Contacts of the helix formed by residues 405 - 410 (chain D) in PDB entry 1EJI
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 THR 405 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331D VAL* 2.8 32.5 + - - +
334D ASN* 4.1 1.6 - - - +
335D CYS* 3.8 28.4 - - - +
338D LEU* 4.5 8.7 - - + -
357D HIS* 3.1 11.0 + - - +
403D LEU 5.8 0.4 - - - -
404D GLY* 1.3 76.9 - - - +
406D PRO* 1.3 71.6 - - - +
407D ALA 3.2 3.2 + - - -
408D LEU* 3.5 3.3 + - - +
409D THR* 2.8 29.8 + - - -
418D PHE* 3.7 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 406 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D ILE 5.7 0.7 - - - +
52D ALA* 4.5 7.4 - - - +
54D GLU 4.4 5.8 - - - +
55D ASN* 3.5 14.1 - - - +
258D THR* 3.8 19.3 - - + +
327D TYR* 2.9 29.9 + - + +
328D GLN* 5.3 0.2 - - - +
331D VAL* 3.8 15.7 - - + -
357D HIS* 3.7 30.5 - - + -
404D GLY* 3.6 4.5 - - - -
405D THR* 1.3 93.9 - - - +
407D ALA* 1.3 67.2 + - - +
409D THR* 4.5 0.7 - - - -
410D SER* 3.0 14.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 407 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D GLU* 3.5 33.9 - - + +
51D ILE 5.0 4.9 - - - +
54D GLU* 3.9 21.0 + - + +
55D ASN* 4.2 12.6 - - - +
56D PHE* 3.7 19.8 - - + -
404D GLY 5.7 0.9 - - - +
405D THR 3.3 1.0 - - - -
406D PRO* 1.3 84.5 - - - +
408D LEU* 1.3 62.6 + - - +
410D SER* 3.1 15.2 + - - -
411D ARG 3.6 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 408 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D GLY 4.6 2.9 - - - +
48D LEU* 3.8 37.9 - - + -
49D GLU* 3.5 23.3 + - + +
50D LEU* 3.8 27.4 - - + -
405D THR 3.5 3.0 + - - +
407D ALA* 1.3 76.9 - - - +
409D THR* 1.3 66.1 + - - +
411D ARG* 2.9 35.9 + - - +
412D GLY 3.5 3.8 + - - -
413D LEU* 3.5 29.3 + - + +
418D PHE* 3.7 22.2 - - + -
421D VAL* 4.6 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 409 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C TRP* 3.6 13.4 - - + -
327D TYR* 3.5 25.1 - - + -
330D GLN* 3.7 12.8 - - + -
331D VAL* 3.6 27.5 - - + +
334D ASN* 2.8 33.5 + - - +
405D THR* 2.8 23.4 + - - -
406D PRO 3.8 0.4 - - - -
408D LEU* 1.3 76.5 - - - +
410D SER* 1.3 59.7 + - - +
412D GLY* 2.9 17.8 + - - -
413D LEU 4.1 4.3 - - - -
418D PHE* 3.8 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 410 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C TRP* 5.3 0.5 - - - -
18C HIS* 4.4 7.4 - - - -
22C LEU* 4.1 10.1 - - - +
55D ASN* 3.2 16.7 + - - -
56D PHE* 4.8 6.1 - - - -
260D ARG* 3.1 17.7 + - - +
327D TYR* 3.0 35.7 + - - -
406D PRO 3.0 4.9 + - - -
407D ALA 3.1 12.5 + - - -
409D THR* 1.3 75.9 - - - +
411D ARG* 1.3 59.1 + - - +
412D GLY 3.4 0.6 + - - -
477D SER* 4.6 1.9 + - - -
479D PRO* 3.9 16.9 - - - +
----------------------------------------------------------
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