Contacts of the helix formed by residues 396 - 411 (chain B) in PDB entry 3H8E
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 ASN 396 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394B GLY 3.5 0.8 - - - -
395B ASN* 1.3 90.7 - - - +
397B ASP* 1.3 70.6 + - - +
398B ASP* 4.1 12.9 + - - +
399B LEU* 3.4 24.6 + - + +
400B VAL* 3.0 26.5 + - - +
459B ASN* 3.2 41.8 + - + +
460B TRP 4.0 1.5 + - - +
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Residues in contact with ASP 397 (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 ASN 4.3 1.1 - - - -
396B ASN* 1.3 77.8 + - - +
398B ASP* 1.3 62.9 + - - +
400B VAL* 3.4 7.1 + - - +
401B GLY* 2.8 26.7 + - - -
416B GLN* 4.9 10.4 + - - +
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Residues in contact with ASP 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B ASN* 3.3 15.1 + - - +
397B ASP* 1.3 84.4 - - - +
399B LEU* 1.3 58.2 + - - +
401B GLY* 3.3 2.0 + - - -
402B GLN* 3.0 42.2 + - - +
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Residues in contact with LEU 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B ALA* 4.1 13.0 - - + -
371B VAL 4.2 2.9 - - - +
372B ILE* 4.5 3.1 - - + -
396B ASN* 3.4 20.6 + - + +
397B ASP 3.3 0.6 - - - -
398B ASP* 1.3 75.2 - - - +
400B VAL* 1.3 69.2 + - - +
402B GLN* 3.1 11.7 + - - +
403B LEU* 3.0 35.9 + - + +
459B ASN* 3.7 11.2 - - + +
460B TRP* 3.7 39.7 - - - +
461B ALA* 3.8 6.7 - - + +
490B TYR* 3.4 38.1 - - + +
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Residues in contact with VAL 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B LEU* 3.8 21.3 - - + -
393B MET 4.2 4.9 - - - +
394B GLY* 3.9 32.1 - - - +
396B ASN 3.0 22.5 + - - +
397B ASP* 3.8 5.8 - - - +
399B LEU* 1.3 75.8 - - - +
401B GLY* 1.4 63.8 + - - +
403B LEU* 3.2 5.7 + - - +
404B LEU* 2.9 30.3 + - + +
416B GLN* 3.6 37.7 - - + +
460B TRP 5.0 0.2 - - - +
461B ALA* 4.5 7.0 - - + -
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Residues in contact with GLY 401 (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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397B ASP 2.8 17.6 + - - -
398B ASP* 3.7 2.0 - - - -
399B LEU 3.2 0.2 - - - -
400B VAL* 1.4 78.8 - - - +
402B GLN* 1.3 55.5 + - - +
404B LEU* 3.4 12.0 + - - +
405B ASP* 2.9 30.0 + - - +
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Residues in contact with GLN 402 (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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398B ASP* 3.0 25.2 + - - +
399B LEU* 3.4 18.1 - - - +
401B GLY* 1.3 76.5 - - - +
403B LEU* 1.3 58.1 + - - +
405B ASP* 3.4 5.6 + - - +
406B ALA* 2.9 29.3 + - - +
409B ARG* 5.1 0.2 + - - -
490B TYR* 3.6 21.4 + - + -
493B ASP* 4.6 2.8 - - - +
494B ARG* 3.6 44.7 + - - +
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Residues in contact with LEU 403 (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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372B ILE* 3.6 31.0 - - + -
392B LEU* 4.0 21.3 - - + -
399B LEU* 3.0 27.7 + - + +
400B VAL 3.6 5.8 - - - +
402B GLN* 1.3 74.7 - - - +
404B LEU* 1.3 61.1 + - - +
406B ALA* 3.4 4.4 + - - +
407B GLY 2.9 24.3 + - - -
461B ALA* 3.6 31.4 - - + -
463B MET* 4.8 2.9 - - - -
486B LEU* 3.7 32.1 - - + +
487B LEU* 4.7 4.0 - - + -
490B TYR* 3.7 21.3 - - + -
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Residues in contact with LEU 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B LEU* 3.7 16.4 - - + -
400B VAL* 2.9 35.8 + - + +
401B GLY* 3.7 8.5 - - - +
403B LEU* 1.3 78.4 - - - +
405B ASP* 1.4 63.0 + - - +
407B GLY* 3.2 2.5 + - - -
408B LYS* 3.0 38.4 + - - +
414B ALA* 3.5 38.3 + - + +
415B TRP* 3.7 11.0 - - + +
416B GLN* 4.0 13.7 - - + +
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Residues in contact with ASP 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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401B GLY 2.9 17.1 + - - +
402B GLN* 3.9 6.3 - - - +
404B LEU* 1.4 77.1 - - - +
406B ALA* 1.3 63.6 + - - +
408B LYS* 3.2 21.0 + - - +
409B ARG* 2.8 55.2 + - - +
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Residues in contact with ALA 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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402B GLN 2.9 19.0 + - - +
403B LEU* 3.6 4.9 - - - +
405B ASP* 1.3 76.3 - - - +
407B GLY* 1.3 56.9 + - - +
409B ARG* 3.3 6.2 + - - +
410B ALA* 2.9 32.8 + - - +
486B LEU* 3.7 10.5 - - + +
489B GLN* 3.4 12.2 - - + +
490B TYR* 3.6 33.4 - - + +
493B ASP* 3.8 6.7 - - - +
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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 LEU 2.9 11.9 + - - -
404B LEU 3.2 4.2 + - - -
406B ALA* 1.3 76.4 - - - +
408B LYS* 1.3 63.0 + - - +
410B ALA* 4.7 0.2 - - - -
411B ASP* 3.0 3.3 + - - -
412B ASP 2.9 48.1 + - - -
413B ARG* 3.7 7.0 - - - +
414B ALA 4.9 0.7 - - - -
486B LEU* 3.7 14.7 - - - +
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Residues in contact with LYS 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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86B ASP* 4.8 0.5 - - - +
120B ARG* 3.1 17.5 + - - -
404B LEU* 3.0 32.6 + - - +
405B ASP* 3.6 19.9 + - - +
407B GLY* 1.3 76.9 - - - +
409B ARG* 1.3 64.0 + - + +
411B ASP* 3.2 6.4 + - - -
413B ARG* 4.1 20.5 - - + +
415B TRP* 6.4 1.8 - - - -
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Residues in contact with ARG 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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120B ARG* 2.9 28.2 + - - +
128B ARG* 4.7 4.0 + - - +
129B LEU* 4.4 3.5 - - - +
405B ASP* 2.8 51.3 + - - +
406B ALA* 3.8 3.1 - - - +
408B LYS* 1.3 80.2 - - + +
410B ALA* 1.3 59.2 + - - +
489B GLN* 3.3 28.1 + - - +
493B ASP* 2.7 44.8 + - - -
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Residues in contact with ALA 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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90B ARG* 4.2 6.1 + - - -
128B ARG* 4.0 15.7 + - - +
129B LEU* 4.7 4.9 - - - +
132B GLU* 4.5 6.2 - - - +
406B ALA 2.9 17.7 + - - +
407B GLY 4.3 2.2 - - - +
409B ARG* 1.3 76.1 - - - +
411B ASP* 1.3 69.8 + - - +
412B ASP* 4.2 3.4 - - - +
485B PRO* 3.7 39.7 - - + +
486B LEU* 4.1 2.7 - - - +
489B GLN* 3.9 8.3 - - + +
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Residues in contact with ASP 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ASP* 3.9 13.6 - - - +
87B ARG* 2.8 47.0 + - - -
90B ARG* 3.0 31.9 + - - +
120B ARG* 3.8 14.1 - - - +
129B LEU* 4.3 6.7 - - + -
407B GLY 3.0 6.2 + - - -
408B LYS 3.2 9.2 + - - -
409B ARG 3.3 0.6 - - - -
410B ALA* 1.3 81.6 - - - +
412B ASP* 1.3 59.0 + - - +
413B ARG* 3.9 14.1 + - - +
482B ARG* 5.1 0.7 + - - -
485B PRO* 5.7 0.2 - - - +
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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
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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