Contacts of the helix formed by residues 146 - 166 (chain B) in PDB entry 3LRB
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 MET 146 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B HIS* 5.7 2.2 - - + -
139B LEU* 3.1 51.6 - - + +
142B VAL* 3.2 23.3 - - + +
143B GLY* 3.2 20.3 - - - +
144B PRO 2.6 5.3 + - - -
145B LYS* 1.3 74.9 - - - +
147B ILE* 1.3 63.8 + - - +
148B THR 3.3 0.2 - - - -
149B ARG* 3.0 13.0 + - - +
150B VAL* 3.0 34.1 + - + -
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Residues in contact with ILE 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B MET* 4.9 1.1 - - + -
136B PHE* 3.9 19.5 - - + -
139B LEU* 3.4 22.9 + - + +
140B ASN* 2.9 43.5 - - - +
144B PRO* 2.9 17.9 + - + +
146B MET* 1.3 75.1 - - - +
148B THR* 1.3 62.8 + - - +
149B ARG 3.0 0.6 + - - -
150B VAL* 3.1 13.5 + - + -
151B GLN* 2.8 29.2 + - + +
288B GLY 5.1 0.9 - - - +
291B GLY* 3.5 27.1 - - - -
292B GLY 4.3 0.9 - - - +
295B LEU* 4.0 17.9 - - + -
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Residues in contact with THR 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B VAL* 3.7 26.5 - - + +
14B PRO* 3.1 32.2 + - - +
15B VAL* 5.8 0.7 - - - -
18B MET* 3.7 21.5 - - + -
144B PRO 2.9 24.5 - - - +
145B LYS* 3.9 4.6 + - - +
147B ILE* 1.3 77.2 - - + +
149B ARG* 1.3 57.3 + - - +
151B GLN* 3.2 10.1 - - - +
152B ALA* 2.8 29.8 + - - +
295B LEU* 5.0 4.9 - - + -
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Residues in contact with ARG 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B VAL* 6.2 1.4 - - - +
14B PRO* 5.4 11.6 - - + +
145B LYS* 3.1 53.8 + - - +
146B MET* 3.0 20.7 + - - +
147B ILE 3.0 0.4 - - - -
148B THR* 1.3 80.2 + - - +
150B VAL* 1.3 63.3 + - - +
151B GLN 3.4 0.3 + - - -
152B ALA* 3.5 5.8 + - - +
153B VAL* 3.4 25.2 + - - +
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Residues in contact with VAL 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B PHE* 4.1 15.5 - - + -
139B LEU* 3.3 26.0 - - + -
146B MET* 3.0 27.4 + - + +
147B ILE* 3.4 10.5 - - + +
149B ARG* 1.3 74.5 - - - +
151B GLN* 1.3 67.0 + - - +
153B VAL* 3.2 9.8 + - - +
154B ALA* 3.1 19.4 + - - +
287B LEU* 3.5 30.2 - - + +
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Residues in contact with GLN 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B PRO 5.2 0.2 - - - +
17B LEU 4.9 0.2 - - - +
18B MET* 4.1 25.1 - - + +
21B GLY* 4.0 7.9 + - - -
22B ASN* 3.8 7.8 + - - +
147B ILE* 2.8 18.1 + - + +
148B THR* 3.2 11.2 - - - +
150B VAL* 1.3 74.3 - - - +
152B ALA* 1.3 70.6 + - - +
153B VAL 3.2 0.2 + - - -
154B ALA* 3.3 1.4 + - - +
155B THR* 3.0 57.5 + - + +
288B GLY* 2.4 42.3 - - - +
289B SER* 3.3 5.8 - - - +
292B GLY* 3.0 24.9 + - - -
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Residues in contact with ALA 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B PRO* 4.4 13.0 - - + +
17B LEU* 3.7 37.8 - - + +
148B THR 2.8 21.4 + - - +
149B ARG* 3.8 6.5 - - - +
151B GLN* 1.3 71.9 - - - +
153B VAL* 1.3 67.2 + - + +
155B THR* 3.5 2.2 + - - -
156B VAL* 3.1 21.8 + - - +
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Residues in contact with VAL 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B ARG 3.4 15.9 - - - +
150B VAL* 3.2 9.8 + - - +
151B GLN 3.1 0.6 - - - -
152B ALA* 1.3 77.1 - - + +
154B ALA* 1.3 66.3 + - - +
156B VAL* 2.9 21.1 + - + +
157B LEU* 3.0 28.0 + - + +
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Residues in contact with ALA 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B VAL 3.1 9.0 + - - +
153B VAL* 1.3 78.9 - - - +
155B THR* 1.3 65.0 + - - +
157B LEU* 2.9 32.8 + - + +
158B ALA* 3.1 5.7 + - - +
284B ALA* 3.0 27.3 - - - +
287B LEU* 3.8 16.2 - - + -
288B GLY* 3.4 23.8 - - - +
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Residues in contact with THR 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B LEU* 3.6 24.5 + - - +
21B GLY* 3.8 23.8 - - - +
24B MET* 6.1 4.0 - - + -
151B GLN* 3.0 42.1 + - - +
152B ALA* 3.5 5.0 + - - -
154B ALA* 1.3 75.1 - - - +
156B VAL* 1.3 60.1 + - - +
158B ALA* 3.0 10.2 + - - +
159B LEU* 2.9 32.2 + - - +
284B ALA 4.8 0.9 - - - -
285B GLY* 4.3 13.9 - - - +
288B GLY* 4.4 1.6 - - - -
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Residues in contact with VAL 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B LEU* 4.3 21.1 - - + -
152B ALA 3.1 14.6 + - - +
153B VAL* 2.9 14.6 + - + +
155B THR* 1.3 77.3 + - - +
157B LEU* 1.3 66.7 + - + +
159B LEU* 3.1 27.5 + - + +
160B ILE* 3.4 10.9 + - + +
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Residues in contact with LEU 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B VAL* 3.0 22.7 + - + +
154B ALA* 2.9 29.2 + - + +
156B VAL* 1.3 80.5 - - + +
158B ALA* 1.3 56.4 + - - +
159B LEU 3.3 0.2 - - - -
160B ILE* 3.3 32.3 - - + +
280B PHE* 4.2 29.2 - - + -
281B CYS* 3.1 26.4 - - - +
284B ALA* 4.2 10.3 - - + -
287B LEU* 6.1 4.0 - - + -
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Residues in contact with ALA 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B MET* 5.6 3.5 - - + +
154B ALA 3.1 4.8 + - - +
155B THR* 3.0 9.9 + - - +
157B LEU* 1.3 75.3 - - - +
159B LEU* 1.3 68.1 + - + +
160B ILE 3.2 1.1 - - - -
161B PRO* 3.2 12.0 - - - +
162B ILE* 3.7 15.8 + - - +
281B CYS 3.0 25.6 - - - +
282B ALA* 5.3 0.2 - - - -
285B GLY* 4.0 23.1 - - - +
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Residues in contact with LEU 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B LEU* 5.7 7.6 - - + -
20B SER* 6.0 0.9 - - - +
24B MET* 3.6 34.8 - - + -
155B THR* 2.9 18.6 + - - +
156B VAL* 3.1 22.4 + - + +
158B ALA* 1.3 79.5 - - - +
160B ILE* 1.3 69.6 + - - +
162B ILE* 5.0 0.7 - - + -
163B VAL* 2.9 45.7 + - + +
164B GLY 3.7 0.2 + - - -
234B ILE* 5.1 10.5 - - + -
238B CYS* 4.6 4.9 - - - -
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Residues in contact with ILE 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B VAL* 3.4 9.3 + - + +
157B LEU* 3.3 32.5 - - + +
159B LEU* 1.3 81.0 - - - +
161B PRO* 1.3 75.3 - - + +
163B VAL 3.8 0.3 - - - -
164B GLY* 2.8 18.9 + - - -
277B ILE* 4.9 11.0 - - + -
281B CYS* 4.1 13.7 - - - -
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Residues in contact with PRO 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B PHE* 6.2 1.6 - - + -
157B LEU 3.4 4.5 - - - +
158B ALA* 3.2 18.8 - - - +
160B ILE* 1.3 98.3 - - + +
162B ILE* 1.3 58.1 + - + +
164B GLY* 2.5 28.2 + - - -
165B ILE* 2.9 12.4 + - - +
278B VAL* 3.4 31.0 - - + -
281B CYS* 3.4 25.8 - - + +
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Residues in contact with ILE 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B MET* 3.8 24.5 - - + -
28B VAL* 3.4 39.0 - - + -
158B ALA 4.1 12.8 - - - +
159B LEU* 3.4 2.5 + - - +
161B PRO* 1.3 80.3 - - + +
163B VAL* 1.3 66.4 + - + +
165B ILE* 2.9 24.3 + - - +
166B ALA* 3.1 11.0 + - + +
238B CYS* 3.9 34.8 - - + +
242B SER* 4.2 14.9 - - - +
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Residues in contact with VAL 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159B LEU* 2.9 40.4 + - + +
160B ILE 3.8 1.1 - - - -
162B ILE* 1.3 71.7 - - + +
164B GLY* 1.3 62.8 + - - +
165B ILE 3.3 0.2 - - - -
166B ALA* 3.7 23.8 + - + -
167B VAL* 4.0 18.5 + - + +
168B PHE* 5.0 1.7 - - - -
237B VAL* 6.4 2.0 - - + -
238B CYS* 4.1 21.3 - - - -
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Residues in contact with GLY 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B ILE 2.8 14.7 + - - -
161B PRO* 2.5 19.7 + - - -
163B VAL* 1.3 74.3 - - - +
165B ILE* 1.3 54.5 + - - -
168B PHE* 2.6 48.3 + - - +
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Residues in contact with ILE 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B PRO 2.9 10.6 + - - +
162B ILE* 2.9 10.5 + - - +
164B GLY* 1.3 75.6 - - - +
166B ALA* 1.3 57.4 + - - +
167B VAL 2.9 9.3 + - - -
169B GLY* 2.8 36.8 + - - +
170B TRP* 3.0 5.5 + - - +
241B LEU 4.1 13.1 - - - +
242B SER* 4.9 6.5 - - - +
245B ALA* 3.8 30.5 - - + -
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Residues in contact with ALA 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B ILE* 3.1 10.1 + - + +
163B VAL* 3.7 32.3 - - + -
164B GLY 3.5 0.8 - - - -
165B ILE* 1.3 74.6 - - - +
167B VAL* 1.3 62.5 + - + +
170B TRP* 4.2 10.3 - - - +
237B VAL* 5.9 0.9 - - + -
238B CYS* 5.9 2.5 - - - +
241B LEU* 3.7 49.7 - - + +
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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
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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) + - + + + + + -
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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