Contacts of the helix formed by residues 448 - 466 (chain A) in PDB entry 4OWW
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 LEU 448 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288A ILE* 4.1 8.7 - - + -
289A LEU* 4.1 25.4 - - + -
292A LEU* 3.8 26.5 - - + -
401A PHE* 4.1 14.1 - - + -
445A TYR* 2.7 45.9 + - + +
447A PRO* 1.3 78.6 - - + +
449A GLU* 1.3 63.4 + - - +
450A GLY 3.3 2.7 - - - -
451A HIS* 3.0 28.4 + - + +
452A VAL* 3.0 22.1 + - + +
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Residues in contact with GLU 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A ILE 3.8 13.4 - - - +
442A PRO* 3.4 36.7 - - + +
445A TYR 3.4 3.6 + - - -
446A PRO* 3.0 20.3 + - + +
447A PRO 3.4 1.0 - - - -
448A LEU* 1.3 76.3 - - - +
450A GLY* 1.3 58.5 + - - +
452A VAL* 3.0 3.3 + - - +
453A ARG* 2.9 65.0 + - - +
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Residues in contact with GLY 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A PRO 5.2 0.6 + - - -
448A LEU 3.3 0.6 - - - -
449A GLU* 1.3 79.3 - - - +
451A HIS* 1.3 60.7 + - - +
453A ARG* 4.0 10.7 - - - +
454A GLN* 3.2 22.5 + - - +
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Residues in contact with HIS 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A LEU* 3.8 30.8 - - + +
293A GLN* 4.2 12.5 + - - -
400A LEU 3.6 4.6 - - - +
401A PHE* 3.7 20.4 - + + -
447A PRO 5.4 0.4 + - - -
448A LEU* 3.0 29.2 + - + +
450A GLY* 1.3 75.5 - - - +
452A VAL* 1.3 61.5 + - - +
454A GLN* 3.3 7.5 + - + +
455A GLY* 2.9 24.1 + - - -
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Residues in contact with VAL 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A LEU* 3.3 33.3 - - + +
401A PHE* 3.6 28.3 - - + -
440A ILE 4.4 2.5 - - - +
441A ILE* 3.7 36.1 - - + +
444A PHE* 4.4 14.8 - - + -
445A TYR 5.1 2.2 - - - +
448A LEU* 3.0 21.0 + - + +
449A GLU* 3.0 5.8 + - - +
451A HIS* 1.3 73.7 - - - +
453A ARG* 1.3 64.8 + - - +
455A GLY 3.1 1.0 + - - -
456A VAL* 3.0 23.5 + - + +
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Residues in contact with ARG 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441A ILE* 3.8 26.6 - - + +
449A GLU* 2.9 49.0 + - - +
450A GLY* 4.0 9.8 - - - +
452A VAL* 1.3 75.8 - - - +
454A GLN* 1.3 60.4 + - - +
456A VAL* 3.3 1.6 + - - +
457A PHE* 2.9 35.2 + - + +
492A LYS* 3.6 38.7 + - - +
493A PHE* 5.1 6.0 - - + -
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Residues in contact with GLN 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450A GLY 3.2 17.3 + - - +
451A HIS* 3.3 8.9 + - + +
453A ARG* 1.3 80.5 - - - +
455A GLY* 1.3 57.3 + - - +
457A PHE* 3.7 23.9 - - - +
458A SER* 2.8 56.2 + - - +
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Residues in contact with GLY 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A TRP 3.1 15.4 - - - +
400A LEU 3.5 11.4 - - - -
401A PHE* 4.3 1.3 - - - -
402A PHE* 3.7 18.3 - - - +
451A HIS 2.9 11.6 + - - -
452A VAL 3.1 0.4 + - - -
454A GLN* 1.3 73.9 - - - +
456A VAL* 1.3 59.1 + - - +
458A SER* 3.2 2.6 + - - -
459A SER* 2.8 31.9 + - - -
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Residues in contact with VAL 456 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396A PHE* 6.5 0.2 - - + -
399A TRP* 3.5 28.0 + - + +
400A LEU* 4.8 5.4 - - + -
437A MET* 4.0 21.8 - - + +
440A ILE* 5.4 1.6 - - + -
441A ILE* 3.8 22.4 - - + -
452A VAL* 3.0 21.9 + - + +
453A ARG 3.9 2.9 - - - +
455A GLY* 1.3 74.6 - - - +
457A PHE* 1.3 57.3 + - - +
459A SER* 3.2 6.1 + - - -
460A LEU* 2.9 34.2 + - + +
493A PHE* 3.6 25.6 - - + -
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Residues in contact with PHE 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453A ARG* 2.9 21.9 + - + +
454A GLN* 3.7 26.2 - - - +
456A VAL* 1.3 77.8 - - - +
458A SER* 1.3 60.7 + - - +
460A LEU* 3.4 3.8 + - - +
461A ASN* 2.9 51.3 + - + +
493A PHE* 4.5 14.3 - + + -
495A GLU* 3.1 34.1 - - + -
496A PHE* 3.5 30.1 - + - -
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Residues in contact with SER 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402A PHE* 3.7 25.0 + - - -
404A PRO* 4.6 11.9 - - - +
454A GLN* 2.8 38.5 + - - +
455A GLY 3.6 4.5 - - - -
457A PHE* 1.3 75.8 - - - +
459A SER* 1.3 57.8 + - - +
461A ASN* 3.8 5.4 - - - +
462A HIS* 2.9 32.7 + - - +
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Residues in contact with SER 459 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399A TRP* 3.3 34.5 + - - -
402A PHE* 3.1 20.4 - - - +
412A ILE* 3.7 20.3 - - - +
455A GLY 2.8 23.2 + - - -
456A VAL 3.2 8.9 + - - -
458A SER* 1.3 71.9 - - - +
460A LEU* 1.3 57.5 + - - +
462A HIS 3.1 1.7 + - - -
463A ILE* 2.9 35.5 + - - +
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Residues in contact with LEU 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A TRP* 3.5 27.8 - - + -
416A ILE* 4.4 7.0 - - + -
437A MET* 4.6 2.7 - - - -
456A VAL* 2.9 27.4 + - + +
457A PHE 3.8 2.9 - - - +
459A SER* 1.3 72.7 - - - +
461A ASN* 1.3 63.2 + - - +
463A ILE* 3.3 8.9 + - + +
464A VAL* 3.1 26.7 + - - +
472A LEU* 3.8 23.5 - - + +
476A PHE* 3.9 33.9 - - + -
493A PHE* 3.9 33.2 - - + -
496A PHE* 4.0 9.9 - - + -
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Residues in contact with ASN 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A PHE* 2.9 36.9 + - + +
458A SER* 3.8 6.1 - - - +
460A LEU* 1.3 77.8 - - - +
462A HIS* 1.3 57.7 + - - +
464A VAL* 3.3 6.2 + - - +
465A GLU* 2.9 44.0 + - - +
496A PHE* 3.8 23.8 - - + -
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Residues in contact with HIS 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A PHE* 3.6 24.5 - + + -
404A PRO* 4.1 27.8 + - + +
407A ASP 5.6 0.4 - - - -
409A ILE* 3.4 29.9 - - + +
412A ILE* 4.8 0.4 - - + -
458A SER 2.9 19.7 + - - +
459A SER 3.7 2.7 - - - +
461A ASN* 1.3 73.5 - - - +
463A ILE* 1.3 60.2 + - - +
465A GLU* 3.7 25.1 - - + +
466A LYS* 3.0 74.1 + - + +
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Residues in contact with ILE 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399A TRP* 3.6 34.5 - - + -
409A ILE* 4.0 11.4 - - + -
412A ILE* 4.0 18.8 - - + -
413A GLU 5.3 0.7 - - - +
416A ILE* 3.6 28.3 - - + -
459A SER 2.9 22.0 + - - +
460A LEU* 3.4 10.8 - - - +
462A HIS* 1.3 77.5 - - - +
464A VAL* 1.3 60.0 + - + +
466A LYS 3.9 0.2 - - - -
467A ARG 3.3 1.6 + - - -
468A VAL* 3.0 35.3 + - + +
469A LEU* 3.4 31.3 + - + +
472A LEU* 5.1 3.4 - - + -
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Residues in contact with VAL 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460A LEU 3.1 15.6 + - - +
461A ASN* 3.5 9.6 - - - +
462A HIS 3.2 0.2 - - - -
463A ILE* 1.3 77.7 - - + +
465A GLU* 1.3 61.0 + - + +
467A ARG* 3.0 28.8 + - - -
469A LEU 3.6 16.0 - - - +
470A ALA* 3.6 18.7 - - - +
472A LEU* 3.7 26.9 - - + +
496A PHE* 4.7 7.9 - - + -
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Residues in contact with GLU 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A PRO* 5.9 1.2 - - - +
461A ASN* 2.9 35.0 + - - +
462A HIS* 3.7 27.4 - - + +
464A VAL* 1.3 77.8 - - + +
466A LYS* 1.3 64.4 + - + +
467A ARG* 3.4 5.6 - - - +
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Residues in contact with LYS 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409A ILE* 3.6 26.4 - - + +
462A HIS* 3.0 55.2 + - + +
463A ILE 3.9 0.2 - - - -
465A GLU* 1.3 82.1 - - + +
467A ARG* 1.3 70.0 + - - +
468A VAL* 3.0 8.9 + - + +
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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
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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