Contacts of the helix formed by residues 1148 - 1154 (chain A) in PDB entry 4N78
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 THR1148 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1142A VAL* 3.8 25.4 - - + +
1146A GLU 4.7 2.5 - - - +
1147A PHE* 1.3 79.2 - - - +
1149A VAL* 1.3 64.8 + - - +
1150A GLU* 3.0 38.4 + - - +
1151A GLN* 3.4 15.2 + - - +
1152A CYS* 3.3 22.3 + - - +
1207A ARG* 4.2 14.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
990A LYS* 5.8 7.2 - - - +
994A PHE* 4.0 9.9 - - + -
1138A TYR* 3.7 36.3 - - + +
1148A THR* 1.3 75.6 - - - +
1150A GLU* 1.3 73.1 + - - +
1152A CYS* 4.5 0.7 - - - -
1153A PHE* 2.8 52.0 + - + +
1154A GLY 4.7 0.5 - - - +
1157A LEU* 3.6 22.4 - - + -
1158A HIS* 4.8 3.8 - - - +
1207A ARG* 4.3 0.8 - - - +
1211A PHE* 4.0 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
856A CYS* 4.5 2.8 - - - +
1148A THR* 3.0 25.4 + - - +
1149A VAL* 1.3 85.1 - - + +
1151A GLN* 1.3 57.8 + - + +
1152A CYS 3.1 4.3 - - - -
1154A GLY* 3.1 34.2 + - - +
1155A ASP* 5.6 3.6 - - - +
1158A HIS* 5.6 2.7 - - + +
1207A ARG* 3.2 39.7 + - - -
1211A PHE* 3.7 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
856A CYS* 4.2 7.7 - - - -
866A ARG 4.9 1.7 - - - +
867A THR* 4.4 1.4 - - - -
868A VAL* 3.6 22.8 + - + +
1146A GLU 4.4 2.3 - - - +
1147A PHE* 3.3 31.1 - - + +
1148A THR* 3.4 18.7 + - - +
1149A VAL 3.3 0.4 - - - -
1150A GLU* 1.3 81.7 - - + +
1152A CYS* 1.3 58.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS1152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
856A CYS* 3.2 4.6 - - - -
867A THR* 2.7 26.4 + - - -
868A VAL* 3.9 6.7 - - + -
871A PHE* 3.5 38.1 - - - -
998A ARG* 3.0 12.6 + - - -
1147A PHE* 4.0 15.0 - - + -
1148A THR 3.3 15.8 + - - +
1149A VAL* 4.5 0.2 - - - -
1150A GLU 3.1 0.4 - - - -
1151A GLN* 1.3 79.8 - - - +
1153A PHE* 1.3 87.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
855A TYR 4.0 0.2 - - - +
856A CYS* 3.7 13.4 - - - -
871A PHE* 3.7 11.7 - + - -
990A LYS* 3.4 28.7 - - + -
994A PHE* 3.5 33.0 - + + -
995A GLN* 3.4 32.5 - - - -
998A ARG* 3.4 40.1 - - + +
1002A ASN* 5.0 0.2 - - - +
1147A PHE* 6.1 0.2 - + - -
1149A VAL* 2.8 32.7 + - + +
1152A CYS* 1.3 98.2 - - + +
1154A GLY* 1.3 63.4 + - - +
1156A GLY 4.0 4.5 + - - -
1157A LEU* 4.0 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
856A CYS* 3.5 16.2 - - - +
857A TYR 3.8 5.8 - - - -
1149A VAL 3.8 1.5 + - - +
1150A GLU* 3.1 27.8 + - - -
1153A PHE* 1.3 83.4 - - - +
1155A ASP* 1.3 66.6 + - - -
1156A GLY 3.4 0.2 + - - -
1157A LEU* 3.8 7.6 + - - +
1158A HIS* 3.9 13.1 + - - -
----------------------------------------------------------
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