Contacts of the helix formed by residues 147 - 159 (chain B) in PDB entry 3M9M
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 ASN 147 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1B MET* 5.2 2.0 - - + -
3B VAL* 3.6 14.8 - - - +
145B SER 3.3 2.0 + - - -
146B LYS* 1.3 91.3 - - - +
148B LYS* 1.3 62.8 + - - +
149B VAL* 3.1 2.0 + - - -
150B PHE* 2.6 55.2 + - - +
151B ALA* 3.1 21.7 + - - +
228B LEU* 4.6 0.2 - - - +
231B ASP* 5.4 1.6 + - - -
233B TYR* 3.5 50.3 + - + +
234B ASN* 4.5 5.4 - - - +
235B GLU 5.5 0.9 - - - +
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Residues in contact with LYS 148 (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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3B VAL* 3.8 4.0 - - + +
100B GLU* 3.1 35.9 + - - +
108B TYR* 3.5 49.2 - - + +
147B ASN* 1.3 74.2 - - - +
149B VAL* 1.3 59.0 + - - +
151B ALA* 3.2 0.5 + - - +
152B LYS* 2.9 32.3 + - - +
233B TYR* 4.1 8.9 + - + +
235B GLU* 3.5 37.3 + - - +
236B PRO 3.8 5.1 + - - -
237B ILE* 3.6 26.2 - - + -
240B ARG* 5.3 0.6 - - - +
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Residues in contact with VAL 149 (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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147B ASN* 3.1 6.8 + - - +
148B LYS* 1.3 77.6 - - - +
150B PHE* 1.3 58.9 + - + +
152B LYS* 3.7 5.2 - - - +
153B ILE* 2.9 47.3 + - + +
183B VAL* 4.5 2.0 - - + -
184B PRO* 4.1 11.7 - - + +
202B LEU* 6.4 0.2 - - + -
224B TYR* 3.2 31.2 - - + +
228B LEU* 3.7 25.6 - - + -
233B TYR* 3.3 33.7 - - + +
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Residues in contact with PHE 150 (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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145B SER* 3.8 19.9 - - - +
146B LYS* 5.1 1.1 - - + -
147B ASN* 2.6 36.4 + - - +
149B VAL* 1.3 73.2 - - + +
151B ALA* 1.3 59.1 + - - +
153B ILE* 3.7 21.1 - - + -
154B ALA* 3.0 5.7 + - - +
166B ILE* 2.8 32.7 - - + +
171B VAL* 3.6 35.7 - - + -
174B LEU* 4.0 33.9 - - + -
175B ILE* 4.0 6.7 - - + -
178B LEU* 4.9 1.6 - - + -
202B LEU* 4.0 23.3 - - + -
228B LEU* 4.0 27.4 - - + -
231B ASP* 5.8 1.1 - - - -
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Residues in contact with ALA 151 (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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3B VAL* 3.7 26.5 - - + +
5B PHE* 3.8 9.6 - - + +
143B GLY* 3.5 28.2 - - - +
145B SER* 3.9 8.0 - - - +
147B ASN 3.1 19.6 + - - +
148B LYS 3.2 4.2 + - - +
150B PHE* 1.3 74.1 - - - +
152B LYS* 1.3 68.7 + - - +
154B ALA* 3.1 17.7 - - - +
155B ALA 3.2 3.6 + - - -
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Residues in contact with LYS 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B PHE* 3.3 27.7 - - + +
7B ASP* 4.3 2.2 + - - -
106B GLU* 2.7 23.8 + - - -
108B TYR* 3.3 22.2 - - + +
148B LYS 2.9 16.4 + - - +
149B VAL* 3.7 5.8 - - - +
151B ALA* 1.3 76.2 - - - +
153B ILE* 1.3 65.0 + - - +
155B ALA* 2.9 15.4 + - - +
156B ASP* 2.9 20.6 + - - +
184B PRO* 3.7 29.4 - - + -
356B CA 4.7 5.4 - - - -
12P A 4.4 4.3 - - - -
13P G 2.6 30.2 + - - -
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Residues in contact with ILE 153 (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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149B VAL* 2.9 36.0 + - + +
150B PHE* 3.7 28.7 - - + +
152B LYS* 1.3 76.4 - - - +
154B ALA* 1.3 63.7 + - - +
156B ASP* 3.1 20.6 + - + +
157B MET* 3.1 26.3 + - + +
166B ILE* 4.2 8.5 - - + -
174B LEU* 4.8 3.8 - - + -
178B LEU* 3.9 35.2 - - + -
182B ASP 4.6 5.4 - - - +
183B VAL* 4.9 4.5 - - + -
184B PRO* 3.6 22.0 - - + -
202B LEU* 6.0 0.2 - - + -
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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
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143B GLY* 3.5 18.8 - - - -
144B ILE 4.1 2.7 - - - +
150B PHE 3.0 8.4 + - - +
151B ALA* 3.1 12.8 - - - +
152B LYS 3.0 0.4 - - - -
153B ILE* 1.3 75.6 - - - +
155B ALA* 1.3 61.6 + - - +
157B MET* 3.0 21.2 + - - +
158B ALA* 3.1 13.3 + - - +
164B LYS* 4.0 12.2 - - + +
166B ILE* 3.2 32.9 - - + +
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Residues in contact with ALA 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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5B PHE* 3.5 29.6 - - + -
7B ASP* 4.6 7.9 - - + -
141B THR* 3.7 22.4 - - + +
142B VAL 4.4 1.1 - - - -
143B GLY* 3.9 10.7 - - - +
151B ALA 3.2 1.3 + - - +
152B LYS 2.9 9.2 + - - +
154B ALA* 1.3 75.8 - - - +
156B ASP* 1.3 66.6 + - - +
158B ALA 3.0 0.2 + - - -
159B LYS* 2.8 32.7 + - - +
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Residues in contact with ASP 156 (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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5B PHE* 5.5 0.3 - - - -
7B ASP* 5.1 0.5 - - - +
152B LYS* 2.9 31.1 + - - +
153B ILE* 3.1 21.0 + - + +
155B ALA* 1.3 77.8 - - - +
157B MET* 1.3 61.7 + - + +
159B LYS* 3.4 34.5 + - - +
182B ASP 4.5 10.9 - - - +
184B PRO* 4.6 3.3 - - - +
356B CA 3.6 21.4 - - - -
13P G 5.0 0.7 + - - -
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Residues in contact with MET 157 (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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153B ILE* 3.1 17.9 + - + +
154B ALA* 3.0 29.6 + - - +
155B ALA 3.0 0.6 - - - -
156B ASP* 1.3 80.5 - - + +
158B ALA* 1.3 58.6 + - - +
159B LYS 4.3 3.0 - - - +
164B LYS* 3.7 28.5 - - + +
166B ILE* 3.4 20.9 - - + -
170B GLU* 6.0 1.3 - - - +
174B LEU* 5.0 14.6 - - - -
178B LEU* 6.0 3.1 - - + -
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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
----------------------------------------------------------
141B THR* 3.8 18.6 - - + -
154B ALA 3.1 10.8 + - - +
155B ALA* 3.0 2.2 + - - -
157B MET* 1.3 76.1 - - - +
159B LYS* 1.3 69.1 + - - +
160B PRO 3.2 11.4 - - - +
162B GLY* 4.2 4.2 - - - -
163B ILE 4.1 13.0 - - - +
164B LYS* 3.9 22.0 - - + -
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Residues in contact with LYS 159 (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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7B ASP* 2.9 36.0 + - - -
9B ASP* 4.1 4.7 - - - +
48B TYR* 4.2 5.4 - - + +
141B THR* 3.2 14.0 - - - +
155B ALA* 2.8 23.7 + - - +
156B ASP* 3.4 35.0 + - - +
157B MET 4.3 4.2 - - - +
158B ALA* 1.3 76.9 - - - +
160B PRO* 1.3 69.3 - - + +
2001B CTP 2.8 39.6 + - - +
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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
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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