Contacts of the strand formed by residues 295 - 300 (chain B) in PDB entry 1DE8
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 295 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B PRO* 3.1 25.2 - - - +
252B SER* 3.9 29.8 - - - +
255B HIS* 4.9 2.0 - - + -
256B LEU* 3.9 28.3 - - + +
287B LEU* 4.3 9.6 - - + -
291B LEU 3.0 8.0 + - - +
292B LEU* 3.0 28.3 + - + +
294B ALA* 1.3 74.9 - - - +
296B CYS* 1.3 65.6 + - - +
297B ASP 3.2 18.6 - - - +
314B LEU* 3.4 26.0 - - + -
315B TYR 3.4 4.0 - - - +
316B LEU* 3.8 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 296 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B HIS* 3.5 31.0 - - - +
53B THR 3.7 13.8 - - - +
54B SER* 3.3 19.3 - - - +
55B PRO* 5.5 1.0 - - - +
60B ALA* 3.4 20.0 - - + -
256B LEU* 4.5 7.6 - - - +
294B ALA 3.5 0.4 - - - -
295B LEU* 1.3 77.3 - - - +
297B ASP* 1.3 64.7 + - - +
315B TYR* 2.9 16.8 + - + +
316B LEU 3.6 0.9 - - - -
317B ALA* 3.2 36.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 297 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B PRO 3.7 1.2 - - - +
51B HIS* 3.1 37.2 + - + +
256B LEU* 3.8 8.2 - - - +
257B TYR* 2.8 28.3 + - - -
295B LEU* 3.2 5.5 - - - +
296B CYS* 1.3 83.8 - - - +
298B SER* 1.3 81.4 + - - +
299B LYS* 3.1 30.4 + - - +
313B THR 4.0 0.6 - - - +
314B LEU* 3.2 6.1 - - - +
315B TYR* 2.8 36.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 298 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B SER* 3.6 35.8 - - - -
253B PHE* 3.7 36.7 + - - +
256B LEU* 3.6 4.4 - - - +
257B TYR* 4.0 2.9 - - - -
285B PHE* 3.9 15.4 - - - -
297B ASP* 1.3 88.5 + - - +
299B LYS* 1.3 67.8 + - - +
300B ILE* 5.6 0.3 - - - +
313B THR 3.5 4.0 - - - -
314B LEU* 3.9 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 299 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ASP* 3.4 15.4 + - - +
48B PRO* 2.6 49.9 + - - +
49B PRO 3.5 5.7 + - - -
50B ASP* 3.4 24.9 - - - +
257B TYR* 3.9 4.0 + - - -
297B ASP* 3.1 26.0 + - - +
298B SER* 1.3 84.4 + - - +
300B ILE* 1.3 67.7 + - - +
301B ARG* 3.4 36.1 - - - +
312B ILE* 3.5 7.8 - - - +
313B THR* 2.8 32.4 + - - +
315B TYR* 4.2 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 300 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B TYR* 4.7 5.8 - - + +
47B ASP* 3.2 25.9 + - + +
253B PHE* 3.8 51.1 - - + -
263B ALA* 4.3 12.1 - - + +
264B TYR 3.4 23.1 - - - +
265B THR* 3.9 18.6 - - + -
281B ARG* 4.5 3.8 - - - +
283B ASP 5.8 0.4 - - - +
298B SER* 5.2 0.7 - - - +
299B LYS* 1.3 80.5 - - - +
301B ARG* 1.3 57.6 + - - +
302B SER* 2.9 21.7 + - - +
310B CYS* 3.7 15.5 - - - -
311B PRO 4.0 2.0 - - - -
312B ILE* 4.3 4.7 - - + -
----------------------------------------------------------
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