Contacts of the helix formed by residues 395 - 406 (chain B) in PDB entry 6IEH
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 395 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393B SER* 3.3 3.6 - - - +
394B PHE* 1.3 81.0 - - - +
396B LYS* 1.3 66.9 + - - +
397B LYS* 3.6 11.4 + - - +
398B ASP* 3.2 32.2 + - - +
399B CYS* 3.2 20.1 + - - +
482B THR* 4.7 3.2 + - - -
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Residues in contact with LYS 396 (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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394B PHE 4.2 0.4 + - - -
395B SER* 1.3 75.7 + - - +
397B LYS* 1.3 63.0 + - - +
399B CYS* 3.3 11.4 + - - +
400B GLU* 3.4 12.0 + - - +
456B HIS* 1.8 56.6 - - + +
457B GLY* 4.5 6.8 - - - +
458B GLY* 3.7 17.2 - - - +
482B THR* 4.4 9.8 + - - +
916B GLU* 5.3 3.6 + - - -
989B PHE* 3.7 21.5 - - + -
992B SER* 5.1 7.3 + - - -
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Residues in contact with LYS 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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213A LYS 6.1 1.1 - - - +
395B SER* 3.2 8.6 + - - +
396B LYS* 1.3 81.4 - - - +
398B ASP* 1.3 64.6 + - - +
400B GLU* 3.4 9.5 + - - +
401B ALA* 3.0 23.0 + - - +
989B PHE* 5.3 8.4 - - + -
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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
----------------------------------------------------------
393B SER* 4.0 8.8 - - - -
394B PHE 5.6 0.5 + - - -
395B SER* 3.2 29.1 + - - +
396B LYS 3.2 1.0 - - - -
397B LYS* 1.3 78.2 - - - +
399B CYS* 1.3 63.4 + - - +
401B ALA* 3.6 6.9 - - - +
402B TYR* 2.9 48.7 + - + -
499B THR* 5.5 1.0 + - - -
500B ASN* 5.3 6.8 + - - -
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Residues in contact with CYS 399 (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 SER* 3.7 15.0 + - - +
395B SER 3.2 10.3 + - - +
396B LYS* 3.4 12.1 - - - +
397B LYS 3.2 0.2 - - - -
398B ASP* 1.3 79.7 - - - +
400B GLU* 1.3 61.4 + - + +
402B TYR* 3.9 1.4 - - - +
403B ALA* 3.4 15.9 + - - +
454B ILE* 4.5 5.6 - - - -
455B HIS 4.4 5.8 - - - -
456B HIS* 4.7 7.2 - - + -
480B PHE* 2.5 57.4 - - - +
481B ALA* 3.3 16.6 - - - -
482B THR* 3.9 3.8 - - - +
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Residues in contact with GLU 400 (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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213A LYS 4.6 2.9 - - - +
214A LYS* 3.0 32.2 - - - +
215A HIS* 3.3 37.7 + - + +
396B LYS 3.4 7.9 + - - +
397B LYS* 3.4 11.1 + - - +
398B ASP 3.2 0.2 - - - -
399B CYS* 1.3 79.5 - - - +
401B ALA* 1.3 64.0 + - - +
402B TYR 3.2 0.4 - - - -
403B ALA* 3.4 13.1 + - - +
404B LEU* 3.4 19.5 + - - +
454B ILE* 4.3 20.3 - - + +
456B HIS* 3.5 25.5 + - + +
459B LEU* 3.6 5.5 - - - +
989B PHE* 5.4 0.3 - - - -
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Residues in contact with ALA 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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213A LYS* 6.6 0.2 - - - -
397B LYS 3.0 18.0 + - - +
398B ASP* 3.2 9.6 + - - +
400B GLU* 1.3 78.8 - - - +
402B TYR* 1.3 64.2 + - + +
404B LEU* 3.7 9.6 + - - +
405B GLN* 3.3 24.1 + - - +
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Residues in contact with TYR 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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373B ASN* 5.8 2.2 - - - -
374B VAL* 3.4 38.4 - - + +
393B SER* 4.0 10.5 - - - -
398B ASP* 2.9 43.1 + - + +
399B CYS 3.9 0.9 - - - +
401B ALA* 1.3 81.4 - - + +
403B ALA* 1.3 63.6 + - - +
405B GLN* 3.2 36.9 + - - +
406B MET* 3.3 6.2 + - - +
480B PHE* 3.6 27.8 - + + -
499B THR* 4.0 25.2 + - + -
500B ASN* 5.6 2.8 + - - -
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Residues in contact with ALA 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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399B CYS 3.4 5.6 + - - +
400B GLU 3.4 8.0 + - - +
401B ALA 3.3 0.4 - - - -
402B TYR* 1.3 80.0 - - - +
404B LEU* 1.3 62.2 + - + +
406B MET* 3.3 8.5 + - - +
407B THR* 3.5 7.6 + - - -
447B LEU* 4.2 8.4 - - + +
452B ILE* 3.5 26.2 - - + +
454B ILE* 3.5 32.1 - - + -
480B PHE* 4.0 15.5 - - + -
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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
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213A LYS* 5.5 3.1 - - + -
214A LYS 6.0 0.2 - - - -
215A HIS* 5.4 7.2 - - + -
220A VAL* 3.2 40.2 - - + -
223A TYR* 5.5 8.4 - - + +
224A PHE* 2.6 50.4 - - + -
400B GLU 3.4 12.9 + - - +
401B ALA* 3.8 11.2 - - - +
402B TYR 3.2 0.2 - - - -
403B ALA* 1.3 74.4 - - + +
405B GLN* 1.3 65.8 + - + +
406B MET 3.0 1.6 - - - -
407B THR* 2.8 22.3 + - - -
408B LYS* 4.3 6.6 + - - +
447B LEU* 4.8 4.0 - - + -
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Residues in contact with GLN 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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373B ASN* 4.2 16.7 + - - +
374B VAL* 6.3 0.2 - - - +
375B PHE* 2.7 43.2 - - + +
401B ALA* 3.3 19.3 - - - +
402B TYR* 3.2 29.9 + - + +
404B LEU* 1.3 77.3 - - + +
406B MET* 1.3 61.7 + - - +
408B LYS* 3.2 14.4 - - - +
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Residues in contact with MET 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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374B VAL* 5.1 1.8 - - - -
375B PHE* 3.5 54.5 - - + +
378B VAL* 3.7 26.9 - - + -
379B LYS 4.5 0.2 - - - +
402B TYR 3.3 6.0 + - - +
403B ALA 3.3 5.3 + - - +
404B LEU 3.0 0.8 - - - -
405B GLN* 1.3 81.1 - - - +
407B THR* 1.3 55.9 + - - +
408B LYS 3.2 0.7 - - - -
409B LEU* 3.0 54.8 + - + +
411B PHE* 4.3 7.7 - - + -
452B ILE* 2.8 28.8 - - + +
480B PHE* 3.7 25.4 - - + -
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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