Contacts of the helix formed by residues 125 - 136 (chain D) in PDB entry 1A4Y
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 GLY 125 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123D LEU 3.6 1.4 - - - -
124D LEU* 1.3 81.7 - - - +
126D ASP* 1.3 66.0 + - - -
127D ALA* 3.0 4.5 - - - -
129D LEU 3.0 14.0 + - - -
151D CYS 3.1 9.5 + - - -
152D SER* 3.8 18.1 - - - -
153D LEU* 3.5 12.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 126 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125D GLY* 1.3 70.3 - - - -
127D ALA* 1.3 64.7 + - - +
129D LEU* 4.0 1.7 - - - +
130D GLN* 3.2 31.3 + - - +
152D SER 4.3 2.1 + - - +
153D LEU* 3.6 0.8 - - - -
154D SER* 2.7 46.9 + - - -
156D ALA* 3.6 18.2 - - + +
157D SER* 2.4 36.1 + - - +
160D PRO* 6.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 127 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D GLY* 5.7 2.7 - - - -
124D LEU 4.8 2.2 - - - +
125D GLY* 3.0 2.2 - - - -
126D ASP* 1.3 76.2 - - - +
128D GLY* 1.3 67.6 + - - +
130D GLN* 3.0 26.5 - - - +
131D LEU* 3.4 6.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 128 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D GLY* 4.0 10.2 - - - -
101D CYS* 3.6 28.3 - - - +
124D LEU 3.3 19.0 + - - -
127D ALA* 1.3 79.8 - - - +
129D LEU* 1.3 62.2 + - - +
130D GLN 2.9 1.7 + - - -
131D LEU* 3.0 16.6 + - - +
132D LEU* 3.0 9.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 129 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101D CYS* 4.5 1.9 - - - -
124D LEU* 4.7 6.5 - - + +
125D GLY 3.0 16.5 + - - +
126D ASP 4.2 0.9 - - - +
128D GLY* 1.3 73.7 - - - +
130D GLN* 1.3 61.4 + - - +
132D LEU* 3.6 15.9 - - + +
133D CYS* 3.1 33.1 + - - -
136D LEU* 6.4 0.2 - - + -
146D LEU* 5.8 0.2 - - + -
148D LEU* 3.4 40.2 - - + -
153D LEU* 3.7 23.6 - - + -
157D SER* 3.5 40.4 - - - +
160D PRO* 4.6 2.9 - - + -
161D LEU* 3.7 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 130 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126D ASP* 3.2 23.0 + - - +
127D ALA* 3.0 16.2 + - - +
128D GLY 2.9 0.4 + - - -
129D LEU* 1.3 75.2 - - - +
131D LEU* 1.3 66.2 + - - +
133D CYS* 3.4 12.1 + - - +
134D GLU* 3.5 17.4 + - - +
156D ALA* 5.3 7.7 + - - +
160D PRO* 4.5 23.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 131 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D GLY 4.9 7.9 - - - +
99D ALA 5.7 0.9 - - - +
101D CYS* 4.3 6.7 - - + +
102D GLY* 3.8 25.8 - - - +
105D SER* 2.9 33.2 + - - +
127D ALA 3.4 5.5 + - - +
128D GLY* 3.0 9.3 + - - +
130D GLN* 1.3 76.8 - - - +
132D LEU* 1.3 65.6 + - - +
134D GLU* 2.9 36.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 132 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101D CYS* 3.8 21.5 - - + +
104D LEU* 3.6 38.4 - - + -
105D SER* 4.1 6.9 + - - +
108D LEU* 4.3 16.2 - - + +
117D LEU* 5.1 0.2 - - + -
119D LEU* 3.7 25.6 - - + -
124D LEU* 5.2 3.4 - - + -
128D GLY 3.0 7.8 + - - +
129D LEU* 3.6 19.3 - - + +
131D LEU* 1.3 78.3 - - - +
133D CYS* 1.3 58.4 + - - +
135D GLY* 2.9 20.3 + - - -
136D LEU* 3.1 25.1 + - + +
146D LEU* 5.0 5.8 - - + -
148D LEU* 4.9 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 133 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129D LEU* 3.1 42.7 + - - +
130D GLN 3.8 5.4 - - - +
131D LEU 3.3 0.6 - - - -
132D LEU* 1.3 78.8 - - - +
134D GLU* 1.3 61.6 + - - +
135D GLY 3.2 0.2 - - - -
136D LEU* 3.7 18.7 - - - +
137D LEU* 3.0 32.8 + - + +
160D PRO* 3.9 23.8 - - + +
161D LEU* 3.9 18.6 - - - -
164D VAL* 3.9 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 134 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D SER* 4.1 3.0 + - - +
109D ARG* 3.6 19.1 + - - +
130D GLN* 3.5 12.1 + - - +
131D LEU* 2.9 35.5 + - - +
133D CYS* 1.3 78.9 - - - +
135D GLY* 1.3 63.8 + - - +
137D LEU* 3.5 13.7 + - + +
138D ASP 3.6 5.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 135 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D SER* 3.3 30.0 + - - -
108D LEU* 4.7 5.8 - - - -
109D ARG* 4.0 12.3 - - - +
132D LEU 2.9 7.2 + - - -
134D GLU* 1.3 78.2 - - - +
136D LEU* 1.3 57.3 + - - +
138D ASP* 2.7 32.1 + - - +
141D CYS* 3.6 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 136 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108D LEU* 3.7 19.2 - - + +
129D LEU* 6.4 0.2 - - + -
132D LEU* 3.1 21.6 + - + +
133D CYS* 3.7 29.8 - - - +
134D GLU 3.4 0.2 - - - -
135D GLY* 1.3 75.8 - - - +
137D LEU* 1.3 61.9 + - - +
138D ASP 3.3 2.8 + - - +
141D CYS* 3.5 27.4 - - - +
143D LEU* 3.5 32.5 - - + -
146D LEU* 4.1 24.0 - - + -
161D LEU* 5.0 1.1 - - + -
164D VAL* 3.7 27.4 - - + +
168D LYS* 5.7 4.5 - - - +
171D PHE* 5.4 4.3 - - + -
----------------------------------------------------------
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