Contacts of the helix formed by residues 691 - 699 (chain A) in PDB entry 3DF0
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 691 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690A ASP* 1.3 74.2 - - - +
692A ILE* 1.3 75.3 - - + +
694A TRP* 3.1 10.0 + - + +
695A LEU* 3.1 42.0 + - + +
206B HIS 5.7 2.2 - - - +
242B PHE* 3.9 26.9 - - + +
245B PHE* 3.3 52.4 - - + -
254B GLY* 3.9 5.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 692 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690A ASP* 4.4 15.5 - - + +
691A LEU* 1.3 88.0 - - + +
693A SER* 1.3 83.3 + - - +
695A LEU* 3.4 8.8 + - - +
696A SER* 3.1 23.6 + - - -
206B HIS 4.2 18.8 - - - +
207B LEU* 5.3 9.5 - - + +
208B ASN* 5.0 19.1 - - - +
211B ILE* 4.2 10.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 693 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
689A LEU* 3.2 15.9 - - - +
690A ASP* 2.9 23.9 + - - -
691A LEU 3.3 0.2 - - - -
692A ILE* 1.3 89.3 - - - +
694A TRP* 1.3 65.4 + - - +
696A SER* 2.9 22.2 + - - -
697A PHE* 3.0 27.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 694 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
689A LEU* 4.0 23.1 - - + -
690A ASP 2.9 20.3 + - - +
691A LEU* 3.5 13.7 - - + +
693A SER* 1.3 78.5 + - - +
695A LEU* 1.3 59.2 + - + +
697A PHE* 3.3 1.6 + - - +
698A SER* 2.6 48.4 + - - -
241B MET* 2.7 45.7 + - + +
244B ALA* 4.2 14.4 - - + -
245B PHE* 3.6 27.1 - + + +
248B LEU* 5.8 1.1 - - + -
256B ILE* 4.1 22.2 - - + -
258B VAL* 4.8 8.3 - - + -
263B TRP* 3.7 35.9 - + - -
266B LEU* 4.3 25.1 - - + -
267B THR* 4.8 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 695 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691A LEU* 3.1 37.2 + - + +
692A ILE* 3.4 9.6 - - - +
694A TRP* 1.3 83.7 - - + +
696A SER* 1.3 58.3 + - - +
697A PHE 3.1 0.2 + - - -
698A SER* 3.5 3.6 - - - -
699A VAL* 2.8 38.7 + - + +
205B PHE* 5.2 2.2 - - + -
207B LEU* 4.0 26.9 - - + -
211B ILE* 5.9 2.7 - - + -
238B LEU* 3.8 35.0 - - + +
241B MET* 4.0 22.7 - - + -
242B PHE* 4.3 18.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 696 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692A ILE 3.1 2.2 + - - -
693A SER* 2.9 29.3 + - - -
695A LEU* 1.3 78.8 - - - +
697A PHE* 1.3 60.9 + - - +
699A VAL* 4.7 4.9 - - - -
700A LEU* 3.3 25.8 + - - +
701A GLY* 3.4 8.1 + - - -
211B ILE* 3.6 30.9 - - - +
214B MET* 4.8 11.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 697 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672A LEU* 5.6 5.0 - - - +
675A ILE* 3.1 42.8 - - + +
679A LEU* 4.0 27.1 - - + -
689A LEU* 3.6 34.1 - - + -
693A SER* 3.0 31.8 + - - +
694A TRP 4.0 1.1 - - - +
696A SER* 1.3 75.4 - - - +
698A SER* 1.3 61.9 + - - +
699A VAL 2.9 11.4 + - - -
700A LEU 3.0 20.8 + - - +
701A GLY 4.3 10.2 - - - +
263B TRP* 3.9 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 698 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672A LEU* 6.2 1.6 - - - -
694A TRP* 2.6 36.6 + - - -
695A LEU* 3.4 6.2 + - - -
697A PHE* 1.3 75.3 - - - +
699A VAL* 1.3 56.3 + - - +
241B MET* 3.4 47.2 - - - +
263B TRP* 5.0 1.6 - - - -
267B THR* 3.8 29.8 - - - +
270B SER* 4.1 7.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 699 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668A ARG* 5.7 3.1 + - - -
695A LEU* 2.8 24.8 + - + +
696A SER* 4.7 0.2 - - - -
697A PHE 3.8 0.2 - - - -
698A SER* 1.3 82.0 - - - +
700A LEU* 1.3 91.3 + - + +
211B ILE* 6.2 1.6 - - + -
215B ILE* 4.6 10.8 - - + -
218B ARG* 4.9 2.9 + - - -
219B TYR* 4.8 9.6 + - + +
237B ARG* 3.5 40.6 - - + +
238B LEU* 4.3 23.6 - - + +
241B MET* 4.8 2.0 - - + -
270B SER* 4.9 5.5 + - - -
----------------------------------------------------------
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