Contacts of the helix formed by residues 92 - 96 (chain 3) in PDB entry 1AR9
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 ASP 92 (chain 3).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3021 TYR* 3.5 2.3 - - - +
853 LEU* 3.3 13.2 - - + +
863 SER* 3.1 31.9 + - - +
883 SER* 2.8 25.3 + - - +
913 SER* 1.3 70.5 + - - +
933 PRO* 1.3 66.2 - - - +
943 ARG* 2.9 52.4 + - - +
953 LEU* 2.8 24.2 + - + -
963 SER 2.9 13.5 + - - -
1813 ASP* 4.4 2.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 93 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2941 LEU* 4.1 3.9 - - + +
2951 SER* 4.1 18.8 - - - +
2961 THR 5.4 0.7 - - - +
2971 LYS* 3.9 35.9 - - + +
543 PRO* 4.8 1.9 - - - +
573 LEU* 3.7 22.8 - - + +
913 SER 3.2 5.1 - - - +
923 ASP* 1.3 96.1 - - - +
943 ARG* 1.3 59.0 + - - +
953 LEU 3.7 0.2 + - - -
963 SER* 3.7 16.3 + - - +
973 HIS* 3.8 15.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 94 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2971 LYS* 3.4 25.1 - - - +
2981 ASP 3.3 17.2 + - - -
2991 LEU 4.1 2.8 + - - -
3011 THR 2.8 29.9 + - - -
3021 TYR* 3.1 11.5 + - - -
533 ILE* 3.4 17.1 - - + +
543 PRO* 3.3 49.3 - - - +
553 PHE* 3.4 21.5 - - + +
573 LEU* 3.9 9.0 - - + -
843 CYS 3.0 20.2 + - - -
853 LEU* 3.9 17.4 - - + +
923 ASP* 2.9 39.8 + - - +
933 PRO* 1.3 78.3 - - - +
953 LEU* 1.3 57.6 + - - +
973 HIS 5.1 0.4 + - - -
983 THR* 3.8 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 95 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533 ILE* 4.3 11.9 - - + -
853 LEU* 3.7 22.0 - - + -
863 SER 3.7 23.3 - - - +
873 LEU* 4.7 5.4 - - + -
883 SER 4.3 2.7 - - - +
893 PRO* 3.4 34.5 - - + +
923 ASP* 2.8 9.6 + - + +
943 ARG* 1.3 76.1 - - - +
963 SER* 1.3 65.9 + - - +
973 HIS 2.9 4.0 + - - -
983 THR* 2.7 28.9 + - - +
1003 LEU* 6.4 0.9 - - + -
1013 GLY* 3.5 3.8 - - - -
1143 LEU* 6.0 0.9 - - + -
1163 PHE* 3.9 34.1 - - + -
2143 VAL* 4.4 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 96 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
893 PRO 3.5 10.4 + - - -
903 ALA 3.1 24.7 - - - -
913 SER* 4.1 5.0 + - - -
923 ASP 2.9 16.0 + - - -
933 PRO* 3.7 7.1 + - - +
943 ARG 3.8 0.2 - - - -
953 LEU* 1.3 75.4 - - - +
973 HIS* 1.3 80.2 + - - +
983 THR 3.6 0.4 - - - -
1013 GLY* 3.3 18.8 - - - -
1023 GLU* 3.3 1.4 - - - +
1053 ASN* 3.7 0.2 + - - -
2303 HIS* 3.2 22.9 - - - -
----------------------------------------------------------
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