Contacts of the helix formed by residues 294 - 301 (chain B) in PDB entry 1DKF
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 ARG 294 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B ARG* 3.7 12.1 - - - +
277B TYR* 4.0 5.3 + - - -
282B ASP* 2.9 51.6 + - - +
293B ASN* 1.3 74.3 - - - +
295B THR* 1.3 52.5 + - - +
297B MET* 3.1 3.3 + - - +
298B HIS* 2.7 35.6 + - - +
306B THR* 3.6 19.0 - - + +
307B ASP* 3.2 30.5 + - - +
310B PHE* 3.5 42.4 - - + +
314B ASN* 4.6 5.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 295 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B GLU* 4.3 9.9 + - + +
216B GLN* 3.6 39.3 - - - +
217B ARG* 3.7 19.4 + - + +
293B ASN* 3.3 12.8 + - - -
294B ARG* 1.3 78.3 - - - +
296B GLN* 1.3 60.3 + - + +
298B HIS* 3.2 7.8 + - - +
299B ASN* 2.8 35.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 296 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B THR* 5.2 2.7 - - - +
210B THR* 4.4 17.8 + - - -
215B GLU* 6.1 5.8 - - + -
224B LEU* 3.5 20.9 - - + +
291B THR 4.5 2.6 + - - +
292B LEU* 3.6 31.9 - - + +
293B ASN* 2.7 63.3 + - - +
295B THR* 1.3 71.2 - - + +
297B MET* 1.3 55.7 + - - +
299B ASN* 3.3 1.9 + - - -
300B ALA* 2.7 37.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 297 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B PHE* 4.8 4.0 - - + -
273B ILE* 4.7 2.5 - - + -
284B MET* 3.9 17.0 - - + -
286B PHE* 3.9 28.5 - - + -
292B LEU* 3.5 28.3 - - + +
293B ASN 2.7 19.0 + - - +
294B ARG 3.4 7.2 - - - +
296B GLN* 1.3 73.1 - - - +
298B HIS* 1.3 65.6 + - - +
300B ALA* 3.3 11.7 + - + +
301B GLY 3.5 1.2 + - - -
302B PHE* 3.2 64.8 + - + +
310B PHE* 3.7 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 298 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B ARG* 3.3 43.2 + - + +
218B VAL 3.2 26.2 - - - -
219B SER* 4.6 5.8 - - - +
294B ARG 2.7 13.2 + - - +
295B THR 3.2 9.2 - - - +
297B MET* 1.3 78.8 - - - +
299B ASN* 1.3 80.8 + - - +
301B GLY* 3.2 4.7 + - - -
303B GLY* 3.1 55.0 + - - -
304B PRO* 5.3 0.4 - - - +
306B THR* 3.1 20.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 299 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B GLU* 3.7 12.0 - - - +
216B GLN 3.0 18.4 - - - +
217B ARG* 3.7 3.0 - - - +
218B VAL* 3.0 37.7 + - + +
220B LEU* 3.5 7.0 - - - +
221B ASP* 2.8 45.0 + - + +
224B LEU* 4.1 6.0 - - + +
295B THR* 2.8 28.3 + - - +
296B GLN* 3.9 3.8 - - - +
298B HIS* 1.3 95.1 + - - +
300B ALA* 1.3 61.3 + - - +
301B GLY 3.2 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 300 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B LEU* 4.0 1.6 - - - -
224B LEU* 3.9 26.0 - - + +
225B TRP* 3.0 31.8 - - - +
228B PHE* 3.4 26.3 - - + -
292B LEU* 4.5 7.2 - - + -
296B GLN 2.7 22.5 + - - +
297B MET* 3.7 9.0 - - - +
298B HIS 3.2 0.6 - - - -
299B ASN* 1.3 74.6 - - - +
301B GLY* 1.3 57.4 + - - +
302B PHE* 6.2 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 301 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B LEU* 4.0 13.2 - - - -
225B TRP* 4.1 11.4 - - - -
228B PHE* 4.5 3.4 - - - -
298B HIS 3.2 1.1 + - - -
299B ASN 3.2 4.4 - - - -
300B ALA* 1.3 81.6 - - - +
302B PHE* 1.3 58.9 + - - +
303B GLY 3.0 2.9 - - - -
394B ARG* 2.6 36.8 + - - +
398B LEU* 4.3 1.1 - - - +
600B BMS 4.0 10.0 - - - +
----------------------------------------------------------
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