Contacts of the helix formed by residues 87 - 94 (chain 9) in PDB entry 3J7Y
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 THR 87 (chain 9).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
859 PRO* 2.8 13.5 + - - +
869 LEU* 1.3 82.9 - - - +
889 ALA* 1.3 70.5 + - - +
899 ALA* 3.8 19.1 + - + +
909 GLN* 3.5 24.8 + - + +
919 LEU* 3.4 16.6 + - - +
230X TYR* 4.7 3.1 + - - -
152Y ALA* 4.4 2.8 - - - +
155Y LEU* 5.8 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 88 (chain 9).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
879 THR* 1.3 78.8 + - - +
899 ALA* 1.3 59.7 + - - +
919 LEU* 3.2 5.7 + - - +
929 PHE* 2.9 28.2 + - - +
226X LEU* 4.4 4.7 - - + -
230X TYR* 3.6 19.6 - - + +
152Y ALA* 4.2 15.0 - - - +
155Y LEU* 4.2 31.4 - - + +
156Y LEU* 3.8 14.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 89 (chain 9).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
879 THR* 3.3 11.6 - - + +
889 ALA* 1.3 76.1 - - - +
909 GLN* 1.3 57.3 + - + +
929 PHE* 3.2 5.8 + - - +
939 SER* 2.9 29.2 + - - -
230X TYR* 3.0 38.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 90 (chain 9).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
849 THR* 4.6 21.8 + - - +
859 PRO 4.1 14.6 + - - +
869 LEU* 3.8 25.4 - - + +
879 THR* 3.5 21.3 + - + +
889 ALA 3.2 0.4 - - - -
899 ALA* 1.3 79.6 - - + +
919 LEU* 1.3 57.9 + - - +
939 SER* 2.5 27.3 + - - +
949 GLU* 2.9 20.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 91 (chain 9).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
869 LEU* 4.3 14.5 - - + +
879 THR 3.4 8.0 + - - +
889 ALA* 3.2 10.7 + - - +
909 GLN* 1.3 80.2 - - - +
929 PHE* 1.3 62.0 + - - +
949 GLU* 3.2 17.5 + - + +
959 ALA* 3.2 12.1 + - + +
187V TYR* 4.5 16.6 - - - +
189V PRO* 5.3 3.3 - - + +
190V CYS 4.1 13.0 - - - +
191V LEU* 3.4 33.7 - - + -
149Y ARG* 4.2 12.6 - - + +
152Y ALA* 3.5 28.0 - - + -
153Y LEU* 4.4 7.9 - - + +
156Y LEU* 3.5 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 92 (chain 9).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
889 ALA 2.9 13.5 + - - +
899 ALA 3.2 8.5 + - - +
919 LEU* 1.3 75.7 - - - +
939 SER* 1.3 58.8 - - - +
959 ALA* 2.9 31.3 + - + +
969 VAL* 3.0 44.6 + - + +
999 ALA* 5.1 4.3 - - + -
227X PHE* 3.8 35.7 - + - -
230X TYR* 3.3 49.8 - + + -
231X VAL* 3.6 24.7 - - + -
234X LEU* 4.1 13.2 - - + -
156Y LEU* 4.3 9.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 93 (chain 9).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
899 ALA 2.9 12.7 + - - -
909 GLN* 2.5 25.4 + - - -
929 PHE* 1.3 77.6 - - - +
949 GLU* 1.3 60.1 + - - +
969 VAL* 3.0 34.5 + - - +
979 ALA 4.3 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 94 (chain 9).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
869 LEU* 6.0 4.3 - - - +
909 GLN* 2.9 16.2 + - + +
919 LEU* 3.2 11.9 + - - +
939 SER* 1.3 84.9 + - - +
959 ALA* 1.3 56.8 + - - +
969 VAL 3.7 0.2 - - - -
979 ALA* 5.5 1.5 - - - +
185V ARG* 5.2 11.3 + - - -
187V TYR* 4.2 16.7 - - - +
189V PRO* 3.3 51.7 - - + +
----------------------------------------------------------
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