Contacts of the helix formed by residues 315 - 321 (chain B) in PDB entry 5DO7
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 SER 315 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A GLU* 4.8 0.2 - - - +
104B ILE* 4.2 9.6 - - - +
270B HIS 6.1 0.2 - - - -
271B GLN* 5.2 2.0 - - - -
272B PRO* 3.9 26.3 - - - +
273B ARG 4.8 2.3 + - - -
285B LEU* 5.1 0.9 - - - -
313B ARG* 3.4 35.0 + - - +
314B TYR* 1.3 78.5 - - - +
316B ASN* 1.3 54.7 + - - +
317B PRO* 3.3 3.4 - - - -
318B ALA* 2.8 41.7 + - - +
319B ASP* 3.3 3.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 316 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A SER* 4.3 9.6 + - - +
255A GLU* 4.4 17.4 - - - +
310B PRO* 3.2 28.9 - - + +
312B PRO* 4.2 16.2 - - - +
313B ARG* 3.8 19.5 + - - +
315B SER* 1.3 73.7 - - - +
317B PRO* 1.3 63.4 - - + +
319B ASP* 2.8 28.0 + - - +
320B PHE* 2.8 45.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 317 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B LEU* 4.8 3.1 - - + +
292B ILE* 5.4 0.3 - - - +
304B PHE* 4.1 10.3 - - + -
309B TYR* 2.4 60.1 - - + +
310B PRO* 5.1 0.9 - - + -
313B ARG 4.1 2.5 - - - +
314B TYR 3.2 17.7 - - - +
315B SER 3.3 1.3 - - - -
316B ASN* 1.3 93.8 - - + +
318B ALA* 1.3 54.0 + - - +
320B PHE* 3.1 16.3 + - + +
321B TYR* 2.8 38.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 318 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A ARG* 6.2 1.6 - - - +
104B ILE 5.2 3.4 - - - +
106B SER* 6.2 5.4 - - - +
285B LEU* 3.6 39.5 - - + +
286B MET 6.1 0.4 - - - +
287B THR* 3.4 9.8 + - - +
315B SER* 2.8 24.6 + - - +
317B PRO* 1.3 72.9 - - - +
319B ASP* 1.3 55.3 + - - +
321B TYR* 2.9 25.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 319 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A ASN* 5.8 1.5 + - - -
253A ARG* 3.9 15.8 + - - +
255A GLU* 3.2 45.5 - - - +
315B SER 3.3 1.4 + - - +
316B ASN* 2.8 18.0 + - - +
318B ALA* 1.3 75.6 - - - +
320B PHE* 1.3 76.4 + - - +
321B TYR 3.1 8.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 320 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B ILE* 6.2 5.8 - - + -
308B GLY 5.2 9.0 - - - -
309B TYR* 5.7 3.1 - + - -
310B PRO* 4.4 13.5 - - + -
316B ASN* 2.8 50.1 + - - -
317B PRO* 3.1 17.7 + - + +
319B ASP* 1.3 80.3 - - - +
321B TYR* 1.3 70.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 321 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B THR* 3.4 23.9 - - - +
292B ILE* 3.6 50.0 - - + -
304B PHE* 5.1 9.2 - + - -
307B ILE* 3.9 34.9 - - + +
317B PRO* 2.8 17.7 + - + +
318B ALA 2.9 19.7 - - - +
319B ASP 3.6 6.6 - - - +
320B PHE* 1.3 85.5 - - + +
----------------------------------------------------------
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