Contacts of the helix formed by residues 310 - 316 (chain B) in PDB entry 2PDA
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 SER 310 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A PRO* 4.9 6.9 - - - +
308B PHE* 3.2 16.9 + - - -
309B VAL* 1.3 71.6 - - - +
311B GLU* 1.3 57.6 + - - +
313B PHE* 2.8 26.7 + - - +
314B PHE* 2.9 23.3 + - - -
346B SER* 5.4 0.2 + - - -
347B ALA* 3.5 28.9 - - - +
350B GLU* 5.6 6.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 311 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B VAL* 4.0 16.0 - - + +
310B SER* 1.3 79.5 - - - +
312B ALA* 1.3 59.8 + - + +
314B PHE* 3.7 5.0 + - - +
315B ALA* 3.2 25.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 312 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B LEU* 4.1 18.6 - - + -
261B PHE* 3.9 23.8 - - + +
309B VAL* 3.2 22.4 + - + +
310B SER 3.1 0.8 - - - -
311B GLU* 1.3 80.6 - - + +
313B PHE* 1.3 69.0 + - - +
315B ALA* 3.4 13.9 + - - +
316B ALA* 3.7 6.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 313 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B PHE* 4.0 30.2 - + + -
274B VAL* 4.1 22.0 - - + -
300B ILE* 3.9 25.2 - - + +
308B PHE* 4.3 15.7 - + + -
309B VAL 3.0 12.5 + - - +
310B SER* 2.8 14.0 + - - +
312B ALA* 1.3 75.5 - - - +
314B PHE* 1.3 98.4 + + - +
316B ALA* 2.9 19.8 + - - +
317B LEU* 3.5 10.6 + - + +
324B ILE* 4.5 2.9 - - + -
344B VAL* 3.8 26.5 - - + -
347B ALA* 4.7 4.9 - - + -
348B PHE* 4.0 16.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 314 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B SER* 2.9 26.7 + - - +
311B GLU* 4.1 5.4 - - - +
313B PHE* 1.3 91.7 - + - +
315B ALA* 1.3 53.0 + - - +
316B ALA 2.6 13.7 + - - -
317B LEU* 2.8 33.0 + - + +
347B ALA* 3.7 37.7 - - + -
348B PHE* 3.6 32.1 - + - -
351B ARG* 3.4 47.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 315 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B LYS* 6.2 0.3 - - - +
311B GLU* 3.2 19.3 + - + +
312B ALA* 3.9 10.3 - - - +
313B PHE 3.2 1.0 + - - -
314B PHE* 1.3 72.9 - - - +
316B ALA* 1.3 57.8 + - - +
317B LEU 5.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 316 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B PHE* 3.8 26.0 - - + +
263B TYR* 3.1 49.0 - - - +
300B ILE* 3.6 14.3 - - + +
312B ALA 3.7 4.0 + - - +
313B PHE 2.9 9.6 + - - +
314B PHE 2.6 7.3 + - - -
315B ALA* 1.3 75.9 - - - +
317B LEU* 1.3 56.6 + - - +
318B PRO* 3.3 1.0 - - - +
----------------------------------------------------------
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