Contacts of the helix formed by residues 468 - 485 (chain C) in PDB entry 3IAD
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 ASN 468 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467C ASP* 1.3 86.4 + - + +
469C TYR* 1.3 65.0 + - - +
470C SER* 3.2 26.6 + - - +
471C ASP* 2.8 34.9 + - - +
472C ARG* 3.3 20.4 + - - +
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Residues in contact with TYR 469 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355C GLU* 5.9 2.0 - - - -
428C LYS* 3.6 30.8 - - + +
429C MET* 3.9 29.7 - - + +
432C ASP* 2.7 27.8 + - - -
467C ASP 3.9 0.6 + - - -
468C ASN* 1.3 73.4 - - - +
470C SER* 1.3 61.8 + - - +
472C ARG* 3.2 13.4 + - + +
473C ILE* 2.9 58.0 + - + +
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Residues in contact with SER 470 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468C ASN* 3.2 18.0 + - - +
469C TYR* 1.3 84.7 - - - +
471C ASP* 1.3 58.7 + - - +
473C ILE* 3.6 8.2 - - - +
474C GLN* 3.2 42.0 + - - +
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Residues in contact with ASP 471 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452C MET* 3.1 29.6 - - + +
466C LEU* 4.0 21.7 - - + +
467C ASP 5.4 0.2 + - - -
468C ASN* 2.8 33.2 + - - +
469C TYR 3.3 0.4 - - - -
470C SER* 1.3 78.7 + - - +
472C ARG* 1.3 64.9 + - - +
474C GLN* 3.5 4.5 + - - +
475C VAL* 3.3 28.4 + - - +
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Residues in contact with ARG 472 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350C VAL* 3.0 24.7 + - - +
351C PHE* 3.4 20.1 - - + -
352C THR* 4.6 9.0 - - - +
355C GLU* 2.7 47.6 + - - +
466C LEU* 3.6 38.5 + - + +
467C ASP 4.2 6.8 + - - -
468C ASN 3.3 15.0 + - - +
469C TYR* 3.2 18.3 + - + +
471C ASP* 1.3 79.0 - - - +
473C ILE* 1.3 60.9 + - - +
475C VAL* 3.4 13.2 + - - +
476C LEU* 3.4 19.7 + - + +
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Residues in contact with ILE 473 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429C MET* 3.8 33.0 - - + +
432C ASP* 3.8 17.5 - - + +
433C ILE* 3.9 13.2 - - + -
469C TYR* 2.9 55.4 + - + +
470C SER* 3.6 10.1 - - - +
472C ARG* 1.3 75.1 - - - +
474C GLN* 1.3 64.0 + - - +
475C VAL 3.2 0.2 - - - -
476C LEU* 3.4 16.1 + - + -
477C GLN* 2.9 43.8 + - + +
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Residues in contact with GLN 474 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445C LEU* 5.6 1.6 - - + -
448C ASP* 3.1 44.1 + - + +
452C MET* 3.5 29.1 - - + +
470C SER* 3.2 32.3 + - - +
471C ASP* 3.7 3.1 - - - +
472C ARG 3.3 0.8 - - - -
473C ILE* 1.3 83.8 - - - +
475C VAL* 1.3 58.0 + - - +
477C GLN* 3.6 16.1 + - - +
478C ASN* 2.6 40.5 + - - +
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Residues in contact with VAL 475 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347C LEU* 4.7 9.2 - - + -
351C PHE* 3.7 24.0 - - + -
449C LEU* 5.4 1.1 - - + -
452C MET* 3.7 21.1 - - - -
464C LEU* 4.6 1.6 - - + -
466C LEU* 4.0 15.3 - - + -
471C ASP 3.3 15.6 + - - +
472C ARG 3.6 8.1 - - - +
473C ILE 3.2 0.2 - - - -
474C GLN* 1.3 75.8 - - - +
476C LEU* 1.3 54.4 + - - +
478C ASN* 3.4 3.7 + - - +
479C MET* 2.8 34.4 + - + +
550C TRP* 3.7 24.8 - - + -
553C LEU* 4.4 13.5 - - + -
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Residues in contact with LEU 476 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342C LEU* 4.4 9.0 - - + -
351C PHE* 3.7 37.5 - - + -
355C GLU* 4.4 28.7 - - + +
358C ALA* 5.7 0.2 - - + -
359C ALA* 4.2 18.8 - - + -
429C MET* 5.1 3.8 - - - -
433C ILE* 3.9 20.2 - - + -
472C ARG 3.4 16.2 + - - +
473C ILE* 3.8 22.2 - - + +
474C GLN 3.4 0.2 - - - -
475C VAL* 1.3 73.8 - - - +
477C GLN* 1.3 66.1 + - - +
479C MET* 3.4 7.5 - - + +
480C VAL* 2.9 30.5 + - - +
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Residues in contact with GLN 477 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432C ASP* 2.9 41.2 + - - +
433C ILE* 4.1 13.4 - - + +
436C ALA* 3.6 22.5 - - + +
437C THR* 5.9 0.7 - - - +
445C LEU* 4.0 18.5 - - + +
473C ILE* 2.9 34.0 + - + +
474C GLN* 3.6 19.8 + - - +
475C VAL 3.3 0.2 - - - -
476C LEU* 1.3 77.3 - - - +
478C ASN* 1.3 57.7 + - - +
480C VAL* 3.9 1.6 - - - +
481C HIS* 2.9 30.9 + - - +
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Residues in contact with ASN 478 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445C LEU* 3.4 46.2 + - - +
446C LEU 4.2 0.5 + - - -
449C LEU* 3.7 42.9 - - + +
474C GLN* 2.6 35.8 + - - +
475C VAL 3.9 3.1 - - - +
477C GLN* 1.3 76.4 - - - +
479C MET* 1.3 56.3 + - - +
481C HIS* 3.8 7.0 - - - +
482C CYS* 2.7 41.3 + - - +
546C LEU* 4.5 6.6 - - - +
550C TRP* 4.4 3.4 - - + -
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Residues in contact with MET 479 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338C THR* 4.1 13.0 - - + +
341C LEU* 3.4 30.1 - - + +
342C LEU* 3.5 44.0 - - + -
347C LEU* 3.6 31.0 - - + -
351C PHE* 4.1 10.8 - - + -
359C ALA* 5.3 1.3 - - - -
475C VAL* 2.8 20.6 + - + +
476C LEU* 3.2 14.3 + - + +
478C ASN* 1.3 74.0 - - - +
480C VAL* 1.3 53.5 + - + +
482C CYS* 3.2 7.1 + - - +
483C ALA* 2.8 30.1 + - - +
550C TRP* 3.7 20.1 - - + -
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Residues in contact with VAL 480 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334C VAL* 4.3 9.1 - - + +
338C THR* 3.5 19.1 - - + +
359C ALA* 4.0 14.8 - - + +
362C ALA 5.3 0.7 - - - -
363C SER* 3.5 32.8 - - - +
366C HIS* 5.4 2.9 - - + -
433C ILE* 3.6 27.8 - - + -
437C THR* 4.3 15.3 - - + -
476C LEU 2.9 18.8 + - - +
477C GLN 4.2 0.9 - - - +
479C MET* 1.3 74.5 - - + +
481C HIS* 1.3 60.8 + - - +
483C ALA* 3.4 2.9 + - - +
484C ASP* 2.8 26.7 + - + +
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Residues in contact with HIS 481 (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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436C ALA 4.3 12.2 + - - +
437C THR* 4.8 10.2 + - + +
438C ASP 5.6 0.4 - - - -
439C MET* 3.7 22.8 - - + +
442C HIS* 3.1 34.2 + - + +
445C LEU* 3.9 25.8 - - + -
477C GLN 2.9 20.7 + - - +
478C ASN* 3.8 7.0 - - - +
480C VAL* 1.3 75.4 - - - +
482C CYS* 1.3 63.7 + - - +
484C ASP* 3.1 9.8 + - - +
485C LEU* 3.0 43.0 + - + +
546C LEU* 3.7 26.5 - - + -
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Residues in contact with CYS 482 (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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341C LEU* 4.4 3.4 - - + -
478C ASN* 2.7 27.9 + - - +
479C MET* 3.4 5.4 - - - +
481C HIS* 1.3 72.5 - - - +
483C ALA* 1.3 62.2 + - - +
485C LEU 3.0 22.7 - - - -
486C SER 3.1 1.0 + - - -
546C LEU* 3.6 38.4 - - - -
547C TRP* 3.3 33.6 - - + -
550C TRP* 4.0 30.1 - - + -
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Residues in contact with ALA 483 (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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330C HIS* 5.5 0.2 - - - -
333C ASP* 5.2 0.3 - - - +
334C VAL* 3.9 27.4 - - + +
337C SER* 3.9 14.3 - - - -
338C THR* 3.5 25.8 - - - +
341C LEU* 4.2 4.6 - - + +
479C MET 2.8 14.0 + - - +
480C VAL 3.4 8.7 - - - +
481C HIS 3.3 0.2 - - - -
482C CYS* 1.3 73.5 - - - +
484C ASP* 1.3 57.6 + - - +
486C SER* 2.6 29.5 + - - -
547C TRP* 4.9 0.2 - - - -
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Residues in contact with ASP 484 (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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325C TYR* 4.1 15.4 + - - -
330C HIS* 3.0 12.3 + - - -
334C VAL* 3.9 6.9 - - + +
366C HIS* 3.1 14.0 + - - -
437C THR* 3.9 22.0 - - + +
439C MET* 4.5 10.6 - - - +
480C VAL 2.8 17.5 + - - +
481C HIS* 3.1 15.8 + - + +
483C ALA* 1.3 74.5 - - - +
485C LEU* 1.3 65.9 + - + +
486C SER* 3.3 2.5 + - - -
487C ASN* 4.8 2.4 + - - +
620C ZN 2.2 36.2 - - - -
901C 15X 4.9 5.0 - - - -
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Residues in contact with LEU 485 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439C MET* 3.8 14.4 - - + -
442C HIS* 4.0 11.7 - - + +
481C HIS* 3.0 46.7 + - + +
482C CYS 3.0 4.7 - - - +
484C ASP* 1.3 80.5 - - + +
486C SER* 1.3 56.8 + - - +
487C ASN* 3.6 2.9 - - - +
488C PRO* 4.2 3.8 - - - +
538C PHE* 4.0 15.5 - - + -
542C ILE* 4.3 10.5 - - + -
543C VAL* 4.0 16.7 - - + +
546C LEU* 3.8 16.2 - - + -
547C TRP* 3.0 19.9 + - - -
901C 15X 3.5 33.7 - - + -
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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