Contacts of the helix formed by residues 80 - 84 (chain 3) in PDB entry 4BOG
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 PRO 80 (chain 3).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
783 ARG 3.9 6.3 - - - +
793 ILE* 1.3 99.3 - - + +
813 SER* 1.3 70.8 + - - +
823 GLU 3.5 0.4 - - - -
833 LEU* 2.9 42.3 + - + +
1063 ASN* 4.8 15.7 - - - +
1073 VAL* 4.6 0.9 - - - +
18Z VAL* 3.9 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 81 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
793 ILE 3.7 0.8 + - - -
803 PRO* 1.3 68.1 - - - +
823 GLU* 1.3 84.7 + - - +
833 LEU 2.4 18.5 + - - -
843 LEU 3.5 2.1 + - - -
863 LEU* 3.2 29.1 - - - +
1033 TYR* 4.7 3.8 - - - -
1043 TYR* 3.4 38.1 + - - +
1053 ALA 3.7 17.7 + - - -
1073 VAL* 4.2 6.8 - - - +
1173 TRP* 5.9 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 82 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163 LYS* 4.5 12.3 - - - +
803 PRO* 3.4 0.4 + - + -
813 SER* 1.3 110.7 + - - +
833 LEU* 1.3 72.6 + - + +
843 LEU 3.8 2.5 + - - -
863 LEU* 4.3 3.4 - - - -
1033 TYR* 4.0 20.0 + - - +
1043 TYR* 4.4 10.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 83 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113 LEU* 6.3 1.1 - - + -
143 TYR* 2.6 44.9 + - + +
163 LYS* 4.7 7.0 - - - -
793 ILE* 4.2 25.7 - - + +
803 PRO* 2.9 40.2 - - + +
813 SER 2.4 16.9 + - - -
823 GLU* 1.3 88.0 - - + +
843 LEU* 1.3 72.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 84 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143 TYR* 4.5 2.5 - - + -
163 LYS* 5.3 7.5 + - - +
593 TRP* 2.9 49.8 - - + +
613 ASP* 4.6 13.7 - - + +
643 LEU* 5.1 13.9 - - + -
793 ILE* 4.5 8.5 - - + -
813 SER 3.5 1.8 + - - +
823 GLU 3.8 1.9 + - - -
833 LEU* 1.3 80.1 - - - +
853 TRP* 1.3 57.4 + - - +
863 LEU* 2.7 35.2 - - + +
1073 VAL* 5.3 5.8 - - + -
1093 VAL* 3.8 15.0 - - + -
1153 MET* 3.3 31.6 - - + -
----------------------------------------------------------
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