Contacts of the helix formed by residues 396 - 404 (chain B) in PDB entry 2NUP
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 THR 396 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B PRO* 3.2 2.1 + - - +
395B GLN* 1.3 99.2 - - + +
397B GLN* 1.3 58.9 + - - +
398B ALA* 3.2 11.3 + - - +
399B LEU* 2.8 25.9 + - + +
400B LEU* 2.9 24.6 + - - +
791B VAL* 3.9 9.4 - - - -
794B SER* 4.0 21.5 - - - +
796B THR* 5.7 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 397 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B THR* 1.3 69.0 - - - +
398B ALA* 1.3 67.6 + - - +
400B LEU* 3.4 23.6 - - - +
401B ASN* 2.8 62.0 + - - +
790B SER* 3.1 15.5 - - - -
791B VAL* 2.8 54.4 + - - +
794B SER* 5.4 0.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 398 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B THR* 3.1 10.0 + - - +
397B GLN* 1.3 80.0 - - - +
399B LEU* 1.3 63.2 + - - +
401B ASN* 3.2 8.8 + - - +
402B LYS* 3.1 29.7 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
394B PRO* 4.2 6.5 - - + -
395B GLN* 4.2 2.2 - - + +
396B THR* 2.8 23.4 + - + +
398B ALA* 1.3 76.0 - - - +
400B LEU* 1.3 63.5 + - - +
402B LYS* 3.3 16.0 + - + +
403B ALA* 3.2 20.3 + - - +
828B VAL 3.7 9.2 - - - +
829B SER* 3.3 41.5 - - - +
830B THR 3.8 2.0 - - - +
831B LEU* 3.8 37.0 - - + +
834B VAL* 3.8 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 400 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B LEU* 3.9 12.3 - - + -
394B PRO* 3.8 27.3 - - + +
396B THR 2.9 12.7 + - - +
397B GLN* 3.1 35.4 + - - +
399B LEU* 1.3 77.8 - - - +
401B ASN* 1.3 63.1 + - - +
403B ALA* 3.4 12.9 + - + +
404B LYS* 3.5 8.3 + - - -
405B LEU 3.5 23.1 + - - +
407B LEU* 4.0 31.0 - - + +
789B MET 4.5 2.0 - - - +
790B SER* 4.4 6.5 - - - -
791B VAL* 4.4 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 401 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B GLN* 2.8 53.2 + - - +
398B ALA* 3.6 7.2 - - - +
400B LEU* 1.3 71.9 - - - +
402B LYS* 1.3 67.4 + - + +
404B LYS* 3.2 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 402 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398B ALA* 3.1 19.6 + - + +
399B LEU* 3.3 19.4 + - + +
401B ASN* 1.3 76.3 - - + +
403B ALA* 1.3 64.4 + - - +
404B LYS* 3.2 7.8 + - - +
831B LEU* 4.1 30.6 - - + +
877B ALA* 3.2 22.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 403 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399B LEU 3.2 8.5 + - - +
400B LEU* 3.5 12.8 - - + +
401B ASN 3.2 0.2 - - - -
402B LYS* 1.3 81.4 - - - +
404B LYS* 1.3 68.4 + - - +
405B LEU* 3.2 19.4 + - + +
831B LEU* 3.6 23.0 - - + +
834B VAL* 4.1 22.4 - - + -
835B PHE* 4.1 11.3 - - + -
874B SER* 3.8 9.4 - - - -
877B ALA* 4.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 404 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400B LEU 3.5 3.7 + - - -
401B ASN* 3.2 25.9 + - - +
402B LYS* 3.1 15.8 - - - +
403B ALA* 1.3 78.8 - - - +
405B LEU* 1.3 58.7 + - - +
406B PRO* 4.5 2.0 - - - +
870B ALA* 4.1 9.5 - - - +
873B ASP* 3.2 48.6 - - + +
874B SER* 3.7 11.8 - - - -
877B ALA* 4.0 2.5 - - + -
----------------------------------------------------------
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