Contacts of the helix formed by residues 235 - 244 (chain E) in PDB entry 1NBF
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 235 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231E THR* 2.6 24.8 + - - +
232E LEU* 3.1 18.1 - - - +
233E PHE 3.0 1.4 - - - -
234E PHE* 1.3 75.6 - - - +
236E ASN* 1.3 49.3 + - - +
237E GLN 3.1 1.7 + - - -
238E LEU* 2.7 49.0 + - + +
239E ARG 3.5 1.1 + - - -
323E LEU* 4.9 2.9 - - + -
324E PHE* 3.9 25.2 - - + -
401E VAL* 5.0 6.8 - - + +
403E HIS* 5.7 1.0 + - - -
451E HIS* 5.0 6.7 - - - -
517E VAL* 5.6 1.6 - - - +
519E ILE* 5.9 1.9 - - + +
527E VAL* 4.1 24.5 - - + -
528E LEU* 5.4 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 236 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233E PHE 3.7 1.5 + - - -
234E PHE* 2.6 26.4 - - - +
235E THR* 1.3 70.8 - - - +
237E GLN* 1.3 56.2 + - - +
239E ARG* 2.7 46.8 + - - +
240E LYS* 2.8 19.0 + - - +
471E PRO 5.3 0.9 - - - +
527E VAL 3.4 10.1 + - - +
528E LEU* 4.3 7.2 + - - +
529E GLN 2.5 37.3 + - - +
530E ALA* 4.5 1.4 - - - +
531E VAL* 3.7 11.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 237 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235E THR 3.1 1.4 + - - +
236E ASN* 1.3 75.3 - - - +
238E LEU* 1.3 58.4 + - - +
240E LYS* 3.9 4.0 + - - +
241E ALA* 3.3 21.5 + - - +
319E THR* 4.7 13.7 - - + +
322E LYS* 3.7 25.8 + - - +
323E LEU* 3.1 37.9 - - + +
526E GLU* 3.3 50.6 + - - +
527E VAL* 3.1 12.3 + - - +
529E GLN* 3.7 20.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 238 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232E LEU* 4.4 17.5 - - + +
235E THR* 2.7 32.0 + - + +
237E GLN* 1.3 72.8 - - - +
239E ARG* 1.3 56.7 + - - +
241E ALA* 3.4 7.3 + - + +
242E VAL* 2.9 41.9 + - + +
264E PHE* 5.7 2.2 - - + -
304E LEU* 3.9 23.6 - - + -
307E VAL* 4.8 4.3 - - + -
319E THR* 3.7 21.3 - - - +
320E ILE* 3.8 21.8 - - + -
323E LEU* 4.3 7.5 - - + +
324E PHE* 3.9 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 239 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232E LEU 4.8 1.5 + - - +
233E PHE* 3.0 58.1 + - - +
234E PHE* 4.5 4.8 - - - +
235E THR 3.5 1.6 + - - +
236E ASN* 2.7 35.2 + - - +
238E LEU* 1.3 70.7 - - - +
240E LYS* 1.3 64.5 + - - +
242E VAL* 3.0 19.4 + - - +
243E TYR* 3.2 30.8 + - + +
264E PHE* 4.0 21.8 - - + -
268E GLN* 3.0 46.8 + - - +
531E VAL* 3.2 23.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 240 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236E ASN 2.8 12.5 + - - +
237E GLN* 4.1 3.8 - - - +
239E ARG* 1.3 75.6 - - - +
241E ALA* 1.3 62.3 + - - +
243E TYR* 3.3 20.3 + - - +
244E MET* 3.2 20.2 + - - +
529E GLN* 2.5 40.9 + - + +
530E ALA 4.8 4.6 + - - -
531E VAL* 3.4 39.0 - - + +
535E ASP* 3.3 36.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 241 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237E GLN 3.3 18.5 + - - +
238E LEU* 3.4 8.3 - - + +
239E ARG 3.1 0.4 - - - -
240E LYS* 1.3 80.4 - - - +
242E VAL* 1.3 60.9 + - - +
244E MET* 3.2 17.9 + - - +
245E MET* 3.8 1.7 - - - +
311E MET* 2.9 20.9 - - + +
316E VAL* 3.2 31.4 - - + +
319E THR* 3.2 16.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 242 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238E LEU* 2.9 34.1 + - + +
239E ARG 3.0 8.9 + - - +
241E ALA* 1.3 76.4 - - - +
243E TYR* 1.3 60.5 + - + +
245E MET* 2.9 41.2 - - + +
260E LEU* 4.5 10.1 - - + -
261E GLN* 2.8 34.4 + - + +
264E PHE* 3.4 39.9 - - + -
307E VAL* 4.5 12.3 - - + -
311E MET* 4.4 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 243 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239E ARG* 3.2 25.0 + - - -
240E LYS* 3.3 7.6 + - - +
242E VAL* 1.3 78.0 - - + +
244E MET* 1.3 56.9 + - - +
245E MET 3.1 3.9 + - - +
261E GLN* 2.8 31.1 + - + +
264E PHE* 2.8 42.3 + - + +
265E TYR* 3.6 13.4 + - + -
268E GLN* 2.6 35.0 + - - -
531E VAL* 4.6 3.1 - - + -
535E ASP* 3.4 22.9 - - + +
536E ILE* 3.3 37.0 - - + -
537E PRO* 3.1 29.8 - - + +
540E LEU* 4.9 2.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 244 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240E LYS 3.2 15.9 - - - +
241E ALA* 3.4 15.0 - - - +
242E VAL 3.1 1.4 - - - -
243E TYR* 1.3 74.9 - - - +
245E MET* 1.3 58.4 + - - +
246E PRO* 3.5 9.5 - - - +
314E THR* 4.9 2.9 + - - -
315E CYS* 5.0 17.3 - - - -
316E VAL* 4.0 23.6 - - + +
535E ASP* 3.6 17.5 - - - +
536E ILE 4.8 0.2 - - - -
537E PRO* 3.2 45.8 - - + -
----------------------------------------------------------
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