Contacts of the strand formed by residues 352 - 356 (chain A) in PDB entry 2DOU
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 PHE 352 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A LEU* 6.4 1.6 - - + -
316A TRP* 3.2 49.1 - + + -
317A GLY 3.4 15.5 - - - -
318A ARG* 3.5 56.8 - - + -
319A LEU* 4.5 0.4 - - - +
325A ASP* 3.1 11.1 - - - +
342A GLY* 2.6 27.4 + - - -
348A GLY 3.7 21.8 - - - -
349A GLY* 3.2 6.6 + - - +
350A LYS 3.2 25.8 - - - -
351A GLY* 1.3 82.0 - - - +
353A VAL* 1.3 59.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 353 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A LEU* 3.9 31.2 - - + -
315A LEU 3.6 1.7 - - - +
316A TRP* 3.7 6.6 - - - -
317A GLY 3.1 30.3 + - - +
319A LEU* 3.8 24.0 - - + -
325A ASP* 4.2 9.6 - - + +
328A PHE* 4.5 11.0 - - + -
329A GLY* 5.7 1.8 - - - +
339A LEU* 4.1 24.0 - - + -
340A ALA 3.5 10.1 - - - +
341A PRO* 4.7 2.7 - - + -
342A GLY 3.9 0.4 - - - +
352A PHE* 1.3 79.7 - - - +
354A ARG* 1.3 59.8 + - - +
355A ILE* 4.1 3.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 354 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A LEU 4.0 1.9 - - - +
31A SER 3.0 29.1 + - - -
32A ILE 4.1 0.4 - - - -
33A GLY 3.7 7.3 - - - +
169A ASN* 3.0 20.2 + - - +
170A PRO* 3.3 34.1 - - - +
314A TYR* 3.6 30.0 - - + -
315A LEU 3.3 5.6 - - - +
316A TRP* 3.7 12.5 - - + -
339A LEU* 3.9 5.7 - - - +
340A ALA* 2.9 34.8 + - + +
345A PHE* 3.4 31.6 - - + -
353A VAL* 1.3 73.7 - - - +
355A ILE* 1.3 66.4 + - - +
356A ALA* 4.6 2.2 - - - +
501A EPE 3.0 33.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 355 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A LEU* 3.7 31.2 - - + -
296A MET* 3.8 23.1 - - + -
300A LEU* 3.7 29.4 - - + -
304A LEU* 4.2 15.7 - - + -
306A LEU* 5.3 1.6 - - + -
313A MET 3.5 0.5 - - - +
314A TYR* 3.3 5.9 - - - -
315A LEU* 2.8 51.1 + - + +
339A LEU* 3.8 15.3 - - + -
353A VAL* 4.7 4.7 - - + +
354A ARG* 1.3 79.7 - - - +
356A ALA* 1.3 65.8 + - - +
357A LEU* 3.7 3.8 + - + -
371A ILE* 4.3 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 356 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A LEU* 2.8 44.4 + - - +
32A ILE 3.4 31.2 - - - +
33A GLY* 4.1 8.7 - - - -
313A MET 3.3 6.7 - - - +
314A TYR* 4.5 4.0 - - + -
354A ARG* 4.2 7.6 - - - +
355A ILE* 1.3 72.8 - - - +
357A LEU* 1.3 59.0 + - - +
358A VAL* 2.8 14.9 + - + +
----------------------------------------------------------
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