Contacts of the helix formed by residues 342 - 352 (chain E) in PDB entry 2NYM
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 342 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299E GLU* 3.4 37.7 + - - +
303E ASP* 3.7 19.0 + - - +
338E TYR 5.1 0.4 - - - +
339E TYR* 3.2 18.2 + - - +
340E TRP 3.3 2.0 + - - -
341E ASN* 1.3 75.5 - - - +
343E GLU* 1.3 68.4 + - - +
344E TYR* 2.8 14.9 + - - +
345E ILE* 3.1 34.3 + - + +
346E MSE 2.8 23.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 343 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341E ASN 3.6 5.4 + - - +
342E ASN* 1.3 71.9 + - - +
344E TYR* 1.3 57.2 + - - +
346E MSE 3.8 5.2 - - - +
347E SER* 3.0 25.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 344 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302E LEU 4.3 10.3 - - - -
303E ASP* 4.3 22.0 - - - +
304E VAL 5.8 0.4 - - - -
305E ILE 2.9 24.0 + - - -
306E GLU* 5.9 0.2 - - - -
307E PRO* 3.7 19.5 - - + +
342E ASN* 2.8 13.0 + - - +
343E GLU* 1.3 73.8 - - - +
345E ILE* 1.3 67.4 + - + +
346E MSE 3.1 1.8 - - - -
347E SER* 2.9 10.0 + - - -
348E LEU* 2.9 53.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 345 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299E GLU* 4.0 7.2 - - + +
302E LEU* 3.5 47.3 - - + +
303E ASP* 4.9 0.7 - - - +
310E PHE* 5.6 1.8 - - + -
318E PHE* 4.3 11.0 - - + -
339E TYR* 3.5 31.6 - - + +
342E ASN* 3.0 38.7 + - + +
344E TYR* 1.3 77.7 - - + +
346E MSE 1.3 64.5 + - + +
348E LEU* 3.1 7.8 + - + +
349E ILE* 2.9 39.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 346 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339E TYR* 3.7 8.1 - - + +
340E TRP* 3.4 69.5 - - + +
341E ASN 5.1 0.2 - - - -
342E ASN 2.8 19.6 + - - +
343E GLU* 3.8 5.2 - - - +
345E ILE* 1.3 77.0 - - + +
347E SER* 1.3 63.5 + - - +
349E ILE* 3.2 36.9 + - + +
350E SER* 2.9 24.4 + - - -
386E LEU* 4.9 14.1 - - + +
387E PHE* 4.6 7.2 - - - -
390E MSE 4.5 12.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 347 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343E GLU 3.0 16.5 + - - -
344E TYR* 2.9 19.7 + - - -
346E MSE 1.3 78.2 - - - +
348E LEU* 1.3 62.4 + - - +
350E SER* 3.4 7.5 - - - -
351E ASP* 3.3 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 348 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302E LEU* 4.7 3.4 - - + +
305E ILE* 3.3 21.5 - - + -
307E PRO* 4.3 21.5 - - + -
310E PHE* 3.2 50.7 - - + -
344E TYR* 2.9 42.9 + - + +
345E ILE* 3.5 9.6 - - - +
346E MSE 3.1 0.2 - - - -
347E SER* 1.3 76.2 - - - +
349E ILE* 1.3 69.8 + - - +
350E SER 2.8 2.8 + - - -
351E ASP* 3.0 19.4 + - + +
352E ASN* 3.3 13.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 349 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310E PHE* 4.4 0.6 - - + -
318E PHE* 3.3 40.8 - - + -
339E TYR* 6.4 0.2 - - + -
340E TRP* 5.0 1.1 - - + -
345E ILE* 2.9 15.0 + - + +
346E MSE 3.2 39.2 + - + +
348E LEU* 1.3 74.8 - - - +
350E SER* 1.3 52.1 + - - +
352E ASN 3.0 5.5 - - - -
353E ALA* 2.7 32.3 + - - -
356E ILE* 3.3 36.3 - - + -
387E PHE* 4.2 10.1 - - + -
390E MSE 4.0 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 350 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346E MSE 2.9 12.5 + - - -
347E SER* 3.4 13.7 - - - -
348E LEU 2.8 0.8 + - - -
349E ILE* 1.3 71.5 - - - +
351E ASP* 1.3 56.9 + - - -
352E ASN 2.4 17.4 + - - -
353E ALA* 2.6 19.6 + - - +
390E MSE 3.9 33.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 351 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347E SER* 3.3 21.0 + - - +
348E LEU* 3.0 13.6 + - + +
350E SER* 1.3 78.5 + - - +
352E ASN* 1.3 70.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 352 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310E PHE* 3.9 19.2 - - + -
311E VAL* 4.3 15.9 - - - +
314E MSE 3.7 33.5 - - - +
348E LEU* 3.3 7.0 + - - +
349E ILE 3.0 7.9 + - - +
350E SER 2.4 16.2 + - - -
351E ASP* 1.3 80.8 - - - +
353E ALA* 1.3 64.6 + - - +
354E ALA* 3.1 6.9 + - - -
355E LYS* 3.3 11.7 + - + +
356E ILE* 3.3 12.7 + - + +
----------------------------------------------------------
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