Contacts of the helix formed by residues 537 - 551 (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 PRO 537 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243E TYR* 3.1 34.3 - - + +
244E MET* 3.2 26.4 - - + -
245E MET 5.9 0.2 - - - +
248E GLU* 4.9 10.3 - - - +
536E ILE* 1.3 83.4 - - + +
538E GLN* 1.3 60.9 + - - +
539E GLN* 4.5 2.7 - - + +
540E LEU* 3.1 17.0 + - + +
541E VAL* 2.9 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 538 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536E ILE 3.3 6.6 + - - +
537E PRO* 1.3 72.1 - - - +
539E GLN* 1.3 60.8 + - - +
541E VAL* 3.1 33.9 + - - +
542E GLU* 3.0 38.2 + - - +
545E GLN* 5.1 4.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 539 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248E GLU* 2.8 59.5 + - + +
537E PRO* 3.2 3.2 - - + +
538E GLN* 1.3 79.4 - - - +
540E LEU* 1.3 62.5 + - - +
542E GLU* 3.5 4.8 + - - +
543E ARG* 3.4 19.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 540 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243E TYR* 5.0 2.7 - - + +
245E MET 5.8 1.3 - - - +
247E THR* 3.9 20.6 - - - +
248E GLU* 5.1 5.3 + - + +
258E LEU* 4.0 13.7 - - + -
261E GLN* 3.8 35.4 - - + +
265E TYR* 4.5 3.8 - - + -
536E ILE* 4.0 20.9 - - + -
537E PRO* 3.1 18.3 + - + +
539E GLN* 1.3 76.5 - - - +
541E VAL* 1.3 68.9 + - - +
542E GLU 3.2 1.4 + - - -
543E ARG* 3.6 8.2 + - + +
544E LEU* 3.4 42.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 541 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265E TYR* 3.3 36.3 + - + +
269E HIS* 5.7 1.1 - - + +
533E ASP 5.9 0.7 - - - +
536E ILE* 3.4 30.7 - - + +
537E PRO 2.9 26.2 + - - +
538E GLN* 3.1 32.5 + - - +
540E LEU* 1.3 77.6 - - - +
542E GLU* 1.3 56.3 + - - +
544E LEU* 5.3 0.2 - - - -
545E GLN* 2.8 33.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 542 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538E GLN* 3.0 25.4 + - - +
539E GLN* 3.5 5.7 + - - +
540E LEU 3.2 0.2 - - - -
541E VAL* 1.3 78.9 - - - +
543E ARG* 1.3 55.3 + - - +
545E GLN* 3.3 22.0 - - + +
546E GLU* 2.7 35.7 + - + +
549E ARG* 4.7 13.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 543 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247E THR 4.1 14.0 + - - -
248E GLU* 4.7 8.1 + - - +
250E ASP 2.8 32.5 + - - +
252E SER* 3.0 33.0 + - - +
258E LEU* 4.1 19.3 - - + +
539E GLN 3.4 11.9 + - - +
540E LEU* 3.6 12.1 + - + +
542E GLU* 1.3 77.7 - - - +
544E LEU* 1.3 65.4 + - + +
546E GLU* 3.0 28.3 + - - +
547E GLU* 3.0 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 544 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258E LEU* 4.3 17.7 - - + +
261E GLN 4.2 0.7 - - - +
262E ARG* 3.9 46.0 - - + +
265E TYR* 4.0 25.4 - - + -
540E LEU* 3.4 42.8 + - + +
541E VAL 5.0 1.3 - - - +
543E ARG* 1.3 80.3 - - + +
545E GLN* 1.3 61.4 + - - +
547E GLU* 3.5 24.0 + - - +
548E LYS* 3.2 32.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 545 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265E TYR* 4.5 12.6 + - + +
538E GLN* 5.1 3.6 + - - -
541E VAL* 2.8 33.8 + - - +
542E GLU* 3.3 29.0 - - - +
543E ARG 3.1 0.2 - - - -
544E LEU* 1.3 81.2 - - - +
546E GLU* 1.3 59.8 + - - +
548E LYS* 3.4 25.4 - - + +
549E ARG* 3.3 31.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 546 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542E GLU 2.7 20.0 + - - +
543E ARG* 3.0 15.1 + - - +
545E GLN* 1.3 71.3 - - - +
547E GLU* 1.3 61.3 + - - +
548E LYS 3.0 2.2 - - - -
549E ARG* 2.8 48.7 + - + +
550E ILE* 3.2 25.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 547 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252E SER* 3.6 11.1 + - - -
258E LEU* 5.1 1.2 - - - +
262E ARG* 3.8 30.8 + - - +
278E LYS* 4.6 5.2 + - - -
543E ARG* 3.0 47.7 + - + +
544E LEU* 3.8 18.3 - - - +
545E GLN 3.5 0.4 - - - -
546E GLU* 1.3 71.8 - - + +
548E LYS* 1.3 56.3 + - + +
549E ARG 2.8 10.6 + - - -
550E ILE* 3.5 18.2 - - + -
551E GLU* 3.0 37.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 548 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262E ARG* 6.3 0.4 - - - +
265E TYR* 3.8 29.2 - - - -
266E GLU* 3.3 33.1 + - - +
269E HIS* 5.4 2.6 - - - +
270E SER* 5.4 3.4 - - - -
544E LEU* 3.2 19.0 + - - +
545E GLN* 3.4 20.3 - - + +
546E GLU 3.0 1.2 - - - -
547E GLU* 1.3 75.6 - - - +
549E ARG* 1.3 59.2 + - - +
551E GLU* 5.4 0.4 - - - -
552E ALA* 3.1 20.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 549 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542E GLU* 4.3 13.1 + - - +
545E GLN* 3.3 44.8 + - - +
546E GLU* 2.9 39.1 + - + +
547E GLU 2.8 1.6 - - - -
548E LYS* 1.3 83.0 - - - +
550E ILE* 1.3 55.8 + - + +
551E GLU 3.4 4.0 - - - -
552E ALA* 3.6 7.2 - - - +
553E GLN* 3.0 34.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 550 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546E GLU* 3.2 37.0 + - + +
547E GLU* 3.5 20.0 - - + -
549E ARG* 1.3 75.0 - - + +
551E GLU* 1.3 61.2 + - + +
552E ALA 3.5 0.2 - - - -
553E GLN* 3.8 24.7 - - - +
554E LYS 3.4 15.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 551 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262E ARG* 4.5 8.4 + - - +
278E LYS* 3.3 29.1 + - - -
547E GLU* 3.0 22.5 + - + +
548E LYS* 5.4 0.4 - - - -
550E ILE* 1.3 81.1 - - + +
552E ALA* 1.3 62.6 + - - +
553E GLN 2.7 6.1 + - - -
554E LYS* 3.1 29.6 + - - +
----------------------------------------------------------
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