Contacts of the helix formed by residues 287 - 292 (chain E) in PDB entry 1FMO
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 GLY 287 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282E GLY* 3.9 23.2 + - - -
284E LEU 3.1 16.4 + - - -
285E LYS 2.9 8.1 - - - -
286E ASN* 1.3 76.0 - - - +
288E VAL* 1.3 64.5 + - - +
290E ASP* 3.1 20.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 288 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151E VAL* 4.4 10.8 - - + +
155E GLU* 3.6 44.0 - - + +
158E HIS* 5.8 2.0 - - + -
221E TRP* 3.8 28.3 - - + +
282E GLY* 4.4 6.5 + - - +
286E ASN 3.3 0.6 + - - -
287E GLY* 1.3 69.8 - - - -
289E ASN* 1.3 56.7 + - - +
290E ASP 2.6 13.3 + - - -
291E ILE* 2.6 29.9 + - + +
292E LYS* 3.3 22.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 289 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155E GLU* 4.5 6.1 + - - +
286E ASN* 3.1 35.9 + - - +
288E VAL* 1.3 74.9 - - - +
290E ASP* 1.3 58.9 + - - +
291E ILE 3.2 0.2 - - - -
292E LYS* 4.1 24.0 + - + +
293E ASN* 3.0 39.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 290 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281E PHE* 3.4 41.8 - - + -
282E GLY 4.8 2.4 + - - +
284E LEU* 3.6 34.2 - - - +
286E ASN* 3.3 27.3 + - - +
287E GLY 3.1 11.7 + - - +
288E VAL 2.6 7.5 + - - -
289E ASN* 1.3 77.9 - - - +
291E ILE* 1.3 60.1 + - - +
293E ASN* 4.1 2.5 - - - +
294E HIS* 3.6 12.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 291 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151E VAL* 3.9 31.4 - - + -
221E TRP* 3.3 42.8 - - + -
224E LEU* 4.7 3.8 - - + -
268E LEU* 4.8 4.7 - - + -
272E LEU* 4.0 18.8 - - + -
281E PHE* 4.0 22.2 - - + -
282E GLY* 4.1 15.3 - - - +
288E VAL* 2.6 9.8 + - - +
290E ASP* 1.3 74.6 - - - +
292E LYS* 1.3 61.3 + - - +
293E ASN 3.1 1.3 - - - -
294E HIS* 2.9 28.1 + - - +
297E PHE* 3.6 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 292 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E VAL* 4.9 12.1 - - - +
151E VAL* 3.8 5.6 - - + -
152E LEU* 3.6 28.6 - - - +
155E GLU* 3.5 28.7 + - - +
288E VAL* 3.3 27.5 + - + +
289E ASN* 4.2 16.1 + - - +
291E ILE* 1.3 79.1 - - - +
293E ASN* 1.3 61.8 + - - +
294E HIS 3.3 1.1 + - - -
297E PHE* 3.7 8.7 - - - +
302E TRP* 3.2 67.7 + - + +
----------------------------------------------------------
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