Contacts of the strand formed by residues 282 - 287 (chain D) 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 LEU 282 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94D LYS* 4.4 6.3 - - - +
95D VAL* 4.9 4.5 - - + -
99D GLN* 3.5 39.0 - - + +
100D MET 2.8 17.8 + - - +
101D LEU* 3.7 18.2 - - + -
102D ALA* 2.8 30.1 + - - +
280D PHE* 4.1 2.8 - - - +
281D ASP* 1.3 82.1 + - - +
283D VAL* 1.3 58.8 - - - +
294D LEU* 5.1 3.1 - - + -
295D GLY* 3.6 28.0 - - - +
296D ALA* 3.8 7.9 - - + +
353D VAL* 3.8 28.5 - - + -
354D ARG* 5.0 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 283 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101D LEU* 3.7 3.1 - - - -
102D ALA 3.4 5.6 - - - +
104D ILE* 3.4 26.9 - - + -
277D PHE* 4.3 6.3 - - + -
280D PHE* 3.9 26.5 - - + -
282D LEU* 1.3 79.5 - - - +
284D LEU* 1.3 63.6 + - - +
285D LEU 4.2 0.4 - - - -
293D TYR 4.2 0.6 - - - +
294D LEU* 3.6 5.0 - - - +
295D GLY 2.8 46.0 + - - +
296D ALA 4.0 1.1 - - - +
297D ALA* 3.8 23.3 - - - +
300D MET* 4.9 7.9 - - + -
314D TYR* 4.1 17.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 284 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D LEU* 5.1 1.6 - - + -
93D PHE* 3.4 37.2 - - + -
101D LEU* 3.8 8.5 - - + +
102D ALA 2.8 10.7 + - - +
103D ILE* 3.4 18.1 - - + +
104D ILE* 2.8 29.4 + - - -
114D LEU* 5.0 0.9 - - + -
283D VAL* 1.3 74.3 - - - +
285D LEU* 1.3 72.6 + - - +
286D MET* 3.9 23.4 + - - -
291D PRO* 4.1 19.7 - - + -
293D TYR 4.2 1.1 - - - -
294D LEU* 3.6 30.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 285 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104D ILE* 3.2 24.9 - - + +
283D VAL 4.2 0.2 - - - -
284D LEU* 1.3 77.8 - - - +
286D MET* 1.3 73.5 + - - +
291D PRO* 3.6 2.9 - - - +
292D ILE* 2.8 47.2 + - + -
293D TYR 3.4 16.3 + - - +
300D MET* 5.2 0.7 - - - -
304D PHE* 4.3 17.0 - - + -
314D TYR* 2.8 31.2 + - + +
317D PRO* 4.5 5.6 - - + +
318D ALA* 3.6 38.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 286 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D ILE* 5.3 3.8 - - + -
91D LEU* 3.7 24.2 - - + -
103D ILE* 4.6 5.6 - - + -
105D GLY* 3.0 15.9 - - - -
106D SER* 2.8 27.2 + - - -
109D CYS* 4.1 13.0 - - - +
114D LEU* 4.2 19.1 - - + -
284D LEU* 3.9 28.3 - - + -
285D LEU* 1.3 82.4 - - - +
287D THR* 1.3 60.7 + - - +
288D SER 4.0 5.1 + - - +
289D GLY* 2.9 31.0 - - - +
290D THR 2.8 24.2 - - - +
291D PRO* 3.8 0.9 - - + -
292D ILE* 4.1 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 287 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D SER* 3.2 8.0 + - - +
285D LEU* 5.2 0.2 - - - +
286D MET* 1.3 72.1 + - - +
288D SER* 1.3 76.4 + - - +
289D GLY 3.1 0.2 + - - -
290D THR* 3.1 22.7 + - - -
292D ILE* 3.8 11.3 - - - +
318D ALA* 3.4 13.0 + - - -
321D TYR* 2.9 40.9 + - - +
322D VAL* 3.3 32.1 - - + -
323D ASP* 3.5 10.5 - - - +
----------------------------------------------------------
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