Contacts of the helix formed by residues 395 - 405 (chain B) in PDB entry 2EZT
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 395 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B VAL* 1.3 75.3 - - - +
396B ASP* 1.3 67.2 + - - -
397B ILE* 3.0 4.5 + - - +
398B ASN* 3.0 21.8 + - - +
479B TRP* 3.6 28.8 - - - -
1614B TDM 3.7 19.3 - - - -
1615B FAD 4.5 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 396 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B ARG* 4.9 0.3 + - - -
395B GLY* 1.3 70.3 - - - -
397B ILE* 1.3 57.9 + - - +
399B LEU* 3.0 6.6 + - - +
400B ASN* 2.8 41.9 + - - +
474B ASN* 4.3 5.9 + - - +
478B GLY* 3.9 14.4 - - - -
479B TRP* 3.2 33.7 + - - -
482B ASP* 4.2 7.4 - - - +
547B ASP 5.3 1.0 - - - +
549B PRO* 4.2 23.8 - - + +
1614B TDM 2.8 32.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 397 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B LEU* 4.2 15.5 - - + -
392B ILE* 3.9 8.1 - - + -
393B ASP* 3.6 31.2 - - - +
394B VAL 4.0 3.4 - - - +
395B GLY* 3.0 6.8 + - - +
396B ASP* 1.3 77.9 - - - +
398B ASN* 1.3 57.5 + - - +
400B ASN* 4.4 3.8 - - + +
401B ALA* 2.7 42.2 + - + +
444B LEU* 3.7 34.1 - - + +
445B ALA 4.3 0.9 - - - +
446B GLY* 4.4 17.0 - - - +
472B PHE* 3.6 39.3 - - + -
1614B TDM 4.2 3.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 398 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B TYR* 2.9 38.3 + - + +
265B VAL* 3.5 20.9 - - + +
392B ILE* 3.6 3.5 - - - +
393B ASP 3.0 18.8 + - - -
394B VAL* 3.2 8.0 - - - -
395B GLY 3.0 32.6 + - - +
397B ILE* 1.3 75.6 - - - +
399B LEU* 1.3 59.8 + - - +
401B ALA* 4.2 0.4 - - - -
402B ASN* 3.0 32.6 + - - +
415B THR* 3.4 12.7 + - - +
1615B FAD 3.6 15.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 399 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B ARG* 3.6 28.3 - - + +
265B VAL* 3.9 11.9 - - + +
266B ALA 5.0 0.4 - - - +
395B GLY 4.0 0.4 + - - -
396B ASP* 3.0 8.6 + - - +
398B ASN* 1.3 79.3 - - - +
400B ASN* 1.3 79.3 + - - +
402B ASN* 3.6 2.1 + - - +
403B ARG* 3.2 59.7 + - - +
479B TRP* 3.6 28.0 - - + -
549B PRO* 3.8 24.0 - - + +
550B LEU 4.4 4.7 - - - +
551B PRO* 5.7 2.7 - - + -
553B GLU* 5.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 400 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B ALA* 3.5 26.2 - - + +
374B TYR* 3.9 20.2 - - - -
377B LEU* 3.4 20.6 - - + -
396B ASP* 2.8 38.0 + - - +
397B ILE* 4.2 6.2 - - + +
399B LEU* 1.3 84.9 - - - +
401B ALA* 1.3 58.5 + - - +
403B ARG* 3.2 2.9 + - - -
404B HIS* 2.8 41.9 + - + +
472B PHE* 5.9 0.4 - - - -
544B ILE* 5.9 0.4 - - - +
549B PRO* 3.9 10.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 401 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B TYR* 5.3 1.1 - - + +
248B LYS* 3.5 2.4 - - - -
377B LEU* 3.9 6.8 - - - +
392B ILE* 4.0 18.2 - - + -
397B ILE* 2.7 33.8 + - + +
398B ASN* 4.2 1.6 - - - +
400B ASN* 1.3 69.9 - - - +
402B ASN* 1.3 65.9 + - - +
405B LEU* 2.9 55.1 + - + +
444B LEU* 4.5 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 402 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B TYR* 3.4 24.9 - - + +
248B LYS* 2.6 53.6 + - - +
258B TYR* 4.9 1.7 + - - -
261B SER* 2.9 28.2 + - - -
265B VAL* 3.5 16.1 + - + -
266B ALA 3.6 4.9 + - - +
267B GLN* 3.5 23.7 + - - +
398B ASN 3.0 21.4 + - - +
399B LEU 3.6 4.0 - - - +
401B ALA* 1.3 75.8 - - - +
403B ARG* 1.3 58.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 403 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B LYS* 4.7 0.9 + - - -
264B ARG 4.1 2.0 + - - -
266B ALA 3.0 28.4 + - - +
267B GLN* 4.1 13.0 + - + +
356B TRP* 3.7 28.8 - - + -
359B TYR* 5.5 1.2 - - - -
360B LEU* 3.7 33.3 - - + +
364B GLU* 5.1 0.5 - - - +
374B TYR* 6.3 0.4 - - - -
399B LEU* 3.2 44.3 + - - +
400B ASN* 3.2 5.5 + - - +
401B ALA 3.2 0.6 - - - -
402B ASN* 1.3 81.0 - - + +
404B HIS* 1.3 69.5 + - + +
405B LEU 4.4 2.4 - - - +
549B PRO* 4.4 1.6 - - - +
550B LEU* 2.8 48.1 + - - +
552B ALA* 3.7 19.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 404 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B LEU* 3.9 33.0 - - + +
363B LEU* 4.6 1.6 - - + -
364B GLU* 2.7 42.6 + - + +
374B TYR* 3.3 36.4 - + + -
377B LEU* 3.7 32.8 - - + -
381B ASN* 2.9 22.2 + - - +
400B ASN* 2.8 30.6 + - - +
403B ARG* 1.3 84.8 - - + +
405B LEU* 1.3 66.7 + - - +
406B LYS* 3.4 6.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 405 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B LYS* 3.0 29.9 + - - -
253B ASP* 3.3 4.3 - - - +
377B LEU* 4.2 15.5 - - + +
380B VAL* 4.1 13.2 - - + -
381B ASN* 3.7 13.7 - - - +
390B TYR* 3.8 49.1 - - + +
392B ILE* 4.2 8.7 - - + -
401B ALA* 2.9 39.2 + - + +
403B ARG 4.4 1.6 - - - +
404B HIS* 1.3 78.1 - - - +
406B LYS* 1.3 60.6 + - - +
407B LEU* 3.6 14.8 - - + -
444B LEU* 4.1 5.2 - - + -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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