Contacts of the helix formed by residues 395 - 405 (chain B) in PDB entry 1ZXN
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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291B GLU* 2.7 31.3 + - - +
393B GLN 3.6 1.7 + - - -
394B LEU* 1.3 74.1 - - - +
396B GLU* 1.3 56.3 - - - +
397B LYS* 2.9 14.5 + - - +
398B PHE* 2.8 39.8 + - - +
399B ILE* 3.1 12.9 + - - +
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Residues in contact with GLU 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 LEU 3.9 1.2 + - - +
395B SER* 1.3 72.2 - - - +
397B LYS* 1.3 58.9 + - - +
399B ILE* 3.0 27.0 - - + +
400B LYS* 3.3 11.6 + - - +
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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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290B HIS 6.1 0.4 - - - +
395B SER* 2.9 10.9 - - - +
396B GLU* 1.3 80.7 - - - +
398B PHE* 1.3 63.5 + - - +
400B LYS* 3.7 6.2 - - - +
401B ALA* 3.4 22.5 + - + +
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Residues in contact with PHE 398 (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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289B ILE* 3.2 27.8 - - + +
290B HIS 3.6 21.5 - - - -
291B GLU* 3.3 32.8 - - + +
299B VAL* 4.0 18.6 - - + -
301B LEU* 4.2 18.6 - - + -
333B ILE* 4.1 10.3 - - + -
394B LEU* 3.3 33.9 - - + -
395B SER* 2.8 25.7 + - - +
397B LYS* 1.3 80.0 - - + +
399B ILE* 1.3 71.0 + - - +
401B ALA* 3.2 7.4 + - - +
402B ALA* 2.9 25.8 + - + +
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Residues in contact with ILE 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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333B ILE* 6.5 0.4 - - + -
336B LYS* 3.1 35.4 - - + +
394B LEU* 5.3 3.1 - - + +
395B SER 3.1 5.8 + - - +
396B GLU* 3.0 28.7 - - + +
398B PHE* 1.3 79.0 - - + +
400B LYS* 1.3 72.0 + - - +
402B ALA* 2.7 22.3 + - + +
403B ILE* 2.9 32.1 + - + +
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Residues in contact with LYS 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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396B GLU 3.4 14.1 - - - +
397B LYS* 3.7 9.4 - - + +
398B PHE 3.2 0.2 - - - -
399B ILE* 1.3 85.6 - - - +
401B ALA* 1.3 61.3 + - - +
403B ILE* 3.2 23.1 + - - +
404B GLY* 3.6 4.2 + - - -
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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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289B ILE* 3.3 23.4 - - + +
397B LYS* 3.4 13.9 + - + +
398B PHE* 3.2 8.9 + - - +
399B ILE 3.1 0.4 - - - -
400B LYS* 1.3 76.8 - - - +
402B ALA* 1.3 64.7 + - - +
404B GLY* 2.9 12.9 + - - +
405B CYS* 3.3 10.0 + - - -
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Residues in contact with ALA 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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289B ILE* 3.2 16.3 - - + +
301B LEU* 4.3 16.6 - - + -
333B ILE* 4.8 10.8 - - + -
398B PHE* 2.9 18.7 + - + +
399B ILE* 2.7 26.1 + - + +
401B ALA* 1.3 73.1 - - - +
403B ILE* 1.3 59.7 + - + -
404B GLY 3.1 1.2 + - - -
405B CYS* 3.2 21.1 - - - -
407B ILE* 3.3 8.3 - - - +
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Residues in contact with ILE 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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336B LYS 4.6 6.1 - - - +
337B LEU* 5.6 2.2 - - + +
340B VAL* 3.9 43.3 - - + -
399B ILE* 2.9 39.9 + - + +
400B LYS* 3.4 13.9 - - - +
402B ALA* 1.3 76.4 - - + +
404B GLY* 1.3 58.3 + - - +
405B CYS 3.7 0.2 - - - -
407B ILE* 4.1 4.4 - - - +
408B VAL* 3.3 30.4 - - + +
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Residues in contact with GLY 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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400B LYS 3.6 4.5 + - - -
401B ALA* 2.9 9.7 + - - -
403B ILE* 1.3 77.7 - - - +
405B CYS* 1.3 67.7 + - - +
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Residues in contact with CYS 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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287B LYS* 4.7 21.3 - - + +
289B ILE* 3.6 27.6 - - + -
301B LEU* 5.1 11.0 - - - -
302B THR* 5.3 2.0 - - - -
303B MET 5.2 10.3 - - - +
401B ALA 3.3 4.6 + - - +
402B ALA* 3.2 22.9 - - - -
403B ILE 4.3 0.9 - - - +
404B GLY* 1.3 83.5 - - - +
406B GLY* 1.3 57.7 + - - +
407B ILE* 2.5 38.2 + - - +
408B VAL* 4.3 1.4 + - - +
409B GLU* 5.0 4.7 + - - +
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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