TYR* 3.7 11.3 + - - -
476C HIS* 5.7 0.6 - - - -
479C LEU* 4.3 11.3 - - + +
511C LEU* 5.9 0.3 - - - +
515C ARG* 4.9 0.5 + - - -
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Residues in contact with SER 456 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513A HIS* 3.9 3.8 + - - -
381C CYS* 4.1 13.4 - - - +
382C ALA* 4.3 12.6 - - - -
385C GLU* 2.6 33.9 + - - -
452C ILE* 3.0 23.2 + - - +
453C LEU 4.3 0.2 + - - -
454C LEU 3.8 0.4 - - - -
455C ASN* 1.3 78.1 + - - +
457C GLY* 1.3 58.2 + - - +
459C TYR* 5.1 0.3 + - - +
460C THR* 5.1 1.2 + - - +
515C ARG* 3.0 37.0 + - - +
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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