Contacts of the helix formed by residues 428 - 442 (chain A) in PDB entry 5ODS
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 428 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393A ARG* 4.0 6.0 - - - +
426A GLN 3.6 3.7 + - - +
427A LEU* 1.3 73.1 - - - +
429A LYS* 1.3 70.5 + - - +
430A TYR* 3.2 15.1 - - - +
431A GLU* 2.8 46.4 + - + +
432A SER* 3.0 10.9 + - - -
458A GLU* 3.4 16.9 - - - +
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Residues in contact with LYS 429 (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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428A ASN* 1.3 79.2 - - - +
430A TYR* 1.3 61.6 + - - +
432A SER* 3.5 3.5 + - - -
433A LEU* 3.2 29.5 + - + +
458A GLU* 3.3 51.5 + - - +
459A CYS 4.1 7.9 + - - -
460A SER* 3.4 38.5 - - - +
482A ALA 5.9 0.8 + - - -
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Residues in contact with TYR 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A PRO* 3.7 25.8 - - + -
398A ILE* 3.6 32.7 - - + +
399A ARG* 4.3 21.1 + - - +
428A ASN* 3.0 11.0 + - - +
429A LYS* 1.3 76.3 - - - +
431A GLU* 1.3 66.7 + - + +
433A LEU* 3.3 15.0 + - + +
434A GLU* 3.1 55.8 + - + +
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Residues in contact with GLU 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A ARG* 3.3 43.9 + - - +
398A ILE* 4.1 21.3 - - + +
417A TYR* 4.3 2.4 + - - -
418A PHE* 3.5 18.1 - - + -
421A LEU* 3.5 15.1 - - + +
427A LEU* 3.9 20.4 - - + -
428A ASN* 2.8 46.4 + - + +
430A TYR* 1.3 76.2 - - + +
432A SER* 1.3 62.5 + - - +
434A GLU* 3.5 0.7 + - - -
435A LEU* 3.0 25.3 + - - +
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Residues in contact with SER 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A LEU* 3.5 5.0 + - - +
428A ASN 3.0 9.9 + - - -
429A LYS 3.7 8.1 - - - -
431A GLU* 1.3 77.4 - - - +
433A LEU* 1.3 61.1 + - - +
435A LEU* 3.4 10.6 + - - +
436A CYS* 3.2 30.7 + - - -
457A LEU* 3.3 37.9 - - - +
458A GLU 3.3 20.5 + - - -
463A LEU* 4.4 7.9 - - - -
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Residues in contact with LEU 433 (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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429A LYS* 3.2 21.1 + - + +
430A TYR* 3.5 17.7 - - + +
431A GLU 3.3 0.2 - - - -
432A SER* 1.3 81.8 - - - +
434A GLU* 1.3 61.7 + - - +
435A LEU 3.3 0.9 + - - -
436A CYS* 3.5 2.1 + - - +
437A ARG* 3.4 54.2 + - - +
460A SER* 4.9 7.0 - - - +
462A GLU* 3.8 36.6 - - + +
463A LEU* 3.8 36.6 - - + +
466A LEU* 4.4 9.4 - - + +
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Residues in contact with GLU 434 (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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398A ILE* 4.5 10.3 - - + -
402A GLN* 3.1 27.5 + - - +
414A LEU* 5.7 2.3 - - - +
418A PHE* 4.2 18.5 - - + -
430A TYR* 3.1 55.4 + - + +
431A GLU* 4.1 2.9 - - - +
433A LEU* 1.3 75.0 - - - +
435A LEU* 1.3 60.3 + - - +
436A CYS 3.5 0.2 - - - -
437A ARG* 2.7 34.8 + - - +
438A PRO* 3.3 19.2 - - - +
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Residues in contact with LEU 435 (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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415A LEU* 6.4 2.0 - - + -
418A PHE* 3.8 37.9 - - + -
422A LEU* 4.7 5.6 - - + -
427A LEU* 3.9 22.7 - - + -
431A GLU 3.0 17.2 + - - +
432A SER* 3.5 9.6 - - - +
433A LEU 3.1 0.6 - - - -
434A GLU* 1.3 79.1 - - - +
436A CYS* 1.3 65.4 + - - +
438A PRO* 3.4 7.3 - - - +
439A VAL* 3.1 23.2 - - + +
451A TRP* 4.5 42.0 - - + -
457A LEU* 5.7 7.2 - - + -
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Residues in contact with CYS 436 (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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432A SER 3.2 18.9 + - - +
433A LEU 3.5 2.0 + - - +
435A LEU* 1.3 87.1 - - - +
437A ARG* 1.3 57.4 + - - +
438A PRO 3.4 0.4 - - - -
439A VAL* 3.6 7.2 - - - -
440A LEU* 2.8 56.0 + - + +
448A LEU* 4.1 22.2 - - + -
451A TRP* 5.1 6.1 - - - -
457A LEU* 4.8 10.8 - - - -
463A LEU* 3.9 20.2 - - + -
466A LEU* 5.7 0.7 - - + -
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Residues in contact with ARG 437 (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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430A TYR* 5.8 0.2 - - - -
433A LEU* 3.4 46.0 + - - +
434A GLU* 2.7 39.6 + - - +
436A CYS* 1.3 77.6 - - - +
438A PRO* 1.4 69.3 - - + +
440A LEU* 4.2 3.5 - - - +
441A GLN* 3.2 24.0 + - - +
462A GLU* 3.5 22.4 + - - -
466A LEU* 3.6 32.6 - - + +
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Residues in contact with PRO 438 (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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414A LEU* 5.2 13.7 - - + -
434A GLU 3.3 20.2 - - - +
435A LEU 3.4 12.3 - - - +
437A ARG* 1.4 91.2 - - + +
439A VAL* 1.3 60.8 + - + +
441A GLN* 3.4 18.8 - - + +
442A GLN* 4.1 3.8 + - - +
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Residues in contact with VAL 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A LEU* 6.3 3.8 - - + -
435A LEU* 3.1 24.0 - - + +
436A CYS* 3.0 10.9 + - - +
438A PRO* 1.3 80.6 - - + +
440A LEU* 1.3 60.6 - - + +
441A GLN 3.2 0.4 + - - -
442A GLN 4.0 2.8 + - - +
444A ARG* 2.7 52.5 + - + +
447A LEU* 4.3 19.5 - - + -
448A LEU* 4.3 13.9 - - + -
451A TRP* 4.3 20.2 - - + -
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Residues in contact with LEU 440 (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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436A CYS* 2.8 33.3 + - + +
437A ARG* 4.3 4.3 - - - +
439A VAL* 1.3 77.6 - - - +
441A GLN* 1.3 64.7 + - - +
442A GLN 3.4 1.1 + - - -
443A GLY* 3.9 8.8 + - - -
444A ARG 3.7 7.8 + - - +
445A LYS* 4.5 7.2 - - + -
448A LEU* 4.0 23.6 - - + -
463A LEU* 5.5 0.2 - - + -
466A LEU* 4.6 13.2 - - + +
467A VAL* 3.6 34.8 - - + +
470A VAL* 3.7 37.6 - - + +
474A LEU* 5.8 1.3 - - + -
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Residues in contact with GLN 441 (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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437A ARG 3.2 21.8 + - - +
438A PRO* 3.4 15.4 - - + +
439A VAL 3.2 0.2 - - - -
440A LEU* 1.3 78.0 - - - +
442A GLN* 1.3 71.0 + - + +
443A GLY 3.9 1.4 + - - -
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Residues in contact with GLN 442 (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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438A PRO 4.1 3.9 + - - +
439A VAL 4.0 2.8 + - - -
440A LEU 3.4 1.0 - - - -
441A GLN* 1.3 91.4 - - + +
443A GLY* 1.3 65.5 + - - +
444A ARG* 3.0 10.8 + - - +
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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
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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