Contacts of the helix formed by residues 113 - 128 (chain D) in PDB entry 5L08
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 SER 113 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A LYS* 4.5 8.1 - - - +
133A LEU 5.5 5.4 - - - -
111D GLU 3.5 2.5 + - - -
112D VAL* 1.3 77.6 - - - +
114D ARG* 1.3 53.7 + - - +
115D SER* 3.8 7.2 + - - -
116D GLU* 2.9 40.1 + - - +
117D LEU* 2.6 33.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 114 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A LYS* 5.5 1.6 - - - +
134A ASP* 2.7 42.9 + - - -
135A ASP* 5.1 4.6 + - - +
136A ASP* 4.2 16.1 + - - -
113D SER* 1.3 70.6 - - - +
115D SER* 1.3 64.2 + - - +
117D LEU* 3.3 15.3 + - + +
118D ARG* 2.9 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 115 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113D SER* 3.3 6.8 + - - -
114D ARG* 1.3 82.7 + - - +
116D GLU* 1.3 64.2 + - - +
118D ARG* 3.4 18.0 + - - +
119D SER* 3.1 23.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 116 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B GLU* 4.8 11.6 - - - +
111D GLU 3.8 5.4 - - - +
112D VAL* 3.7 14.2 - - + -
113D SER* 2.9 41.4 + - - +
115D SER* 1.3 77.1 - - - +
117D LEU* 1.3 56.3 + - - +
119D SER* 3.0 10.4 + - - -
120D PHE* 2.7 40.4 + - + -
167D ILE* 3.3 21.8 - - + +
168D ASN* 2.9 30.4 + - - +
171D LEU* 5.1 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 117 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112D VAL* 3.6 8.5 - - + +
113D SER 2.6 21.4 + - - +
114D ARG* 3.4 15.7 - - + +
115D SER 3.3 0.2 - - - -
116D GLU* 1.3 72.5 - - - +
118D ARG* 1.3 57.9 + - - +
120D PHE* 3.0 7.1 + - + +
121D LYS* 2.8 27.2 + - + +
135D ASP 5.8 2.7 - - - +
137D MET 3.7 21.1 - - - +
138D ASN* 4.6 5.4 - - - +
139D LEU* 3.6 47.1 - - + +
142D ILE* 4.3 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 118 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114D ARG 2.9 13.3 + - - +
115D SER* 3.5 17.0 + - - +
116D GLU 3.3 0.2 - - - -
117D LEU* 1.3 76.8 - - - +
119D SER* 1.3 56.5 + - - +
121D LYS* 3.2 15.9 + - + +
122D PHE* 2.5 95.3 + - + -
135D ASP* 5.9 3.1 - - - +
39E LYS* 4.6 15.2 - - - +
40E ASP* 2.7 36.7 + - - +
43E MET* 3.6 11.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 119 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B LYS* 5.8 2.1 + - - -
115D SER 3.1 14.2 + - - -
116D GLU* 3.0 15.2 + - - -
118D ARG* 1.3 79.6 + - - +
120D PHE* 1.3 57.8 + - - +
122D PHE* 3.2 11.9 + - - +
123D LEU* 2.8 35.6 + - - +
167D ILE* 3.6 20.2 - - - -
8E TYR* 4.0 18.2 + - - -
12E GLU* 5.1 3.6 + - - -
42E LEU* 5.7 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 120 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108D ILE* 5.1 3.6 - - + -
112D VAL* 3.4 38.1 - - + -
116D GLU 2.7 27.3 + - - -
117D LEU* 3.0 11.2 + - + +
119D SER* 1.3 72.8 - - - +
121D LYS* 1.3 63.6 + - - +
123D LEU* 3.6 4.8 - - + +
124D LEU* 2.9 27.7 + - - +
139D LEU* 4.1 27.6 - - + -
142D ILE* 5.1 4.0 - - + -
143D PHE* 6.2 2.5 - + - -
160D LEU* 6.0 5.4 - - + -
163D VAL* 3.3 33.2 - - + +
164D CYS* 4.7 10.8 - - - -
167D ILE* 3.8 25.4 - - + -
171D LEU* 3.8 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 121 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117D LEU* 2.8 16.2 + - + +
118D ARG* 3.2 20.2 - - + +
120D PHE* 1.3 73.2 - - - +
122D PHE* 1.3 66.3 + - + +
124D LEU* 4.9 0.2 - - - -
125D GLN* 3.1 20.6 + - - +
133D LEU* 3.2 38.2 + - + +
134D ASP* 3.7 38.2 + - - +
135D ASP* 2.7 29.9 + - - +
137D MET* 6.2 1.1 - - + -
142D ILE* 4.9 8.4 - - + +
43E MET* 6.3 1.0 - - - -
46E GLN* 5.0 15.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 122 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118D ARG* 2.5 70.1 + - + -
119D SER* 3.2 8.9 + - - +
121D LYS* 1.3 79.2 - - + +
123D LEU* 1.3 52.0 + - - +
125D GLN* 3.2 9.9 + - - +
126D GLU* 2.7 41.9 + - + +
40E ASP* 4.5 1.1 - - - -
42E LEU* 3.6 35.4 - - + -
43E MET* 2.9 39.3 - - + -
46E GLN* 3.0 47.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 123 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119D SER 2.8 24.5 + - - +
120D PHE* 3.6 6.3 - - - +
122D PHE* 1.3 74.3 - - - +
124D LEU* 1.3 58.3 + - - +
126D GLU* 3.1 23.9 + - - +
127D GLU* 2.8 32.5 + - + +
163D VAL* 3.7 25.1 - - + +
166D GLN* 3.6 30.1 - - + +
167D ILE* 3.5 39.0 - - + -
5E ARG* 5.6 1.8 - - + -
8E TYR* 3.5 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 124 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120D PHE 2.9 16.8 + - - +
121D LYS 3.9 3.4 - - - +
123D LEU* 1.3 72.9 - - - +
125D GLN* 1.3 62.7 + - - +
127D GLU* 3.0 18.1 + - + +
128D ILE* 2.8 32.9 + - + +
131D CYS* 3.6 34.3 - - + -
133D LEU* 3.9 12.1 - - + -
142D ILE* 3.5 32.8 - - + -
146D MET* 4.7 12.8 - - + -
151D ILE* 4.6 20.2 - - + -
163D VAL* 5.7 2.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 125 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D LYS* 3.1 14.0 + - + +
122D PHE* 3.3 11.4 - - - +
124D LEU* 1.3 75.5 - - - +
126D GLU* 1.3 61.8 + - + +
128D ILE* 3.2 23.5 + - - +
129D SER* 4.1 5.9 + - - -
131D CYS 5.2 4.5 - - - +
133D LEU* 4.2 7.9 - - + +
46E GLN* 2.8 40.3 + - - +
49E GLN* 4.1 19.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 126 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122D PHE* 2.7 21.9 + - - +
123D LEU* 3.1 29.6 + - - +
125D GLN* 1.3 75.8 - - + +
127D GLU* 1.3 62.8 + - - +
128D ILE* 3.6 0.5 + - - -
2E ASP* 5.8 0.7 - - - -
4E SER* 3.0 55.4 + - - +
5E ARG* 3.6 19.4 + - + +
7E LEU* 5.9 0.2 - - + -
8E TYR* 3.6 9.0 - - - +
42E LEU* 3.3 34.2 - - + +
56E GLU* 4.5 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 127 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123D LEU 2.8 19.9 + - - +
124D LEU* 3.0 21.7 + - + +
126D GLU* 1.3 77.3 - - + +
128D ILE* 1.3 77.6 + - + +
159D ILE* 4.7 7.7 - - + +
162D ARG* 2.8 35.1 + - - +
163D VAL* 4.3 22.3 - - + +
5E ARG* 2.8 41.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 128 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124D LEU* 2.8 24.0 + - + +
125D GLN* 3.2 15.8 - - - +
126D GLU 3.4 1.8 - - - -
127D GLU* 1.3 99.2 - - + +
129D SER* 1.3 62.2 + - - +
130D LYS* 3.0 37.2 + - + +
131D CYS* 4.1 12.6 + - + +
151D ILE* 5.2 22.4 - - + -
----------------------------------------------------------
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