Contacts of the helix formed by residues 404 - 421 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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369B ASP 3.9 8.7 + - - -
403B GLY* 1.3 71.8 - - - +
405B GLY* 1.3 65.0 + - - +
406B LYS 3.5 2.0 - - - -
407B GLN* 3.3 17.1 + - - +
408B ALA* 3.4 9.0 + - - +
437B GLY 5.4 0.2 - - - +
438B GLY 5.5 0.2 - - - +
439B GLY* 5.9 0.5 - - - -
6G C 3.7 43.9 + - - -
7G T 3.5 12.2 + - - +
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Residues in contact with GLY 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B ASP 5.3 0.6 + - - -
374B ALA* 4.5 6.9 - - - +
399B ILE 4.4 9.2 - - - -
400B ALA* 4.3 9.0 - - - -
402B ASN* 3.2 17.2 + - - -
403B GLY 3.1 3.6 - - - -
404B GLY* 1.3 71.8 - - - +
406B LYS* 1.3 70.4 + - - +
407B GLN 2.9 1.8 - - - -
408B ALA* 2.5 19.9 + - - +
409B LEU* 2.9 18.4 + - - +
6G C 4.6 1.6 + - - -
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Residues in contact with LYS 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B GLN* 3.6 41.7 - - + +
374B ALA* 4.1 9.9 - - - +
376B GLU* 6.0 2.5 - - - -
377B THR* 2.8 36.7 - - + +
405B GLY* 1.3 73.9 - - - +
407B GLN* 1.3 76.4 + - - +
409B LEU* 3.2 2.4 + - - +
410B GLU* 3.0 50.9 + - - +
6G C 3.8 7.4 - - - +
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Residues in contact with GLN 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B GLY 3.4 11.2 - - - +
405B GLY 2.8 3.8 + - - -
406B LYS* 1.3 91.2 - - - +
408B ALA* 1.3 54.3 + - - +
410B GLU* 3.9 12.3 + - - +
411B THR* 2.7 38.3 + - - -
440B LYS* 3.6 35.4 + - + +
6G C 2.9 53.9 + - - +
7G T 3.7 9.4 - - - +
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Residues in contact with ALA 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399B ILE* 3.9 24.5 - - + +
402B ASN* 6.0 1.6 - - + +
404B GLY 3.4 5.9 + - - +
405B GLY* 2.5 16.5 + - - +
407B GLN* 1.3 69.7 - - - +
409B LEU* 1.3 65.4 + - - +
411B THR* 3.3 2.8 + - - -
412B VAL* 2.9 25.6 + - - +
434B ALA* 4.0 15.7 - - + +
436B ASN 5.7 0.2 - - - +
439B GLY* 4.4 15.5 - - - -
440B LYS 4.2 9.5 - - - +
443B LEU* 4.4 1.7 - - - +
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Residues in contact with LEU 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B ALA* 4.0 6.7 - - - +
377B THR* 3.3 38.8 - - + +
378B VAL* 3.9 19.7 - - + +
381B LEU* 4.3 9.0 - - + -
385B LEU* 4.7 11.5 - - + +
396B VAL* 3.9 32.1 - - + +
399B ILE* 3.6 25.1 - - + -
400B ALA* 4.3 9.6 - - + +
405B GLY 2.9 18.3 + - - +
406B LYS* 3.7 3.8 - - - +
408B ALA* 1.3 73.1 - - - +
410B GLU* 1.3 64.3 + - - +
412B VAL* 3.7 5.8 - - - +
413B GLN* 2.9 23.9 + - - +
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Residues in contact with GLU 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B THR* 4.4 5.5 - - + +
381B LEU* 4.1 20.8 - - + +
406B LYS* 3.0 57.5 + - - +
407B GLN* 3.9 17.6 + - - +
409B LEU* 1.3 72.7 - - - +
411B THR* 1.3 58.4 + - - +
413B GLN* 3.4 5.4 + - - +
414B ARG* 3.0 30.1 + - - +
440B LYS* 5.5 2.9 + - - +
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Residues in contact with THR 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407B GLN 2.7 22.6 + - - -
408B ALA 3.7 3.1 - - - -
410B GLU* 1.3 77.4 - - - +
412B VAL* 1.3 57.4 + - - +
414B ARG* 3.3 27.4 + - - +
415B LEU* 2.9 34.0 + - + +
440B LYS* 2.9 38.7 + - + +
443B LEU* 3.6 27.6 - - + -
444B GLU* 4.3 0.9 - - + -
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Residues in contact with VAL 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B LEU* 3.7 20.9 - - + -
391B LEU* 5.0 2.5 - - + -
399B ILE* 4.3 19.5 - - + -
408B ALA 2.9 14.8 + - - +
409B LEU* 3.9 6.1 - - - +
411B THR* 1.3 73.2 - - - +
413B GLN* 1.3 65.5 + - - +
414B ARG 3.1 1.3 - - - -
415B LEU* 4.2 1.6 - - + +
416B LEU* 2.9 42.2 + - + +
430B VAL* 3.7 29.6 - - + +
431B VAL* 5.3 0.7 - - + +
434B ALA* 3.8 25.1 - - + -
443B LEU* 3.9 9.0 - - + -
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Residues in contact with GLN 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B LEU* 3.9 28.0 - - + +
384B VAL* 3.5 33.9 - - + +
385B LEU* 3.7 26.9 - - + -
389B HIS* 3.8 24.0 + - + -
409B LEU 2.9 15.5 + - - +
410B GLU* 3.6 5.8 + - - +
412B VAL* 1.3 80.5 - - - +
414B ARG* 1.3 60.0 + - - +
417B PRO* 4.4 2.6 - - - +
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Residues in contact with ARG 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B GLU 3.0 15.8 + - - +
411B THR* 3.6 32.3 + - - +
412B VAL 3.1 0.4 - - - -
413B GLN* 1.3 78.5 - - - +
415B LEU* 1.3 85.8 + - + +
417B PRO* 4.4 4.4 - - - +
418B VAL* 4.3 7.8 - - - +
440B LYS* 4.3 6.1 - - - +
444B GLU* 3.4 26.3 + - - +
447B GLN* 5.3 1.6 + - - -
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Residues in contact with LEU 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B THR* 2.9 28.5 + - + +
412B VAL* 3.3 2.2 + - + -
414B ARG* 1.3 105.5 - - + +
416B LEU* 1.3 70.6 + - - +
417B PRO* 3.2 4.8 - - - -
418B VAL* 3.3 14.3 + - + +
419B LEU* 3.1 33.3 + - + +
430B VAL* 5.6 0.2 - - - -
443B LEU* 4.1 15.7 - - + +
444B GLU* 4.1 20.9 - - + +
447B GLN* 3.8 39.7 - - + +
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Residues in contact with LEU 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B LEU* 4.9 0.7 - - + -
389B HIS* 4.0 28.7 - - + +
391B LEU* 3.8 34.3 - - + -
412B VAL* 2.9 26.0 + - + +
415B LEU* 1.3 76.8 - - - +
417B PRO* 1.4 65.0 - - + +
419B LEU* 3.4 1.0 + - - +
420B CYS* 2.8 65.9 + - - +
427B PRO* 4.2 11.2 - - + -
430B VAL* 3.9 28.2 - - + +
431B VAL* 5.7 0.7 - - + -
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Residues in contact with PRO 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B HIS* 3.8 25.4 - - + +
413B GLN 4.4 3.8 - - - +
414B ARG 4.4 4.7 - - - +
415B LEU* 3.4 8.1 - - - +
416B LEU* 1.4 90.5 - - + +
418B VAL* 1.3 61.3 + - + +
420B CYS* 3.0 4.2 + - + -
421B GLN* 2.5 60.5 + - + +
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Residues in contact with VAL 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B ARG 4.3 8.3 - - - +
415B LEU* 3.3 24.9 + - + +
417B PRO* 1.3 80.8 - - + +
419B LEU* 1.3 67.2 + - + +
420B CYS 3.0 0.2 + - - -
421B GLN* 4.7 1.6 - - - -
422B ALA* 2.9 35.2 + - + +
423B HIS* 3.7 15.6 + - + -
447B GLN* 4.6 13.7 - - - +
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Residues in contact with LEU 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B LEU* 3.1 32.3 + - + +
416B LEU 3.9 2.9 - - - +
418B VAL* 1.3 80.9 - - + +
420B CYS* 1.3 57.6 + - - +
423B HIS* 3.3 30.4 - - + +
425B LEU* 3.3 27.0 + - + +
430B VAL* 4.2 27.6 - - + -
433B ILE* 5.9 1.6 - - + -
443B LEU* 4.4 21.3 - - + +
446B VAL* 4.5 11.4 - - + -
447B GLN* 3.4 42.0 - - + -
450B LEU* 5.8 2.5 - - + -
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Residues in contact with CYS 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416B LEU* 2.8 49.5 + - - +
417B PRO* 3.6 3.8 - - + +
419B LEU* 1.3 75.7 - - - +
421B GLN* 1.3 74.8 + - + +
424B GLY* 3.2 16.1 + - - -
425B LEU 3.2 27.9 + - - +
427B PRO* 3.8 19.3 - - + -
430B VAL* 4.0 3.6 - - - -
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Residues in contact with GLN 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417B PRO* 2.5 48.8 + - + +
418B VAL* 4.2 1.1 - - - +
420B CYS* 1.3 82.2 - - - +
422B ALA* 1.3 65.7 + - + +
423B HIS 3.3 0.7 + - - -
424B GLY* 3.4 5.2 + - - -
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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