Contacts of the helix formed by residues 404 - 417 (chain B) in PDB entry 3Q36
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 404 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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402B LYS 3.6 3.8 + - - -
403B ILE* 1.3 73.9 - - - +
405B PRO* 1.3 71.7 - - - +
406B GLY* 3.9 3.6 + - - -
407B GLY* 2.8 21.7 + - - -
408B ILE* 2.8 25.5 + - - +
430B MET* 5.2 3.0 - - - +
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Residues in contact with PRO 405 (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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403B ILE 3.5 3.5 - - - +
404B SER* 1.3 84.3 - - - +
406B GLY* 1.3 63.2 + - - +
408B ILE* 3.4 12.9 + - + +
409B SER* 3.1 21.3 + - - -
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Residues in contact with GLY 406 (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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404B SER* 3.0 4.5 + - - -
405B PRO* 1.3 82.6 - - - +
407B GLY* 1.3 58.6 + - - +
409B SER* 3.0 25.2 - - - -
410B GLN* 3.3 13.5 + - - +
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Residues in contact with GLY 407 (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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403B ILE* 4.0 6.3 - - - -
404B SER* 2.8 19.7 + - - -
406B GLY* 1.3 74.5 - - - +
408B ILE* 1.3 65.1 + - - +
409B SER 3.2 0.2 + - - -
410B GLN* 3.2 15.2 + - - +
411B ILE* 3.0 26.3 + - - +
430B MET* 4.2 16.1 - - - +
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Residues in contact with ILE 408 (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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395B LYS* 3.9 16.2 - - + +
398B LEU* 4.0 16.2 - - + -
399B GLN* 3.6 39.9 - - + +
403B ILE* 3.4 33.6 - - + +
404B SER 2.8 15.1 + - - +
405B PRO* 3.8 11.7 - - + +
407B GLY* 1.3 75.8 - - - +
409B SER* 1.3 57.1 + - - +
411B ILE* 3.7 5.2 - - - +
412B LEU* 2.8 51.3 + - + +
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Residues in contact with SER 409 (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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405B PRO 3.1 13.9 + - - -
406B GLY* 3.0 17.5 - - - -
407B GLY 3.1 0.2 - - - -
408B ILE* 1.3 78.8 - - - +
410B GLN* 1.3 61.1 + - - +
412B LEU* 3.4 7.2 + - - +
413B ASP* 3.2 29.5 + - - +
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Residues in contact with GLN 410 (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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435A ASP* 3.0 29.1 + - + +
406B GLY 3.9 9.4 - - - +
407B GLY* 3.2 16.0 + - - +
409B SER* 1.3 76.0 - - - +
411B ILE* 1.3 58.6 + - - +
413B ASP* 2.7 32.5 + - - +
414B LEU* 2.9 18.7 + - + +
426B LYS* 2.8 30.4 + - + +
430B MET* 4.2 6.4 - - - +
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Residues in contact with ILE 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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386B PHE* 3.6 27.8 - - + -
394B LEU* 5.1 1.8 - - + -
398B LEU* 3.8 25.6 - - + -
403B ILE* 4.4 9.9 - - + -
407B GLY 3.0 14.7 + - - +
408B ILE* 3.8 3.8 - - - +
410B GLN* 1.3 79.1 - - - +
412B LEU* 1.3 61.9 + - - +
414B LEU* 3.6 8.5 + - - +
415B VAL* 3.1 24.0 + - + +
423B ALA* 4.0 5.7 - - + +
426B LYS* 3.8 20.6 - - + -
427B TYR* 4.0 22.0 - - + +
430B MET* 3.6 26.0 - - + -
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Residues in contact with LEU 412 (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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391B PRO* 4.0 38.6 - - + +
394B LEU* 4.3 20.0 - - + -
395B LYS* 4.2 20.9 - - + +
398B LEU* 5.4 0.7 - - + -
408B ILE* 2.8 41.0 + - + +
409B SER* 3.9 6.5 - - - +
410B GLN 3.1 0.2 - - - -
411B ILE* 1.3 75.1 - - + +
413B ASP* 1.3 65.2 + - - +
415B VAL* 3.8 6.5 - - + +
416B LYS* 3.2 31.3 + - - +
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Residues in contact with ASP 413 (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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409B SER* 3.2 21.0 + - - +
410B GLN* 2.7 15.5 + - - +
412B LEU* 1.3 75.8 - - - +
414B LEU* 1.3 60.8 + - + +
415B VAL 3.0 1.3 - - - -
416B LYS* 2.6 33.0 + - - +
417B GLY* 2.8 10.6 + - - -
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Residues in contact with LEU 414 (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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435A ASP* 4.5 11.0 - - - +
436A ASP* 5.3 3.1 - - + -
410B GLN* 2.9 17.9 + - + +
411B ILE* 3.9 3.6 - - - +
413B ASP* 1.3 77.4 - - + +
415B VAL* 1.3 54.9 + - - +
417B GLY 3.1 1.9 + - - -
418B THR 3.0 8.3 + - - -
419B HIS* 2.7 61.0 + - + +
422B VAL* 3.7 21.3 - - + -
423B ALA* 3.5 32.1 - - + +
426B LYS* 4.0 25.8 - - + -
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Residues in contact with VAL 415 (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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386B PHE* 3.4 55.2 - - + +
389B SER 5.8 1.1 - - - +
391B PRO* 5.0 15.0 - - + -
394B LEU* 3.9 14.4 - - + -
411B ILE 3.1 20.5 + - - +
412B LEU* 3.8 10.3 - - + +
413B ASP 3.0 0.6 - - - -
414B LEU* 1.3 78.9 - - - +
416B LYS* 1.3 61.9 + - + +
418B THR* 3.4 6.9 + - - -
420B TYR* 3.8 20.3 + - + -
423B ALA* 4.4 4.0 - - + -
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Residues in contact with LYS 416 (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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391B PRO* 5.5 15.7 - - + -
412B LEU* 3.2 18.0 + - - +
413B ASP* 2.6 22.6 + - - +
415B VAL* 1.3 74.7 - - + +
417B GLY* 1.3 56.1 + - - +
418B THR* 3.0 9.2 + - - -
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Residues in contact with GLY 417 (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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413B ASP 2.8 11.0 + - - -
414B LEU 3.1 3.3 + - - -
416B LYS* 1.3 76.3 - - - +
418B THR* 1.3 67.8 + - - +
419B HIS* 3.1 36.9 + - - -
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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
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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