Contacts of the helix formed by residues 407 - 419 (chain B) in PDB entry 3H60
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 407 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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390B GLN* 3.5 5.0 - - - +
392B GLN 3.1 16.8 - - - -
394B GLY 2.7 18.8 + - - -
406B PHE* 1.3 76.2 - - - +
408B PRO* 1.3 75.8 - - - +
409B ASP* 3.2 6.3 - - - -
410B VAL* 3.1 12.3 + - - +
411B THR* 3.3 7.4 + - - -
438B HIS* 3.4 6.3 - - - -
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Residues in contact with PRO 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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390B GLN 3.6 4.9 - - - +
391B PRO 3.3 27.6 - - - +
392B GLN 3.6 9.0 - - - +
393B ASN* 3.7 10.8 - - - +
407B GLY* 1.3 84.2 - - - +
409B ASP* 1.3 56.0 + - - +
411B THR* 3.4 2.1 + - - -
412B LYS* 3.0 28.6 + - - +
438B HIS* 3.4 41.8 - - + +
441B ARG* 6.1 0.7 - - - +
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Residues in contact with ASP 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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393B ASN* 3.3 32.1 + - - +
394B GLY* 2.9 34.8 + - - +
407B GLY* 3.5 5.7 - - - -
408B PRO* 1.3 74.3 - - - +
410B VAL* 1.3 74.7 + - - +
412B LYS* 3.9 6.2 - - - +
413B ALA* 3.1 24.9 + - - +
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Residues in contact with VAL 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B LEU* 4.3 13.9 - - + -
356B PHE 4.4 1.8 - - - +
359B ASP* 4.7 4.4 - - - +
394B GLY 3.5 26.2 - - - +
395B ARG* 3.5 47.3 - - + +
406B PHE* 3.7 23.8 - - + -
407B GLY 3.1 7.8 + - - +
409B ASP* 1.3 86.9 + - - +
411B THR* 1.3 65.2 + - - +
413B ALA* 3.4 4.4 + - - +
414B PHE* 3.0 23.2 + - + +
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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
----------------------------------------------------------
355B LEU* 3.7 17.9 - - + -
406B PHE* 3.5 13.0 - - - -
407B GLY 3.3 1.6 + - - -
408B PRO* 3.4 3.8 + - - -
409B ASP 3.2 0.2 - - - -
410B VAL* 1.3 78.6 - - - +
412B LYS* 1.3 63.4 + - - +
414B PHE* 3.3 1.4 + - - +
415B LEU* 3.0 40.6 + - + +
423B ILE* 4.8 3.6 - - + -
438B HIS* 2.6 34.4 + - - +
441B ARG* 3.6 38.6 - - + +
442B CYS* 4.7 2.7 - - + -
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Residues in contact with LYS 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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408B PRO 3.0 16.8 + - - +
409B ASP* 3.9 6.7 - - - +
410B VAL 3.3 0.2 - - - -
411B THR* 1.3 77.9 - - - +
413B ALA* 1.3 63.2 + - - +
415B LEU* 3.9 2.1 - - - +
416B GLU* 2.4 67.4 + - - +
441B ARG* 3.9 25.7 - - + +
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Residues in contact with ALA 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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359B ASP* 5.2 9.4 - - + +
409B ASP 3.1 17.1 + - - +
410B VAL* 3.9 5.2 - - - +
412B LYS* 1.3 77.3 - - - +
414B PHE* 1.3 62.8 + - - +
416B GLU* 3.9 9.7 + - - +
417B GLU* 3.1 26.4 + - - +
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Residues in contact with PHE 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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349B LEU* 3.6 33.2 - - + -
355B LEU* 3.7 34.5 - - + -
356B PHE* 3.7 27.6 - + - -
361B VAL* 3.3 27.1 - - + -
362B THR* 5.0 0.4 - - - -
363B LEU* 4.7 1.6 - - + -
366B ILE* 4.3 6.7 - - + -
410B VAL* 3.0 19.7 + - + +
411B THR 3.3 2.9 + - - +
413B ALA* 1.3 78.2 - - - +
415B LEU* 1.3 69.9 + - + +
417B GLU* 3.6 3.3 + - - +
418B ASN* 2.9 48.1 + - - +
420B LEU* 3.6 16.8 - - + -
423B ILE* 4.7 2.0 - - + -
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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
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411B THR* 3.0 35.7 + - + +
412B LYS 4.0 2.2 - - - +
414B PHE* 1.3 79.1 - - + +
416B GLU* 1.3 56.4 + - - +
418B ASN 3.2 0.3 + - - -
419B ASN* 2.9 11.1 + - - -
420B LEU* 2.8 61.9 + - + +
421B ASP 3.7 2.9 - - - +
422B TYR* 3.7 24.7 - - - +
423B ILE* 3.9 14.6 - - + -
441B ARG* 3.2 49.6 - - + +
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Residues in contact with GLU 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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412B LYS* 2.4 70.3 + - + +
413B ALA* 3.9 8.1 - - - +
415B LEU* 1.3 74.1 - - - +
417B GLU* 1.3 65.1 + - - +
418B ASN 3.2 0.9 + - - -
419B ASN* 3.3 17.8 + - - +
441B ARG* 4.4 10.2 + - - +
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Residues in contact with GLU 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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360B GLY* 3.3 32.9 + - - +
361B VAL 4.1 4.0 - - - +
362B THR* 3.7 23.6 - - - +
413B ALA 3.1 16.4 + - - +
414B PHE* 3.8 6.0 - - - +
416B GLU* 1.3 79.2 - - - +
418B ASN* 1.3 64.3 + - - +
419B ASN* 3.3 3.3 + - - -
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Residues in contact with ASN 418 (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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346B GLY 4.8 1.0 - - - +
361B VAL 3.2 22.0 + - - -
362B THR* 3.3 9.8 - - - +
363B LEU* 3.1 45.2 + - + +
414B PHE* 2.9 41.9 + - - +
416B GLU 3.1 0.2 - - - -
417B GLU* 1.3 88.2 + - - +
419B ASN* 1.3 71.9 - - - +
420B LEU* 3.4 26.0 + - + +
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Residues in contact with ASN 419 (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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346B GLY 3.3 10.5 - - - +
347B LYS* 3.2 32.2 + - - +
415B LEU 2.9 6.9 + - - -
416B GLU* 3.3 14.3 + - - +
417B GLU 3.3 3.0 + - - -
418B ASN* 1.3 81.4 - - - +
420B LEU* 1.3 57.6 + - - +
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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