Contacts of the helix formed by residues 441 - 458 (chain A) in PDB entry 1O94
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 SER 441 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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428A LEU* 4.9 0.4 - - - -
432A ALA* 3.6 18.0 - - - +
438A GLY 2.9 20.1 + - - -
439A GLU 3.0 0.8 - - - -
440A TRP* 1.3 79.4 - - - +
442A TYR* 1.3 68.5 + - - +
443A HIS 3.1 0.4 - - - -
444A ARG* 3.1 22.7 + - - -
445A ASP* 2.9 34.7 + - - -
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Residues in contact with TYR 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A VAL* 3.5 39.9 - - + +
345A CYS 3.9 9.6 - - - -
346A ILE* 3.8 6.7 - - + -
366A GLN* 3.6 3.2 + - - +
438A GLY 5.0 0.4 - - - -
439A GLU* 3.1 57.4 + - + +
440A TRP 3.0 2.4 + - - -
441A SER* 1.3 84.2 + - - +
443A HIS* 1.3 58.1 + - - +
445A ASP* 3.6 18.1 - - + +
446A TYR* 2.8 33.3 + - - +
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Residues in contact with HIS 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A ILE* 3.8 11.2 - - + +
365A THR* 3.1 35.6 + - + -
366A GLN* 3.7 16.8 - - + +
399A PRO* 3.6 23.9 - - + +
428A LEU* 3.6 15.8 - - + +
440A TRP 3.2 12.7 + - - +
442A TYR* 1.3 81.2 - - - +
444A ARG* 1.3 63.9 + - - +
446A TYR 3.7 0.2 + - - -
447A ARG* 2.9 60.6 + - - -
681A ILE* 4.2 3.7 - - + +
685A THR* 3.0 28.7 + - + -
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Residues in contact with ARG 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A SER* 6.0 0.2 - - - -
423A LYS* 3.6 19.4 - - - +
424A ILE* 2.8 30.9 + - + +
425A GLY* 3.6 23.6 - - - +
428A LEU* 4.2 18.6 - - + +
429A ASN* 3.1 20.7 + - - +
441A SER* 3.1 29.8 + - - +
443A HIS* 1.3 82.1 + - - +
445A ASP* 1.3 88.3 + - - +
447A ARG* 3.1 6.0 + - - +
448A GLU* 2.7 79.5 + - - +
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Residues in contact with ASP 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A SER* 2.9 38.2 + - - +
442A TYR* 3.6 18.1 - - + +
444A ARG* 1.3 110.2 + - - +
446A TYR* 1.3 64.7 + - - +
448A GLU* 3.7 3.6 - - - +
449A THR* 2.9 30.2 + - - +
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Residues in contact with TYR 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A LYS* 5.2 0.3 + - - -
340A ASP 5.0 2.5 - - - -
341A ASP 3.6 22.0 + - - -
342A ILE 3.7 17.5 - - - +
343A ARG* 3.1 48.9 + - + -
344A VAL 5.3 1.1 - - - +
366A GLN* 4.1 8.1 - - - +
406A ARG* 3.2 39.7 + - - -
442A TYR 2.8 22.3 + - - +
443A HIS 3.9 2.2 - - - +
445A ASP* 1.3 74.4 - - - +
447A ARG* 1.3 79.8 + - + +
449A THR* 3.3 4.1 + - - -
450A GLN* 2.8 59.1 + - + +
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Residues in contact with ARG 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A ARG* 4.8 0.4 - - - +
366A GLN* 2.9 47.1 + - - -
399A PRO 4.6 0.4 - - - -
402A SER* 3.4 37.2 - - - +
403A GLU* 2.6 40.7 + - - +
406A ARG* 4.4 9.4 - - - +
424A ILE* 4.6 2.7 - - + -
443A HIS* 2.9 50.6 + - - +
444A ARG* 3.1 8.2 + - - +
446A TYR* 1.3 97.2 - - + +
448A GLU* 1.3 59.7 + - - +
450A GLN* 4.3 3.1 - - - +
451A ILE* 2.8 39.7 + - + +
685A THR* 3.7 6.6 - - - +
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Residues in contact with GLU 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A LYS* 4.6 10.6 - - - +
424A ILE* 3.8 25.6 + - + +
444A ARG* 2.7 60.3 + - - +
445A ASP* 3.7 5.3 - - - +
447A ARG* 1.3 70.7 - - - +
449A THR* 1.3 65.2 + - - +
451A ILE* 3.9 1.0 - - - +
452A THR* 3.0 34.9 + - - +
465A LEU* 6.0 0.7 - - - +
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Residues in contact with THR 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A ASP* 3.8 39.0 - - + +
445A ASP* 2.9 20.2 + - - +
446A TYR* 3.6 5.4 - - - -
448A GLU* 1.3 79.8 + - - +
450A GLN* 1.3 66.5 + - - +
452A THR* 3.4 5.9 + - - -
453A LYS* 3.0 24.3 + - - +
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Residues in contact with GLN 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A ASP 3.1 21.4 + - - -
341A ASP* 3.0 34.1 + - - +
406A ARG* 4.0 22.5 + - + -
410A GLU* 4.1 15.2 - - - +
446A TYR* 2.8 50.2 + - + +
447A ARG 4.0 2.0 - - - +
449A THR* 1.3 77.8 - - - +
451A ILE* 1.3 58.0 + - - +
453A LYS* 3.2 19.7 + - - +
454A LEU* 2.8 34.7 + - + +
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Residues in contact with ILE 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A SER* 3.7 39.5 - - - +
405A ALA* 4.3 1.3 - - + -
406A ARG* 4.5 10.3 - - + +
409A MET* 3.9 27.1 - - + -
417A LEU* 4.1 17.9 - - + -
424A ILE* 4.1 9.9 - - + -
447A ARG* 2.8 22.9 + - + +
448A GLU 4.0 2.5 - - - +
450A GLN* 1.3 78.3 - - - +
452A THR* 1.3 63.4 + - - +
454A LEU* 3.3 2.2 + - - +
455A LEU* 3.0 30.6 + - + +
463A LEU* 4.3 29.2 - - + -
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Residues in contact with THR 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A GLU* 3.0 23.5 + - - +
449A THR* 3.6 6.7 - - - -
451A ILE* 1.3 78.9 - - - +
453A LYS* 1.3 62.3 + - - +
455A LEU* 3.5 19.3 + - + +
456A LYS* 3.6 35.1 + - + +
463A LEU* 5.3 6.6 - - - +
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Residues in contact with LYS 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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338A ARG* 6.2 0.2 - - - +
340A ASP* 2.6 36.0 + - - -
341A ASP* 3.1 30.5 + - - +
449A THR* 3.0 18.2 + - - +
450A GLN* 3.4 24.9 - - - +
452A THR* 1.3 75.9 - - - +
454A LEU* 1.3 71.0 + - + +
456A LYS* 3.4 24.9 + - + +
457A LYS* 3.6 4.7 + - - -
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Residues in contact with LEU 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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406A ARG* 4.6 5.6 - - + +
409A MET* 3.9 30.7 - - + +
410A GLU* 3.7 48.7 - - + +
450A GLN* 2.8 29.8 + - + +
451A ILE* 3.8 3.6 - - - +
453A LYS* 1.3 77.8 - - + +
455A LEU* 1.4 52.1 + - - +
457A LYS* 3.1 2.1 + - - +
458A ASN* 2.7 40.5 + - + +
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Residues in contact with LEU 455 (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 MET* 4.1 10.3 - - + -
451A ILE* 3.0 24.8 + - + +
452A THR* 3.8 15.0 - - + +
453A LYS 3.3 0.2 - - - -
454A LEU* 1.4 75.5 - - - +
456A LYS* 1.3 62.0 + - + +
458A ASN 3.0 20.1 - - - +
459A LYS* 3.9 4.9 + - - -
461A SER* 3.6 17.0 - - - +
462A GLN* 3.5 36.6 - - - +
463A LEU* 3.8 27.4 - - + +
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Residues in contact with LYS 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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452A THR* 3.6 32.4 + - - +
453A LYS* 3.4 15.2 + - + +
454A LEU 3.3 0.4 - - - -
455A LEU* 1.3 79.6 - - + +
457A LYS* 1.3 57.6 + - - +
458A ASN 4.9 0.2 - - - -
459A LYS* 5.0 4.3 + - - +
12C ALA* 6.2 4.0 - - + -
32C MET* 3.9 30.2 - - + +
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Residues in contact with LYS 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 LYS 3.6 5.7 + - - -
454A LEU* 3.1 5.6 + - - +
456A LYS* 1.3 78.6 - - - +
458A ASN* 1.3 60.8 + - - +
459A LYS* 3.5 4.9 + - - +
32C MET* 4.9 9.9 - - - +
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Residues in contact with ASN 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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409A MET* 3.4 30.2 + - + +
412A GLY* 3.8 9.8 + - - -
413A TYR 2.7 26.8 + - - +
414A THR* 4.1 4.9 + - - -
454A LEU* 2.7 21.6 + - + +
455A LEU 3.0 12.3 - - - +
457A LYS* 1.3 72.7 - - - +
459A LYS* 1.3 54.8 + - - +
460A GLU* 4.1 2.4 + - - +
461A SER* 2.6 49.9 + - - +
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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
------------------------------------------------------------
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