Contacts of the helix formed by residues 336 - 348 (chain E) in PDB entry 6V3O
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 336 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335E CYS* 1.3 78.9 - - - +
337E ASP* 1.3 61.1 + - - +
338E GLU* 3.6 17.0 + - - +
339E LEU 3.6 15.7 - - - +
340E ARG* 3.1 26.5 + - - +
418E LEU* 4.7 3.8 + - - +
421E LYS* 4.0 5.1 - - - +
422E SER* 2.9 38.6 + - - +
425E ASP* 2.8 40.6 + - - +
426E CYS* 4.1 1.6 - - - -
931F ASP* 5.9 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 337 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336E ASN* 1.3 72.7 + - - +
338E GLU* 1.3 67.0 + - - +
340E ARG* 3.1 17.6 + - - +
341E VAL* 2.9 44.3 + - - +
931F ASP* 5.9 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 338 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336E ASN* 3.3 12.4 + - + +
337E ASP* 1.3 79.4 + - - +
339E LEU* 1.3 61.1 + - - +
341E VAL* 3.2 26.6 - - + +
342E ARG* 3.3 9.1 + - + +
418E LEU* 3.7 27.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 339 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335E CYS* 4.2 2.2 - - - -
336E ASN* 3.6 18.9 - - + +
337E ASP 3.3 0.2 - - - -
338E GLU* 1.3 78.6 - - - +
340E ARG* 1.3 58.3 + - - +
342E ARG* 3.2 1.9 + - - +
343E ALA* 2.8 28.1 + - + +
370E PRO* 3.5 33.7 - - + -
371E TYR* 3.4 35.9 - - + -
374E ILE* 3.9 22.9 - - + -
418E LEU* 4.0 18.0 - - + +
419E CYS* 4.0 17.3 - - - +
422E SER* 3.6 15.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 340 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335E CYS* 3.8 14.3 - - - -
336E ASN 3.1 20.5 + - - +
337E ASP* 3.1 21.1 + - - +
339E LEU* 1.3 77.7 - - - +
341E VAL* 1.3 72.8 + - - +
343E ALA* 3.3 5.1 + - + +
344E GLU* 3.1 49.7 + - + +
370E PRO* 5.6 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 341 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337E ASP* 2.9 32.4 + - - +
338E GLU* 3.2 19.7 - - + +
340E ARG* 1.3 88.2 - - - +
342E ARG* 1.3 66.3 + - + +
344E GLU* 3.8 2.8 + - - +
345E GLU* 3.2 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 342 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338E GLU 3.3 9.4 + - - +
339E LEU 3.2 7.4 + - - +
340E ARG 3.2 0.8 - - - -
341E VAL* 1.3 82.7 - - + +
343E ALA* 1.3 65.4 + - - +
345E GLU* 3.2 33.1 + - - +
346E LEU* 3.0 48.2 + - - +
374E ILE* 3.5 20.0 - - + +
377E HIS* 3.6 31.7 + - - -
415E PRO* 6.2 2.8 - - - +
418E LEU* 4.5 16.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 343 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339E LEU* 2.8 33.9 + - + +
340E ARG* 3.3 5.6 + - + +
342E ARG* 1.3 73.2 - - - +
344E GLU* 1.3 64.4 + - + +
346E LEU 3.2 2.4 + - - -
347E HIS* 3.1 17.2 + - - +
367E PRO* 5.3 5.3 - - + +
370E PRO* 4.2 24.0 - - + +
373E VAL* 3.5 20.3 - - + +
374E ILE* 4.0 8.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 344 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340E ARG* 3.1 40.1 + - + +
341E VAL* 4.5 2.5 - - - +
343E ALA* 1.3 75.5 - - + +
345E GLU* 1.3 66.5 + - - +
347E HIS* 3.1 26.1 + - - +
348E SER* 3.5 4.7 + - - -
367E PRO* 4.3 25.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 345 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341E VAL* 3.2 17.8 + - - +
342E ARG* 3.4 36.0 + - - +
344E GLU* 1.3 76.1 - - - +
346E LEU* 1.3 58.0 + - + +
348E SER* 2.2 41.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 346 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342E ARG* 3.0 45.4 + - - +
343E ALA 3.2 6.9 + - - +
345E GLU* 1.3 76.8 - - + +
347E HIS* 1.3 60.7 + - - +
348E SER 3.3 10.0 + - - +
350E SER* 4.2 17.3 + - - +
373E VAL* 4.0 17.7 - - + +
374E ILE* 3.6 31.2 - - + -
377E HIS* 3.8 42.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 347 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343E ALA 3.1 9.0 + - - +
344E GLU* 3.1 26.3 + - - +
346E LEU* 1.3 76.0 - - - +
348E SER* 1.3 58.6 + - - +
349E SER 3.6 3.8 + - - -
350E SER* 4.7 3.6 + - - +
364E GLN* 5.9 6.0 - - + +
365E ILE 4.3 12.2 + - - -
367E PRO* 3.5 40.7 - - + +
373E VAL* 4.8 5.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 348 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344E GLU 3.5 4.2 + - - -
345E GLU* 2.2 38.0 + - - +
346E LEU* 3.4 7.8 - - - +
347E HIS* 1.3 78.5 - - - +
349E SER* 1.3 74.2 + - - +
350E SER 3.7 0.2 - - - -
----------------------------------------------------------
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