Contacts of the helix formed by residues 404 - 416 (chain A) in PDB entry 4OSI
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 GLY 404 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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369A ASP 4.0 9.9 + - - -
370A GLY 5.7 0.4 + - - -
403A GLY* 1.3 72.7 - - - +
405A GLY* 1.3 64.3 + - - +
406A LYS 3.3 2.2 - - - -
407A GLN* 3.3 8.4 + - - +
408A ALA* 3.1 20.1 + - - +
438A GLY 5.9 0.2 + - - -
439A GLY 6.0 0.2 + - - -
6I C 3.8 31.2 + - - +
7I T 3.9 19.7 + - - +
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Residues in contact with GLY 405 (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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370A GLY 5.8 0.6 + - - -
374A ALA* 4.6 7.5 - - - +
399A ILE 3.8 17.3 - - - -
400A ALA* 4.0 9.2 - - - -
402A ASN* 3.1 18.5 + - - -
404A GLY* 1.3 73.9 - - - +
406A LYS* 1.3 66.6 + - - +
408A ALA* 3.0 4.0 + - - +
409A LEU* 2.9 30.9 + - - +
6I C 5.0 0.6 + - - -
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Residues in contact with LYS 406 (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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370A GLY 5.7 0.2 + - - -
373A GLN* 3.3 49.5 + - + +
374A ALA* 4.0 7.5 - - - +
376A GLU* 5.5 5.9 + - - +
377A THR* 3.0 40.7 + - + +
405A GLY* 1.3 75.8 - - - +
407A GLN* 1.3 72.4 + - - +
409A LEU* 3.2 2.1 + - - +
410A GLU* 3.0 47.5 + - - +
6I C 3.6 16.3 + - - +
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Residues in contact with GLN 407 (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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404A GLY 3.3 6.9 + - - +
405A GLY 3.2 0.6 - - - -
406A LYS* 1.3 91.3 - - - +
408A ALA* 1.3 55.1 + - - +
410A GLU* 3.5 11.5 + - - +
411A THR* 2.5 38.5 + - - -
440A LYS* 3.5 37.5 + - + +
6I C 2.4 60.4 + - - +
7I T 4.0 5.2 - - - +
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Residues in contact with ALA 408 (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 ILE* 3.4 26.9 - - + +
402A ASN* 6.3 1.1 - - + -
404A GLY 3.1 12.2 + - - +
405A GLY* 3.0 7.0 + - - +
407A GLN* 1.3 74.7 - - - +
409A LEU* 1.3 59.5 + - - +
411A THR* 3.2 2.8 + - - -
412A VAL* 2.9 34.0 + - - +
434A ALA* 3.8 14.4 - - + +
436A ASN 5.4 0.7 - - - +
439A GLY* 4.7 3.6 - - - +
440A LYS* 4.3 19.7 - - - +
443A LEU* 4.3 1.1 - - - +
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Residues in contact with LEU 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A ALA 4.2 1.8 - - - +
377A THR* 3.5 40.6 - - + +
378A VAL* 3.6 18.8 - - + -
381A LEU* 3.6 17.2 - - + +
385A LEU* 4.3 18.0 - - + +
396A VAL* 4.0 23.1 - - + +
399A ILE* 3.7 21.3 - - + -
400A ALA* 4.3 4.9 - - + +
405A GLY 2.9 17.4 + - - +
406A LYS 3.5 5.6 - - - +
408A ALA* 1.3 75.7 - - - +
410A GLU* 1.3 64.1 + - - +
412A VAL* 3.4 4.9 + - + +
413A GLN* 2.9 23.4 + - - +
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Residues in contact with GLU 410 (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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377A THR* 3.9 14.7 - - + +
381A LEU* 4.0 10.2 - - + +
406A LYS* 3.0 45.1 + - - +
407A GLN* 4.0 11.7 + - - +
409A LEU* 1.3 76.1 - - - +
411A THR* 1.3 57.5 + - - +
413A GLN* 3.1 12.2 + - - +
414A ARG* 2.9 40.1 + - - +
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Residues in contact with THR 411 (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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407A GLN 2.5 22.9 + - - -
408A ALA 3.7 3.4 - - - -
410A GLU* 1.3 77.1 - - - +
412A VAL* 1.3 56.3 + - - +
414A ARG* 3.4 17.4 + - - +
415A LEU* 2.9 54.1 + - + +
440A LYS* 2.8 26.9 - - + +
443A LEU* 3.7 22.2 - - + -
444A GLU* 3.8 12.8 - - - +
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Residues in contact with VAL 412 (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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385A LEU* 4.2 17.5 - - + -
391A LEU* 4.4 10.3 - - + -
399A ILE* 4.7 12.3 - - + -
408A ALA 2.9 22.4 + - - +
409A LEU* 3.8 5.4 - - + +
411A THR* 1.3 73.2 - - - +
413A GLN* 1.3 67.3 + - - +
414A ARG 3.0 0.3 + - - -
415A LEU* 3.2 0.8 + - - +
416A LEU* 2.9 55.4 + - + +
430A VAL* 4.6 8.1 - - + -
431A VAL* 5.9 1.6 - - + -
434A ALA* 3.4 29.8 - - + -
443A LEU* 3.9 6.7 - - + -
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Residues in contact with GLN 413 (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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381A LEU* 3.3 37.9 - - + +
384A VAL* 3.6 21.0 - - + +
385A LEU* 4.2 10.7 - - + +
389A HIS* 3.1 39.8 + - + -
409A LEU 2.9 13.6 + - - +
410A GLU* 3.2 15.0 - - - +
412A VAL* 1.3 77.3 - - - +
414A ARG* 1.3 62.8 + - - +
417A PRO* 4.2 1.4 - - - +
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Residues in contact with ARG 414 (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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410A GLU* 2.9 17.7 + - - +
411A THR* 3.5 35.0 + - - +
413A GLN* 1.3 80.1 - - - +
415A LEU* 1.3 79.9 + - + +
417A PRO* 3.3 19.4 - - - +
418A VAL* 4.0 5.0 - - - +
440A LYS* 4.6 6.3 - - - +
444A GLU* 4.0 19.5 + - - -
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Residues in contact with LEU 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A THR* 2.9 33.9 + - + +
412A VAL* 5.3 0.7 - - - -
414A ARG* 1.3 93.0 - - + +
416A LEU* 1.3 65.5 + - - +
417A PRO 3.3 2.9 - - - -
418A VAL* 3.0 25.0 + - + -
419A LEU* 3.3 27.5 + - + +
430A VAL* 5.9 0.7 - - + -
443A LEU* 3.9 26.7 - - + +
444A GLU* 3.4 22.4 - - - +
447A GLN* 3.7 27.8 - - + +
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Residues in contact with LEU 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A HIS* 3.8 41.3 - - + +
391A LEU* 4.6 14.1 - - + -
412A VAL* 2.9 38.4 + - + +
415A LEU* 1.3 77.3 - - - +
417A PRO* 1.4 65.5 - - + +
419A LEU* 3.3 3.3 + - - +
420A CYS* 3.0 41.8 + - + +
427A PRO* 4.9 15.9 - - + -
430A VAL* 3.6 28.4 - - + +
431A VAL* 5.3 2.7 - - + -
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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
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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