Contacts of the helix formed by residues 110 - 122 (chain D) in PDB entry 1L9X
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 CYS 110 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73D GLY* 4.0 3.1 - - - -
74D GLY 5.1 7.4 - - - -
109D THR* 1.3 68.9 - - + +
111D LEU* 1.3 69.1 + - - +
113D PHE* 2.9 14.3 + - - +
114D GLU* 2.9 19.2 + - - +
170D PHE 4.0 17.0 - - - -
171D HIS* 4.3 6.5 - - - -
217D VAL 2.8 14.6 + - - -
218D GLN* 3.7 33.2 + - - +
220D HIS* 3.4 35.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 111 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D GLN* 3.7 22.4 - - - +
72D PRO 3.6 1.6 - - - +
73D GLY* 3.5 3.1 - - - -
74D GLY* 3.4 31.0 - - - +
75D SER* 5.1 0.2 - - - -
76D VAL* 3.7 38.1 - - + +
78D LEU* 3.8 14.8 - - + -
83D TYR* 3.7 31.6 - - + -
109D THR 2.8 2.0 + - - -
110D CYS* 1.3 81.6 - - - +
112D GLY* 1.3 57.4 + - - +
114D GLU* 3.2 20.5 + - - +
115D GLU* 2.9 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 112 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71D PHE* 3.4 36.3 - - - -
83D TYR* 3.6 4.8 + - - -
108D GLY* 3.6 7.3 - - - -
109D THR 2.9 8.7 + - - -
111D LEU* 1.3 81.1 - - - +
113D PHE* 1.3 54.1 + - - +
115D GLU* 3.4 4.8 + - - +
116D LEU* 3.0 33.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 113 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108D GLY* 3.7 9.3 - - - +
110D CYS* 2.9 11.7 + - - +
112D GLY* 1.3 74.7 - - - +
114D GLU* 1.3 69.9 + - + +
116D LEU* 3.1 8.2 + - - +
117D SER* 3.0 21.1 + - - -
175D LEU* 4.1 21.8 - - + -
204D ILE* 3.7 35.4 - - + -
205D SER 4.4 2.7 - - - -
207D MET* 3.6 35.9 - - + +
216D GLY* 3.5 27.1 - - - -
217D VAL 3.4 23.1 - - - +
218D GLN* 3.5 32.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 114 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D VAL 5.2 1.4 - - - +
78D LEU* 3.7 11.1 - - + +
110D CYS* 2.9 19.4 + - - +
111D LEU* 3.4 23.5 - - - +
113D PHE* 1.3 79.2 - - + +
115D GLU* 1.3 61.4 + - - +
117D SER* 2.5 25.7 + - - -
118D LEU* 3.0 10.2 + - - +
126D LEU* 4.2 20.1 - - + +
171D HIS* 5.6 2.8 - - - +
173D TRP* 4.4 15.6 - - - +
218D GLN* 4.9 13.9 - - - +
1006D BME 3.6 23.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 115 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71D PHE* 4.4 5.6 - - + -
78D LEU* 3.4 34.8 - - + +
83D TYR* 4.3 5.4 - - + -
84D ALA* 3.5 27.3 - - - +
87D ALA* 3.6 24.2 - - + +
88D LYS* 4.7 0.2 - - - +
111D LEU 2.9 16.3 + - - +
112D GLY* 3.6 9.4 - - - +
113D PHE 3.2 0.2 - - - -
114D GLU* 1.3 78.0 - - - +
116D LEU* 1.3 56.6 + - - +
118D LEU* 3.3 9.6 + - - +
119D LEU* 2.9 62.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 116 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71D PHE* 4.1 23.3 - - + -
91D TYR* 4.5 7.0 - - + -
106D VAL* 4.1 7.0 - - + -
107D TRP 4.7 1.6 - - - -
108D GLY* 3.8 10.1 - - - +
112D GLY 3.0 19.4 + - - +
113D PHE* 3.1 6.9 + - - +
115D GLU* 1.3 74.0 - - - +
117D SER* 1.3 65.9 + - - +
119D LEU* 4.3 10.1 - - + -
120D ILE* 3.0 32.6 + - + +
190D PHE* 4.2 13.4 - - + -
207D MET* 5.0 2.5 - - + -
214D VAL* 3.6 26.0 - - + -
215D TYR 3.1 34.1 - - - +
216D GLY* 4.2 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 117 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113D PHE* 3.0 14.1 + - - -
114D GLU* 2.5 27.3 + - - -
116D LEU* 1.3 77.1 - - - +
118D LEU* 1.3 52.1 + - - +
121D SER* 2.7 40.5 + - - -
123D GLU 4.5 1.2 + - - -
125D LEU 5.8 0.2 + - - -
175D LEU* 4.3 28.6 - - - +
186D LEU* 3.8 14.5 - - - +
207D MET* 4.6 8.2 - - - +
1006D BME 3.9 11.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 118 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78D LEU* 4.1 26.5 - - + +
79D ARG* 5.8 1.8 - - + -
84D ALA* 5.6 1.1 - - + -
114D GLU 3.0 8.4 + - - +
115D GLU* 3.5 25.1 - - - +
117D SER* 1.3 79.5 + - - +
119D LEU* 1.3 61.6 + - + +
122D GLY* 2.7 37.3 + - - -
123D GLU* 3.4 32.8 - - - +
124D CYS* 4.4 3.1 - - + +
1006D BME 4.0 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 119 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71D PHE* 4.5 1.8 - - + -
87D ALA 4.2 6.7 - - - +
88D LYS* 3.7 37.2 - - + -
91D TYR* 3.7 46.6 - - + -
92D ASN* 5.7 0.2 - - - +
115D GLU* 2.9 53.0 + - + +
116D LEU* 3.3 14.8 + - + +
118D LEU* 1.3 81.2 - - + +
120D ILE* 1.3 64.2 + - + +
122D GLY* 4.4 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 120 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D TYR* 3.4 39.3 - - + +
116D LEU* 3.0 27.7 + - + +
119D LEU* 1.3 79.4 - - + +
121D SER* 1.3 62.3 + - - +
185D LYS* 3.5 43.0 + - + +
186D LEU* 3.8 15.5 - - + -
189D PHE* 3.6 34.5 - - + -
190D PHE* 3.6 19.1 - - + -
214D VAL* 4.9 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 121 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117D SER* 2.7 23.3 + - - -
120D ILE* 1.3 79.8 - - - +
122D GLY* 1.3 59.7 + - - +
123D GLU* 2.9 32.6 + - - +
125D LEU* 4.9 1.8 - - - +
183D ASN* 3.8 18.4 + - - -
185D LYS* 3.9 23.1 + - - +
186D LEU* 3.7 24.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 122 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118D LEU* 2.7 28.4 + - - +
119D LEU 4.4 2.4 + - - -
120D ILE 3.7 1.2 - - - -
121D SER* 1.3 72.9 - - - +
123D GLU* 1.3 62.6 + - - +
185D LYS* 5.9 1.3 - - - -
----------------------------------------------------------
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