Contacts of the helix formed by residues 143 - 159 (chain D) in PDB entry 4G1U
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 143 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141D VAL 3.5 2.8 + - - -
142D LEU* 1.3 76.0 - - - +
144D GLY* 1.3 66.0 + - - +
145D GLY* 4.1 2.0 + - - -
146D GLU* 3.2 35.5 + - - +
147D GLN* 3.0 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 144 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143D SER* 1.3 75.4 - - - +
145D GLY* 1.3 57.6 + - - +
147D GLN* 3.2 10.2 + - - +
148D GLN 3.0 22.7 + - - -
177D ALA 6.0 2.2 - - - -
178D LEU* 3.8 17.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 145 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143D SER* 3.5 3.4 + - - -
144D GLY* 1.3 72.1 - - - +
146D GLU* 1.3 60.2 + - - +
148D GLN* 3.0 8.0 + - - +
149D ARG* 2.9 39.0 + - - +
178D LEU* 4.2 1.2 - - - +
182D HIS* 3.6 41.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 146 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134D LEU* 3.9 20.2 - - + +
137D ARG* 4.6 11.2 + - - -
142D LEU* 3.3 28.7 - - + +
143D SER* 3.2 37.6 + - - +
144D GLY 3.3 0.4 - - - -
145D GLY* 1.3 75.0 - - - +
147D GLN* 1.3 56.6 + - - +
149D ARG* 3.3 28.3 + - - +
150D VAL* 2.9 35.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 147 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92D GLN 4.5 8.6 - - - +
94D SER* 2.4 35.4 + - - -
139D TYR* 3.6 37.8 + - + +
140D ARG* 4.8 6.1 + - - +
142D LEU* 3.9 18.4 + - + +
143D SER 3.0 19.4 + - - +
144D GLY* 3.3 11.9 - - - +
146D GLU* 1.3 73.9 - - - +
148D GLN* 1.3 65.0 + - - +
150D VAL* 3.8 5.7 - - - +
151D GLN* 2.9 31.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 148 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90D MET* 3.6 21.4 - - - +
92D GLN* 3.3 25.6 - - - +
144D GLY 3.0 12.0 + - - +
145D GLY* 3.0 13.9 + - - +
147D GLN* 1.3 77.1 - - - +
149D ARG* 1.3 62.5 + - + +
151D GLN* 4.9 0.2 - - - -
152D LEU* 2.9 30.5 + - - +
171D LEU* 5.8 0.2 - - - +
178D LEU* 3.1 33.1 - - + +
182D HIS* 4.2 12.5 + - + +
183D GLN* 5.0 1.6 - - - +
186D THR* 2.7 43.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 149 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129D THR* 3.2 27.4 + - - +
130D ASP* 2.9 38.7 + - - +
131D CYS* 4.2 5.2 - - - -
134D LEU* 3.8 17.7 - - + +
145D GLY 2.9 21.5 + - - +
146D GLU* 3.8 22.6 + - - +
148D GLN* 1.3 80.9 - - + +
150D VAL* 1.3 58.2 + - + +
152D LEU* 3.6 10.0 + - + +
153D ALA* 2.9 28.2 + - - +
181D TYR* 6.3 0.4 - - - -
182D HIS* 4.6 15.6 + - + -
185D HIS* 4.8 18.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 150 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D VAL* 3.6 31.9 - - + -
105D VAL* 4.4 5.2 - - + -
106D ILE* 4.1 9.4 - - + +
131D CYS* 4.3 10.1 - - - -
134D LEU* 4.4 6.7 - - + -
139D TYR* 3.6 28.3 - - + -
142D LEU* 3.5 21.1 - - + -
146D GLU 2.9 21.4 + - - +
147D GLN 3.9 2.9 - - - +
149D ARG* 1.3 76.8 - - - +
151D GLN* 1.3 58.9 + - - +
153D ALA* 3.3 7.0 + - - +
154D ARG* 2.9 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 151 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A LEU* 5.1 4.9 - - - +
90D MET* 4.0 16.0 - - + +
91D ARG 4.0 19.6 + - - +
92D GLN* 5.2 7.6 - - - +
93D TYR 5.6 2.2 + - - -
94D SER* 4.8 5.3 - - - +
96D LEU* 6.3 0.4 - - - +
105D VAL* 4.4 6.1 - - - +
139D TYR* 2.5 39.3 + - - +
147D GLN* 2.9 18.1 + - - +
148D GLN* 3.9 2.7 - - - +
150D VAL* 1.3 73.2 - - - +
152D LEU* 1.3 66.8 + - - +
154D ARG* 3.0 44.5 + - - +
155D VAL* 3.0 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 152 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90D MET* 3.8 16.0 - - + +
129D THR* 3.9 15.0 - - + +
148D GLN 2.9 18.6 + - - +
149D ARG* 3.6 9.4 - - + +
151D GLN* 1.3 75.9 - - - +
153D ALA* 1.3 57.6 + - - +
155D VAL* 3.0 12.6 - - + +
156D LEU* 2.9 41.4 + - + +
169D LEU* 5.2 1.3 - - + -
186D THR* 3.9 32.3 - - + +
189D LEU* 3.9 29.2 - - + -
190D LEU* 4.0 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 153 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D ILE* 3.7 23.8 - - + -
125D VAL* 3.1 23.5 - - + +
126D MET* 4.8 1.1 - - + -
129D THR* 3.3 19.5 - - - +
131D CYS* 4.1 2.7 - - - -
149D ARG 2.9 18.4 + - - +
150D VAL 3.4 6.5 - - - +
151D GLN 3.1 0.2 - - - -
152D LEU* 1.3 75.1 - - - +
154D ARG* 1.3 65.6 + - - +
156D LEU 3.4 0.2 + - - -
157D ALA* 2.9 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 154 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A LEU* 3.7 30.7 - - - +
224A GLU* 3.8 29.1 + - - +
228A LEU* 3.9 21.6 - - - +
89D VAL 4.1 16.7 + - - -
90D MET* 5.4 0.8 - - - +
91D ARG 5.4 3.2 - - - +
105D VAL* 3.3 37.7 - - + +
106D ILE* 4.0 12.1 - - - +
109D GLY* 4.0 12.8 - - - +
150D VAL 2.9 13.5 + - - +
151D GLN* 3.0 38.7 + - - +
153D ALA* 1.3 75.9 - - - +
155D VAL* 1.3 64.6 + - - +
157D ALA* 3.2 4.5 + - - +
158D GLN* 3.0 28.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 155 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D ALA* 3.7 24.0 - - + -
89D VAL 4.6 6.5 - - - +
90D MET* 3.8 25.8 - - + -
151D GLN 3.0 13.8 + - - +
152D LEU* 3.0 30.3 - - + +
154D ARG* 1.3 79.9 - - - +
156D LEU* 1.3 60.8 + - - +
158D GLN* 3.1 12.4 + - - +
159D LEU* 3.0 19.7 + - + +
169D LEU* 3.5 33.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 156 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125D VAL* 3.6 21.5 - - + +
128D GLN* 3.9 21.5 - - + +
129D THR* 3.6 27.8 - - + -
152D LEU* 2.9 29.0 + - + +
155D VAL* 1.3 77.1 - - - +
157D ALA* 1.3 61.8 + - - +
159D LEU* 3.2 9.6 + - + +
160D TRP* 3.1 18.4 + - - +
167D ARG* 6.1 1.6 - - - +
169D LEU* 3.8 24.2 - - + -
189D LEU* 4.4 3.8 - - + -
190D LEU* 4.7 0.7 - - + -
193D LEU* 3.9 25.1 - - + -
197D GLU* 5.8 1.8 - - - +
199D LEU* 4.9 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 157 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D ILE* 3.9 26.9 - - + +
109D GLY* 4.9 0.2 - - - -
110D ARG* 3.1 34.7 + - + +
121D ALA* 5.2 0.4 - - - -
122D LEU* 4.2 13.7 - - + -
125D VAL* 3.6 13.9 - - + +
153D ALA 2.9 17.7 + - - +
154D ARG 3.4 5.2 - - - +
156D LEU* 1.3 73.7 - - - +
158D GLN* 1.3 65.0 + - - +
159D LEU 3.2 0.5 + - - -
160D TRP* 3.2 4.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 158 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A TYR* 3.5 21.5 + - - +
228A LEU* 3.2 24.0 - - + +
84D ALA* 2.9 26.5 + - - +
85D ARG 4.3 2.8 - - - +
87D ARG 3.4 16.0 + - - -
88D ALA* 3.5 18.9 - - + +
89D VAL 4.7 4.0 + - - +
109D GLY* 3.2 25.2 + - - +
112D PRO* 4.2 4.3 - - + -
113D TYR* 2.8 27.2 + - - -
154D ARG* 3.0 19.0 + - - +
155D VAL* 3.1 11.7 + - - +
157D ALA* 1.3 76.2 - - - +
159D LEU* 1.3 57.5 - - - +
160D TRP 3.4 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 159 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84D ALA 5.3 0.4 - - - +
85D ARG 3.6 13.5 - - - +
86D THR 3.3 27.8 - - - +
87D ARG 4.4 0.4 - - - -
88D ALA* 3.6 25.1 - - + +
113D TYR* 4.2 1.8 - - - -
155D VAL 3.0 10.3 + - - +
156D LEU* 3.4 12.1 - - + +
157D ALA 3.1 0.6 - - - -
158D GLN* 1.3 79.3 - - - +
160D TRP* 1.3 57.7 + - - +
161D GLN 3.7 0.2 + - - -
167D ARG* 2.7 48.1 + - + +
168D TRP 3.9 7.4 - - - +
169D LEU* 3.8 37.2 - - + -
199D LEU* 4.0 15.7 - - + -
----------------------------------------------------------
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