Contacts of the helix formed by residues 351 - 356 (chain E) in PDB entry 2HLO
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 351 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326E TYR* 2.8 24.5 + - - -
345E TYR* 3.5 41.1 - - + +
350E GLY* 1.3 68.7 - - - -
352E ALA* 1.3 57.9 + - - +
354E MET* 3.0 44.2 - - - +
355E ASP* 3.1 34.7 + - + +
439E ASN* 4.2 5.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 352 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350E GLY 2.8 9.1 + - - -
351E ASN* 1.3 71.9 - - - +
353E LEU* 1.3 60.6 + - - +
356E GLY* 3.0 26.3 + - - +
368E THR 4.2 0.3 - - - +
370E HIS* 3.9 4.5 - - - -
409E ALA* 3.8 16.4 - - + +
410E ALA* 4.0 12.3 - - + -
437E TRP* 3.7 25.6 - - + -
439E ASN* 3.0 29.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 353 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310E LEU* 4.7 3.4 - - + -
312E ILE* 4.1 15.3 - - + -
326E TYR* 3.4 36.5 + - + +
340E ILE* 5.0 10.3 - - + -
342E VAL* 4.2 23.6 - - + -
351E ASN 3.4 0.6 - - - -
352E ALA* 1.3 78.0 - - - +
354E MET* 1.3 59.8 + - - +
369E ILE* 3.6 0.2 - - - +
370E HIS* 2.9 55.5 + - + -
371E ASN 3.0 10.4 + - - -
402E TRP* 4.1 19.5 - - + -
410E ALA* 4.4 2.9 - - + -
437E TRP* 4.0 18.6 - - + -
452E MET* 6.3 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 354 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326E TYR* 4.1 9.6 - - + -
342E VAL* 3.7 31.4 - - + +
343E ASN* 3.8 26.5 - - + -
344E LYS 4.6 2.2 - - - +
345E TYR* 4.2 7.0 - - - -
351E ASN* 3.0 30.6 - - - +
353E LEU* 1.3 78.5 - - - +
355E ASP* 1.3 69.7 + - - +
356E GLY 3.8 0.4 - - - -
369E ILE* 3.4 26.1 - - - +
371E ASN* 4.4 15.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 355 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351E ASN* 3.1 28.5 + - + +
354E MET* 1.3 90.9 - - - +
356E GLY* 1.3 61.1 + - - +
365E ARG* 3.0 28.5 - - - +
369E ILE* 3.9 10.1 - - - +
439E ASN* 5.6 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 356 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352E ALA 3.0 18.2 + - - -
354E MET 3.8 0.8 - - - -
355E ASP* 1.3 83.8 - - - +
357E ALA* 1.3 65.0 + - - -
358E SER* 3.2 1.7 + - - -
365E ARG* 3.8 4.9 - - - +
368E THR* 3.2 21.1 - - - -
369E ILE* 4.0 2.0 - - - +
409E ALA* 3.8 8.1 - - - -
439E ASN* 3.0 19.5 - - - +
----------------------------------------------------------
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