Contacts of the helix formed by residues 243 - 255 (chain D) in PDB entry 1UMD
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 ASP 243 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194D GLY 3.6 15.1 + - - +
195D LYS* 3.4 22.3 + - - +
196D ALA* 2.9 43.5 + - + +
236D LEU* 5.1 4.8 + - + +
238D THR 4.5 1.8 + - - -
242D TRP* 1.3 73.4 - - - +
244D TYR* 1.3 61.9 + - - +
245D GLU* 3.6 8.3 + - - +
246D ALA* 3.0 29.8 + - - +
247D VAL* 3.2 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 244 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354C TRP* 3.6 47.0 - + + +
358C ARG* 3.0 25.9 + - - -
242D TRP* 2.9 21.6 + + - -
243D ASP* 1.3 70.9 + - - +
245D GLU* 1.3 80.9 + - + +
247D VAL* 3.3 2.1 + - - +
248D MET* 2.9 72.8 + - + +
276D THR* 3.8 5.4 - - + -
280D ASP* 2.7 36.6 + - - +
281D LEU* 5.5 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 245 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195D LYS* 5.9 3.4 - - - +
243D ASP* 3.3 7.5 + - - +
244D TYR* 1.3 103.5 - - + +
246D ALA* 1.3 58.3 + - - +
248D MET* 3.4 3.2 + - - +
249D ASN* 2.9 52.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 246 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196D ALA* 4.1 6.5 - - + -
234D LEU* 3.8 21.0 - - + +
243D ASP* 3.0 35.5 + - + +
245D GLU* 1.3 74.7 - - - +
247D VAL* 1.3 63.0 + - - +
249D ASN* 3.9 6.4 - - - +
250D SER* 3.1 25.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 247 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208D ILE* 3.7 26.5 - - + -
234D LEU* 3.9 10.3 - - + -
236D LEU* 3.5 29.6 - - + -
242D TRP* 3.8 18.2 - - + -
243D ASP 3.2 12.7 + - - +
244D TYR 3.6 6.7 - - - +
246D ALA* 1.3 77.8 - - - +
248D MET* 1.3 76.6 + - + +
250D SER* 3.3 3.5 + - - -
251D VAL* 3.0 27.9 + - - +
273D VAL* 4.2 2.5 - - + -
277D ILE* 3.9 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 248 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242D TRP* 3.9 10.8 - - + -
244D TYR* 2.9 67.2 + - + +
245D GLU* 4.1 3.4 - - - +
247D VAL* 1.3 78.4 - - + +
249D ASN* 1.3 62.8 - - - +
251D VAL* 5.4 0.2 - - - -
252D ALA* 2.9 32.2 + - - +
276D THR* 3.9 16.6 - - + +
277D ILE* 3.8 32.1 - - + -
280D ASP* 5.1 0.4 - - - -
281D LEU* 3.6 35.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 249 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245D GLU* 2.9 42.0 + - - +
246D ALA* 3.9 6.5 - - - +
248D MET* 1.3 78.6 - - - +
250D SER* 1.3 62.6 + - - +
252D ALA* 3.8 5.4 - - - +
253D LYS* 3.2 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 250 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198D LEU* 5.9 0.7 - - - -
206D THR* 2.8 38.5 + - - +
232D GLU* 2.6 31.8 + - - +
234D LEU* 4.7 9.8 - - - +
246D ALA 3.1 18.2 + - - -
247D VAL 3.7 3.4 - - - -
249D ASN* 1.3 75.0 - - - +
251D VAL* 1.3 59.8 + - - +
253D LYS* 3.1 7.4 + - - +
254D THR* 3.0 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 251 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206D THR* 3.9 7.6 - - + -
247D VAL* 3.0 19.8 + - + +
250D SER* 1.3 73.6 - - - +
252D ALA* 1.3 59.9 + - - +
254D THR* 3.9 6.5 - - - -
255D GLY* 2.7 33.0 + - - -
257D VAL* 4.0 29.4 - - + -
277D ILE* 4.0 27.1 - - + -
281D LEU* 4.0 14.4 - - + -
284D MET* 4.3 2.1 - - + +
285D LEU* 3.7 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 252 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248D MET 2.9 20.3 + - - +
249D ASN* 3.8 7.2 - - - +
251D VAL* 1.3 77.8 - - - +
253D LYS* 1.3 62.8 + - - +
255D GLY* 4.2 3.6 + - - -
281D LEU* 4.1 5.6 - - + +
284D MET* 3.5 45.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 253 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201D GLU* 5.2 5.1 + - - +
202D GLY 3.0 20.7 + - - +
203D LYS* 4.0 22.5 - - + +
232D GLU* 2.6 38.2 + - - -
249D ASN 3.2 11.9 + - - +
250D SER* 3.1 7.5 + - - +
252D ALA* 1.3 82.6 - - - +
254D THR* 1.3 61.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 254 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202D GLY 4.1 6.1 - - - +
203D LYS* 3.5 38.4 - - - +
204D ASP* 4.1 1.7 - - - +
205D LEU* 3.7 25.4 - - - +
206D THR* 2.7 29.8 + - - +
232D GLU* 4.8 2.7 - - + -
250D SER* 3.0 7.3 + - - +
251D VAL* 3.9 1.9 + - - -
253D LYS* 1.3 79.0 - - + +
255D GLY* 1.3 60.1 + - - +
256D ARG* 3.1 29.7 + - - -
286D LEU* 4.0 7.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 255 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251D VAL 2.7 25.0 + - - -
252D ALA 4.2 2.2 + - - -
253D LYS 3.5 1.2 - - - -
254D THR* 1.3 71.7 + - - +
256D ARG* 1.3 61.6 + - - +
284D MET 3.3 17.5 - - - -
285D LEU* 3.5 9.9 - - - +
286D LEU* 2.7 36.2 + - - +
287D ALA 3.6 1.6 + - - -
----------------------------------------------------------
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