Contacts of the helix formed by residues 120 - 124 (chain D) in PDB entry 3BRW
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 120 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A LYS* 6.3 3.1 - - + -
85A PRO* 5.3 0.2 - - - -
84D ILE* 4.1 6.3 - - - +
85D THR* 4.1 15.9 + - - +
117D LYS* 3.2 23.0 + - + +
118D CYS 4.5 0.7 - - - -
119D ASP* 1.3 82.5 - - - +
121D GLU* 1.3 64.0 + - - +
122D ASP* 3.2 9.2 - - - +
123D GLU* 3.0 44.0 + - + +
124D ARG 3.5 6.9 + - - -
149D LYS* 6.0 1.8 - - + +
171D GDP 3.5 34.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 121 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A PRO* 4.5 15.2 - - + +
86A THR* 4.6 14.6 - - + -
89A ILE* 4.5 7.0 - - + -
139A HIS* 3.2 41.9 + - + +
84D ILE* 4.6 0.8 - - - +
118D CYS* 3.8 15.3 + - - +
119D ASP 3.2 5.6 + - - +
120D LEU* 1.3 75.0 - - - +
122D ASP* 1.3 59.1 + - - +
124D ARG* 3.1 65.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 122 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A LYS* 4.4 5.7 + - - -
85A PRO* 3.3 37.2 + - - +
88A ARG* 3.5 24.4 + - + -
89A ILE* 3.7 28.4 - - + +
92A LYS* 3.2 18.6 + - + -
93A HIS* 2.9 27.5 + - - -
128A ARG* 5.5 0.7 - - - -
139A HIS* 5.7 0.2 - - - -
120D LEU* 4.6 5.2 - - - +
121D GLU* 1.3 77.8 + - - +
123D GLU* 1.3 72.1 + - - +
124D ARG 3.4 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 123 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A LYS* 5.9 2.9 - - - +
92A LYS* 4.4 13.7 - - - +
93A HIS* 4.9 2.2 - - - -
128A ARG* 4.8 1.1 - - - -
275B THR* 5.8 4.0 - - - +
85D THR* 3.4 39.8 + - + +
120D LEU* 3.0 41.1 + - + +
122D ASP* 1.3 90.3 - - - +
124D ARG* 1.3 66.8 + - - +
125D VAL* 3.3 13.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 124 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ARG* 2.4 35.9 + - - -
139A HIS* 4.3 7.7 + - + -
140A ASP* 3.9 11.5 + - - -
141A VAL* 3.6 13.3 - - + +
84D ILE* 3.4 41.1 - - + +
118D CYS* 4.5 2.2 - - - +
120D LEU 3.5 3.7 + - - -
121D GLU* 3.1 46.7 + - - +
122D ASP 3.4 0.8 - - - -
123D GLU* 1.3 76.8 - - - +
125D VAL* 1.3 53.9 + - - +
126D VAL 3.2 25.1 + - - +
127D GLY* 4.5 0.2 - - - -
128D LYS* 3.4 24.7 - - - +
145D GLU* 2.7 44.6 + - - -
----------------------------------------------------------
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