Contacts of the helix formed by residues 146 - 165 (chain B) in PDB entry 6EBT
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 146 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B GLN* 3.3 16.2 - - - -
143B THR* 3.0 9.7 + - - -
144B GLY 3.4 1.0 + - - -
145B SER* 1.3 78.5 - - - +
147B THR* 1.3 65.8 + - - +
148B GLN 3.2 4.0 + - - -
149B THR 3.3 2.1 + - - -
150B ASN* 3.1 18.8 + - - +
187B SER 5.1 0.2 - - - -
191B PHE* 3.6 28.4 - - - -
410B PRO* 4.1 5.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 147 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A HIS* 5.0 2.6 + - - -
143B THR* 3.0 14.0 + - + -
145B SER* 2.7 22.7 + - - -
146B GLY* 1.3 76.5 - - - +
148B GLN* 1.3 59.6 + - + +
150B ASN* 3.1 8.8 + - + +
151B MET* 2.8 46.1 + - + +
187B SER* 3.0 39.8 + - - -
188B ASN* 4.3 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 148 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B THR* 5.0 1.0 + - - -
75B SER* 3.1 30.0 + - - +
78B ASN* 6.1 0.2 - - - +
79B PHE* 3.2 30.0 - - - -
138B LEU* 3.3 17.8 - - + +
142B GLN* 3.5 27.6 + - - +
143B THR* 3.2 28.7 + - + +
146B GLY 3.2 1.0 - - - -
147B THR* 1.3 77.8 - - + +
149B THR* 1.3 51.4 + - - +
151B MET* 3.2 20.9 + - + +
152B ASN 2.7 29.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 149 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B MET* 3.2 22.8 - - + +
93B ILE* 3.8 26.5 - - + -
96B PHE* 3.8 23.1 - - + -
138B LEU* 3.8 6.5 - - - +
142B GLN* 2.9 30.8 + - - -
146B GLY 3.3 6.5 + - - -
148B GLN* 1.3 72.8 - - - +
150B ASN* 1.3 60.3 + - - +
152B ASN* 3.1 9.5 + - + +
153B VAL* 2.8 29.5 + - + +
191B PHE* 4.4 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 150 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B PHE* 3.6 16.7 - - + -
100B LYS* 2.9 29.6 + - - -
146B GLY 3.1 12.2 + - - +
147B THR* 3.1 13.3 + - - +
149B THR* 1.3 77.7 - - - +
151B MET* 1.3 60.8 + - - +
153B VAL* 3.3 2.8 + - - +
154B ASN* 2.9 40.2 + - - +
182B ASN* 3.2 22.6 + - - +
187B SER* 4.1 16.5 - - - +
190B THR* 3.3 23.7 + - - +
191B PHE* 5.6 0.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 151 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B GLN* 3.3 54.1 - - + +
72B THR* 4.4 1.8 - - - +
75B SER* 4.5 3.8 - - - +
147B THR* 2.8 26.7 + - + +
148B GLN* 3.6 35.7 - - + +
150B ASN* 1.3 74.3 - - - +
152B ASN* 1.3 66.9 + - - +
154B ASN* 3.7 11.5 - - - +
155B GLU* 2.9 30.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 152 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B TYR* 3.7 4.6 - - - +
72B THR* 3.3 25.8 + - - +
135B HIS 3.1 21.6 + - - -
136B PHE* 3.4 33.7 - - + +
137B PRO* 3.4 9.7 - - - +
138B LEU* 3.6 14.6 + - + +
148B GLN 2.7 17.6 + - - +
149B THR* 3.3 15.2 + - + +
151B MET* 1.3 72.9 - - - +
153B VAL* 1.3 60.1 + - - +
155B GLU* 4.0 0.7 - - - +
156B VAL* 3.0 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 153 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B ILE* 4.8 4.3 - - + +
96B PHE* 3.6 37.9 - - + -
97B GLY 5.0 0.4 - - - +
100B LYS* 3.6 22.9 - - + -
127B VAL* 5.2 1.3 - - + -
136B PHE* 3.5 28.0 - - + -
149B THR* 2.8 24.4 + - + +
150B ASN 3.7 3.4 - - - +
152B ASN* 1.3 69.2 - - - +
154B ASN* 1.3 68.0 + - - +
157B ILE* 3.0 47.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 154 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B GLN* 6.1 0.2 - - - +
100B LYS* 3.1 26.3 + - - -
150B ASN* 2.9 30.9 + - - +
151B MET* 3.2 11.4 + - - +
153B VAL* 1.3 77.5 - - - +
155B GLU* 1.3 56.9 + - + +
158B SER* 3.0 31.0 + - - -
177B PRO* 3.5 29.8 + - + +
178B ASN* 5.3 0.6 - - - +
181B VAL* 3.4 17.9 - - - +
182B ASN* 3.0 28.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 155 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B GLU* 5.1 0.3 - - - +
67B TYR 3.1 8.8 - - - +
68B TYR* 4.2 0.4 - - - -
69B GLY* 2.7 40.2 + - - +
70B ALA* 3.5 4.7 + - - +
71B GLN* 3.0 46.1 + - - +
72B THR* 2.7 25.4 + - - -
151B MET 2.9 17.2 + - - +
152B ASN 4.0 2.5 - - - +
154B ASN* 1.3 75.1 - - - +
156B VAL* 1.3 60.5 + - - +
158B SER* 3.7 1.6 - - - -
159B ASN* 2.9 31.2 + - - +
177B PRO* 4.3 18.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 156 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B TYR* 3.5 18.6 - - + +
68B TYR 3.8 15.0 - - - +
127B VAL* 4.3 3.8 - - + -
132B LEU* 4.0 23.6 - - + -
135B HIS* 3.3 33.2 - - + +
136B PHE* 3.9 23.3 - - + -
152B ASN* 3.0 27.0 + - - +
153B VAL 4.0 1.3 - - - +
155B GLU* 1.3 76.4 - - - +
157B ILE* 1.3 57.1 + - - +
160B ARG* 2.9 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 157 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B GLY* 4.9 2.5 - - - -
100B LYS* 3.6 24.7 - - + -
120B ILE* 3.8 31.0 - - + +
123B ALA* 3.6 9.5 - - + +
124B ALA* 4.1 15.0 - - - +
127B VAL* 4.0 22.7 - - + -
153B VAL* 3.0 41.1 + - + +
156B VAL* 1.3 76.5 - - + +
158B SER* 1.3 58.0 + - - +
160B ARG* 4.6 0.4 - - - -
161B ALA* 2.9 29.6 + - - +
181B VAL* 3.7 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 158 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B ASN 3.0 21.0 + - - -
155B GLU 3.7 3.5 + - - -
157B ILE* 1.3 77.4 - - - +
159B ASN* 1.3 60.8 + - - +
161B ALA 3.4 0.7 + - - -
162B ILE* 2.8 38.8 + - - +
172B LYS* 4.8 0.5 - - - -
175B VAL* 2.7 41.1 + - - +
177B PRO* 3.8 25.7 - - - +
181B VAL* 4.1 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 159 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B ARG* 3.7 14.6 - - - +
53B GLU* 4.4 3.8 + - - -
67B TYR* 2.6 38.6 + - - +
68B TYR 4.0 5.7 + - - -
69B GLY* 4.4 2.8 - - - +
155B GLU* 2.9 14.0 + - - +
158B SER* 1.3 76.7 + - - +
160B ARG* 1.3 60.6 + - - +
162B ILE* 3.4 11.9 + - - +
163B GLU* 2.9 23.6 + - - +
169B LEU* 3.3 25.3 - - + +
170B GLY* 2.8 32.1 + - - +
172B LYS 5.2 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 160 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B TYR* 3.6 36.8 + - + -
123B ALA* 3.6 22.4 - - + -
126B GLU* 2.7 40.9 + - - +
132B LEU* 4.3 10.2 - - + +
156B VAL 2.9 18.4 + - - +
159B ASN* 1.3 77.0 - - - +
161B ALA* 1.3 56.0 + - - +
163B GLU* 2.8 34.5 + - - +
164B MET* 3.0 57.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 161 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B ALA* 3.7 34.0 - - + +
120B ILE* 4.0 4.0 - - - +
123B ALA* 4.0 1.3 - - - +
157B ILE 2.9 18.8 + - - +
158B SER 3.7 1.1 - - - +
160B ARG* 1.3 73.3 - - - +
162B ILE* 1.3 66.6 + - - +
164B MET* 3.2 6.0 + - - +
165B LEU* 3.0 26.9 + - - +
175B VAL* 3.7 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 162 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B SER* 2.8 30.8 + - - +
159B ASN* 3.5 20.6 - - - +
161B ALA* 1.3 76.1 - - - +
163B GLU* 1.3 64.0 + - - +
165B LEU* 3.0 12.4 + - - +
167B GLY* 2.9 39.9 + - - +
168B GLU 3.3 25.1 - - - +
169B LEU* 4.2 2.2 - - + +
172B LYS 3.8 9.0 - - - +
173B ILE 3.3 34.3 - - - +
174B PRO* 4.1 1.3 - - - -
175B VAL* 3.5 27.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 163 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B TYR* 2.5 35.9 + - - -
159B ASN 2.9 14.6 + - - +
160B ARG* 2.8 30.5 + - - +
162B ILE* 1.3 77.5 - - - +
164B MET* 1.3 62.9 + - - +
166B GLY* 3.0 13.6 + - - +
167B GLY 4.6 7.0 - - - +
169B LEU* 4.3 16.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 164 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B ALA* 4.1 17.9 - - + +
122B LYS* 3.9 35.7 - - + -
123B ALA 4.1 9.2 - - - +
126B GLU* 3.4 30.5 - - - +
160B ARG* 3.0 49.9 + - + +
161B ALA* 3.2 9.2 + - - +
163B GLU* 1.3 75.9 - - - +
165B LEU* 1.3 61.9 + - + +
166B GLY 3.3 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 165 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B LYS* 4.3 27.6 - - + +
116B ILE* 4.6 7.9 - - + -
119B ALA* 3.9 20.9 - - + -
161B ALA 3.0 17.4 + - - +
162B ILE 3.0 6.4 + - - +
164B MET* 1.3 79.7 - - + +
166B GLY* 1.3 62.5 + - - +
167B GLY* 3.3 2.2 + - - -
174B PRO* 3.5 34.6 - - + +
175B VAL* 3.9 14.1 - - + -
----------------------------------------------------------
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