Contacts of the helix formed by residues 386 - 399 (chain B) in PDB entry 3N2Z
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 386 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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384B SER* 3.4 11.7 + - - +
385B TRP* 1.3 78.5 - - - +
387B LEU* 1.3 60.8 + - - +
388B LYS* 3.3 12.3 + - - +
389B GLU* 3.0 50.0 + - + +
390B LEU* 3.2 22.6 + - - +
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Residues in contact with LEU 387 (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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368B VAL* 4.4 3.4 - - + -
385B TRP* 3.9 35.7 + - + +
386B ASN* 1.3 68.9 + - - +
388B LYS* 1.4 55.3 + - - +
390B LEU* 3.2 19.1 + - + +
391B SER* 2.8 38.4 + - - -
402B PRO* 4.5 10.5 - - + -
404B PRO* 3.8 38.1 - - + -
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Residues in contact with LYS 388 (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 ASN* 3.3 9.3 + - - +
387B LEU* 1.4 76.3 - - - +
389B GLU* 1.3 63.1 + - - +
391B SER* 3.3 8.5 + - - -
392B ASP* 2.8 63.7 + - - +
401B ARG* 5.3 0.8 - - - +
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Residues in contact with GLU 389 (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 ASN* 3.0 39.5 + - - +
388B LYS* 1.3 74.7 - - - +
390B LEU* 1.4 60.1 + - - +
392B ASP* 3.2 9.8 + - - +
393B ASP* 2.9 46.0 + - - +
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Residues in contact with LEU 390 (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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363B ALA 4.8 6.3 - - - +
368B VAL* 3.9 26.5 - - + -
385B TRP* 3.9 24.9 - - + -
386B ASN 3.2 14.6 + - - +
387B LEU* 3.2 12.3 + - + +
389B GLU* 1.4 74.3 - - - +
391B SER* 1.4 60.2 + - - +
393B ASP* 3.3 11.7 + - - +
394B CYS* 3.1 37.4 + - - -
402B PRO* 4.0 18.4 - - + -
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Residues in contact with SER 391 (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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387B LEU* 2.8 23.3 + - - -
388B LYS* 3.4 10.5 - - - -
390B LEU* 1.4 73.1 - - - +
392B ASP* 1.4 56.9 + - - +
394B CYS* 3.3 4.5 + - - +
395B PHE* 3.0 27.0 + - - +
401B ARG* 3.5 32.9 + - - +
402B PRO* 3.6 23.7 + - - +
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Residues in contact with ASP 392 (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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388B LYS* 2.8 49.5 + - - +
389B GLU* 3.2 8.7 + - - +
391B SER* 1.4 71.3 - - - +
393B ASP* 1.4 61.4 + - - +
395B PHE* 3.5 5.4 + - - +
396B GLN* 3.0 32.1 + - - +
401B ARG* 3.0 29.3 + - - +
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Residues in contact with ASP 393 (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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364B CYS* 5.3 0.2 - - - -
389B GLU* 2.9 41.6 + - - +
390B LEU* 3.3 8.6 + - - +
392B ASP* 1.4 77.1 - - - +
394B CYS* 1.4 59.3 + - - +
396B GLN* 3.3 7.4 + - - +
397B GLN* 3.0 30.8 + - - +
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Residues in contact with CYS 394 (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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363B ALA 4.9 0.2 - - - -
364B CYS* 2.0 62.1 - - + -
390B LEU* 3.1 30.8 + - - +
391B SER 3.4 9.0 - - - +
392B ASP 3.3 0.2 - - - -
393B ASP* 1.4 73.9 - - - +
395B PHE* 1.4 55.7 + - - +
397B GLN 3.5 0.2 + - - -
398B TRP* 2.8 36.9 + - - +
399B GLY 3.5 2.8 + - - -
400B VAL 3.4 11.8 - - - +
402B PRO* 3.9 10.5 - - + -
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Residues in contact with PHE 395 (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 SER 3.0 13.8 + - - +
392B ASP 3.7 4.5 - - - +
393B ASP 3.4 0.2 - - - -
394B CYS* 1.4 74.7 - - - +
396B GLN* 1.3 69.5 + - - +
399B GLY* 2.8 49.5 + - - +
400B VAL* 3.2 9.5 + - - +
401B ARG* 3.2 51.6 - - + +
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Residues in contact with GLN 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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392B ASP* 3.0 19.6 + - - +
393B ASP* 3.6 8.7 - - - +
394B CYS 3.3 0.4 - - - -
395B PHE* 1.3 88.7 + - - +
397B GLN* 1.4 61.1 + - - +
399B GLY 4.8 0.2 + - - -
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Residues in contact with GLN 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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357B LEU* 5.0 8.5 - - - +
360B SER* 3.4 19.8 + - - -
364B CYS* 5.5 1.2 - - - -
393B ASP 3.0 16.4 + - - +
394B CYS* 5.1 0.2 - - - -
396B GLN* 1.4 77.3 - - - +
398B TRP* 1.3 95.8 + - + +
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Residues in contact with TRP 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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136B PHE* 4.4 13.2 - + + -
138B ASP 6.3 0.7 - - - -
139B SER* 3.5 24.4 + - - -
142B LEU* 3.6 31.2 - - + -
357B LEU* 3.3 52.0 - - + -
360B SER* 3.4 24.5 + - - -
361B TYR* 3.8 21.0 - + + +
364B CYS* 3.8 28.9 - - + -
394B CYS 2.8 16.7 + - - +
396B GLN 5.2 0.2 - - - -
397B GLN* 1.3 106.9 + - + +
399B GLY* 1.3 61.0 + - - +
400B VAL* 3.7 15.0 - - + +
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Residues in contact with GLY 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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139B SER* 4.0 7.9 + - - -
394B CYS 3.5 0.6 + - - -
395B PHE* 2.8 49.8 + - - -
396B GLN 4.8 0.2 + - - -
398B TRP* 1.3 74.2 - - - +
400B VAL* 1.4 63.5 + - - +
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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