Contacts of the helix formed by residues 436 - 457 (chain C) in PDB entry 3IW4
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 LYS 436 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434C LYS 4.1 0.6 + - - -
435C PHE* 1.3 73.9 - - - +
437C GLU* 1.3 66.4 + - - +
438C PRO* 3.1 30.5 - - + +
439C GLN* 2.9 52.0 + - + +
440C ALA 3.1 8.3 + - - -
613C PRO* 3.7 16.4 + - - +
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Residues in contact with GLU 437 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435C PHE 3.6 2.4 + - - -
436C LYS* 1.3 70.0 - - - +
438C PRO* 1.3 70.3 - - + +
441C VAL* 2.6 47.5 + - + +
532C LEU* 3.9 17.6 - - + +
562C SER* 2.7 40.6 + - - -
564C GLU* 4.0 1.7 - - - +
565C ALA* 3.9 7.3 - - - +
596C PHE* 4.1 21.6 - - + +
598C ARG* 3.9 22.2 + - - -
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Residues in contact with PRO 438 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436C LYS* 3.1 35.4 - - + +
437C GLU* 1.3 98.9 - - + +
439C GLN* 1.3 59.1 + - - -
441C VAL* 3.4 8.5 - - + +
442C PHE* 3.1 19.6 + - - +
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Residues in contact with GLN 439 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432C VAL* 4.3 9.5 - - - +
434C LYS 5.0 0.2 + - - -
435C PHE* 3.0 43.6 - - + +
436C LYS* 2.9 38.8 + - + +
438C PRO* 1.3 71.5 - - - +
440C ALA* 1.3 63.2 + - - -
441C VAL 3.0 1.3 - - - -
442C PHE* 3.1 5.3 + - - +
443C TYR* 2.8 46.0 + - + -
613C PRO* 3.3 34.3 - - + +
614C PHE* 3.8 13.6 - - - -
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Residues in contact with ALA 440 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435C PHE* 4.0 12.2 - - + +
436C LYS 3.1 8.4 + - - +
437C GLU 3.5 2.9 - - - +
439C GLN* 1.3 77.3 - - - +
441C VAL* 1.3 52.1 + - - +
443C TYR* 3.2 1.7 + - - +
444C ALA* 2.6 38.6 + - - +
528C LEU* 6.1 0.4 - - + -
531C MET* 3.7 24.1 - - + +
532C LEU* 3.1 38.8 - - + -
596C PHE* 4.8 2.5 - - + -
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Residues in contact with VAL 441 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437C GLU* 2.6 55.5 + - + +
438C PRO* 3.4 7.9 - - + +
440C ALA* 1.3 72.8 - - - +
442C PHE* 1.3 58.4 + - - +
444C ALA* 3.2 3.1 + - - +
445C ALA* 2.8 30.2 + - - +
596C PHE* 3.5 45.1 - - + +
597C PHE* 3.9 15.6 - - + -
600C ILE* 4.3 15.9 - - + -
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Residues in contact with PHE 442 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438C PRO 3.1 10.2 + - - +
439C GLN* 3.1 8.9 + - - +
441C VAL* 1.3 79.9 - - - +
443C TYR* 1.3 74.6 + + - +
445C ALA* 3.1 6.8 + - - +
446C GLU* 3.0 62.4 + - - +
475C GLY 4.1 11.4 - - - -
476C HIS* 4.1 6.3 - + - -
600C ILE* 4.8 7.8 - - + +
605C LEU* 4.2 10.1 - - + -
610C ILE* 3.9 34.8 - - + -
611C GLN 4.2 6.5 - - - -
612C PRO* 3.7 16.8 - - + -
613C PRO* 3.2 30.3 - - + -
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Residues in contact with TYR 443 (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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425C LEU* 4.3 8.5 - - + -
435C PHE* 3.6 41.7 - + - -
439C GLN* 2.8 37.6 + - + -
440C ALA 3.6 4.3 - - - +
442C PHE* 1.3 90.0 - + - +
444C ALA* 1.3 70.9 + - - +
445C ALA 2.7 2.9 + - - -
446C GLU 3.2 0.2 + - - -
447C ILE* 3.0 27.9 + - + +
471C LEU* 3.7 30.0 - - + +
475C GLY 4.1 4.2 + - - -
477C ILE* 3.6 27.4 - - + +
531C MET* 3.7 14.4 - - + -
613C PRO* 3.6 14.8 - - + +
614C PHE* 3.6 18.5 + - - -
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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 ALA 2.6 21.5 + - - +
441C VAL 3.4 5.4 - - - +
443C TYR* 1.3 73.8 - - - +
445C ALA* 1.3 55.9 + - - +
447C ILE* 4.6 1.6 - - - -
448C SER* 3.1 15.9 + - - -
524C TYR* 2.3 31.1 + - - +
528C LEU* 3.2 41.5 - - + -
531C MET* 3.9 2.5 - - - +
596C PHE* 4.1 4.3 - - + -
597C PHE* 4.1 10.1 - - + -
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Residues in contact with ALA 445 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441C VAL 2.8 15.6 + - - +
442C PHE* 3.3 7.6 - - - +
443C TYR 2.7 4.9 + - - -
444C ALA* 1.3 71.2 - - - +
446C GLU* 1.3 65.1 + - - +
447C ILE 3.1 1.1 + - - -
448C SER* 2.7 24.2 + - - -
449C ILE* 3.4 4.2 + - - +
597C PHE* 4.1 16.8 - - + -
600C ILE* 4.4 6.5 - - + -
602C TRP* 4.1 6.5 - - + -
605C LEU* 3.6 31.6 - - + +
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Residues in contact with GLU 446 (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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399C PHE* 3.0 60.8 - - + +
442C PHE* 3.0 46.2 + - + +
443C TYR 4.2 0.9 - - - +
445C ALA* 1.3 74.4 - - - +
447C ILE* 1.3 61.8 + - - +
449C ILE* 3.4 5.4 - - - +
476C HIS* 2.6 29.3 + - - -
477C ILE* 2.9 37.0 + - + +
605C LEU* 3.8 19.1 - - + +
608C ARG* 4.3 0.5 - - - +
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Residues in contact with ILE 447 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425C LEU* 4.8 1.6 - - + -
443C TYR* 3.0 23.6 + - + +
444C ALA* 3.7 5.2 - - - +
446C GLU* 1.3 72.1 - - - +
448C SER* 1.3 70.2 + - - +
449C ILE 2.9 1.8 - - - -
450C GLY* 2.8 15.4 + - - -
451C LEU* 3.2 11.4 + - + -
464C LEU* 4.6 11.7 - - + -
469C VAL* 4.2 16.8 - - + -
477C ILE* 3.5 33.9 - - + -
479C ILE* 4.2 20.3 - - + +
524C TYR* 3.5 24.2 - - + -
527C LEU* 4.2 25.6 - - + -
528C LEU* 5.9 0.2 - - + -
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Residues in contact with SER 448 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444C ALA 3.1 5.3 + - - -
445C ALA* 2.7 18.8 + - - -
447C ILE* 1.3 78.0 - - - +
449C ILE* 1.3 51.0 + - - +
451C LEU* 2.8 12.9 + - - +
452C PHE* 2.7 65.4 + - - -
521C TRP* 4.3 4.0 - - - -
524C TYR* 3.5 26.2 - - - -
591C VAL* 4.7 3.8 - - - -
602C TRP* 3.6 11.8 - - - -
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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
----------------------------------------------------------
397C PRO* 3.7 18.4 - - + -
398C PRO* 5.5 0.2 - - + -
399C PHE* 3.6 25.4 - - + -
445C ALA 3.4 11.4 + - - +
446C GLU 3.4 8.7 - - - +
447C ILE 2.8 1.2 + - - -
448C SER* 1.3 81.6 + - - +
450C GLY* 1.3 62.7 + - - +
452C PHE* 3.4 20.2 + - + +
453C PHE* 3.1 22.4 + - + +
592C ARG* 4.0 10.3 - - - +
602C TRP* 4.0 13.7 - - + -
605C LEU* 4.1 12.3 - - + -
606C GLU* 3.7 34.1 - - + +
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Residues in contact with GLY 450 (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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397C PRO* 4.7 2.5 - - - -
399C PHE* 4.8 2.4 - - - +
400C LEU* 3.6 29.8 - - - -
446C GLU 3.7 3.4 + - - -
447C ILE 2.8 14.7 + - - -
449C ILE* 1.3 74.3 - - - +
451C LEU* 1.3 62.8 + - - -
453C PHE* 3.1 5.9 + - - +
454C LEU* 2.9 28.5 + - - +
479C ILE* 4.5 5.8 - - - -
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Residues in contact with LEU 451 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447C ILE* 3.2 10.5 + - + +
448C SER 2.8 13.2 + - - +
450C GLY* 1.3 71.6 - - - +
452C PHE* 1.3 63.5 + - - +
454C LEU* 3.3 6.7 + - + +
455C HIS* 2.8 39.4 + - + +
461C TYR* 4.4 16.6 - - + -
464C LEU* 3.6 30.5 - - + -
479C ILE* 5.2 4.2 - - + +
520C ASP* 3.9 36.3 - - + +
521C TRP* 3.9 31.9 - - + -
524C TYR* 3.9 11.4 - - + -
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Residues in contact with PHE 452 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448C SER* 2.7 46.3 + - - -
449C ILE* 3.6 18.6 - - + +
451C LEU* 1.3 71.9 - - - +
453C PHE* 1.3 58.6 + - - +
455C HIS* 3.9 3.6 - - - +
456C LYS* 2.9 37.1 + - - +
521C TRP* 3.4 28.7 - + - -
588C GLU* 3.5 56.9 - - + +
591C VAL* 4.0 14.1 - - + -
592C ARG* 3.5 35.0 - - + +
602C TRP* 4.6 1.3 - + - -
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Residues in contact with PHE 453 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393C LEU* 4.2 17.0 - - + -
394C LEU 3.5 15.7 - - - -
395C ASP* 3.1 18.4 - - + -
396C LYS* 3.5 29.4 - - + -
397C PRO* 3.3 34.1 - - + -
400C LEU* 3.6 12.8 - - + -
449C ILE 3.1 7.2 + - - +
450C GLY 3.5 1.8 - - - +
452C PHE* 1.3 82.6 - - - +
454C LEU* 1.3 70.9 + - + +
456C LYS* 3.2 12.3 + - + +
457C ARG* 3.2 53.6 + - + +
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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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390C VAL* 4.0 14.4 - - + +
393C LEU* 4.2 6.7 - - + -
400C LEU* 4.4 12.1 - - + -
450C GLY 2.9 20.3 + - - +
451C LEU* 3.9 7.4 - - + +
453C PHE* 1.3 91.7 - - + +
455C HIS* 1.3 64.9 + - + +
457C ARG* 3.1 10.7 + - - +
458C GLY 3.4 0.2 + - - -
459C ILE* 3.0 62.1 + - + +
461C TYR* 4.8 18.6 - - + +
479C ILE* 6.3 1.1 - - + -
482C PHE* 3.9 28.3 - - + -
485C CYS* 5.4 0.2 - - - -
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Residues in contact with HIS 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 LEU* 2.8 33.2 + - + +
452C PHE* 3.9 4.0 + - - +
454C LEU* 1.3 75.6 - - + +
456C LYS* 1.3 56.4 + - - +
458C GLY* 2.6 26.9 + - - -
459C ILE 3.3 20.9 - - - -
460C ILE* 4.7 0.2 - - - -
489C MET 5.0 1.0 - - - +
490C MET* 5.3 1.2 - - - +
517C LYS* 3.7 39.0 - - + +
520C ASP* 2.7 37.1 + - + +
521C TRP* 3.4 43.0 + + - -
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Residues in contact with LYS 456 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452C PHE* 2.9 23.3 + - - +
453C PHE* 3.4 10.1 - - + +
455C HIS* 1.3 76.8 - - - +
457C ARG* 1.3 62.5 + - + +
458C GLY 3.3 3.6 + - - -
490C MET* 4.6 9.4 - - - +
588C GLU* 3.4 36.3 + - - -
592C ARG* 5.0 1.2 - - - +
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Residues in contact with ARG 457 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393C LEU* 3.9 30.2 - - + +
394C LEU* 3.0 36.6 + - - +
395C ASP* 3.7 16.6 + - - +
453C PHE* 3.5 39.2 - - + +
454C LEU* 3.1 9.8 + - - +
455C HIS 3.1 1.0 - - - -
456C LYS* 1.3 79.1 - - + +
458C GLY* 1.3 61.3 + - - +
459C ILE* 3.3 13.3 + - + +
488C HIS* 5.5 1.4 + - - -
490C MET* 4.7 6.0 - - - +
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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