Contacts of the helix formed by residues 150 - 164 (chain B) in PDB entry 1L9W
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 150 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148B THR 3.8 0.4 + - - -
149B PRO* 1.3 80.5 - - - +
151B ALA* 1.3 62.3 + - - +
152B GLU* 3.3 10.4 + - - +
153B GLU* 3.1 23.1 + - - +
154B MET* 3.2 18.9 + - - +
183B THR* 4.0 4.7 - - - -
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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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150B SER* 1.3 73.2 - - - +
152B GLU* 1.3 65.1 + - - +
154B MET* 3.3 13.8 + - - +
155B VAL* 2.9 29.3 + - - +
183B THR* 3.6 15.6 - - + +
186B THR* 4.8 9.2 - - + -
187B ALA* 4.0 20.4 - - + +
190B GLU* 4.6 11.2 - - - +
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Residues in contact with GLU 152 (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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150B SER* 3.6 9.4 - - - +
151B ALA* 1.3 81.0 - - - +
153B GLU* 1.3 61.9 + - - +
155B VAL* 3.3 7.6 + - - +
156B SER* 3.1 28.6 + - - +
190B GLU* 5.5 6.8 - - - +
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Residues in contact with GLU 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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118B PHE* 5.1 1.7 - - - -
149B PRO* 3.7 15.3 - - + -
150B SER* 3.1 18.2 + - - +
152B GLU* 1.3 76.5 - - - +
154B MET* 1.3 63.1 + - - +
156B SER* 3.3 11.1 + - - -
157B ARG* 2.5 68.3 + - - +
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Residues in contact with MET 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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148B THR* 3.9 6.3 - - + -
149B PRO* 3.4 37.5 - - + +
150B SER 3.2 11.5 + - - +
151B ALA* 3.7 2.2 - - - +
153B GLU* 1.3 79.6 - - - +
155B VAL* 1.3 62.7 + - - +
157B ARG* 3.2 4.0 + - - +
158B LEU* 3.0 28.3 + - + +
171B ILE* 4.2 23.3 - - + +
173B VAL* 4.0 21.8 - - + -
183B THR* 3.7 24.2 - - + +
184B LEU* 3.9 23.6 - - - -
187B ALA* 3.9 22.9 - - + -
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Residues in contact with VAL 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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151B ALA 2.9 24.2 + - - +
152B GLU* 3.8 6.7 - - - +
154B MET* 1.3 72.1 - - - +
156B SER* 1.3 56.8 + - - +
158B LEU* 3.3 7.6 + - + +
159B ARG* 2.8 48.0 + - + +
187B ALA* 3.8 26.9 - - + +
190B GLU* 4.0 26.5 - - + +
191B MET* 4.3 7.4 - - + +
195B TYR* 3.8 22.4 - - + -
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Residues in contact with SER 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B GLU* 3.1 20.0 + - - +
153B GLU* 3.3 17.6 + - - -
155B VAL* 1.3 76.7 - - - +
157B ARG* 1.4 55.3 + - - +
159B ARG* 3.2 12.9 + - - +
160B LYS* 2.7 35.2 + - - +
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Residues in contact with ARG 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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117B LEU* 4.4 14.5 - - + +
118B PHE* 4.1 21.3 - - + -
142B ASN* 2.8 36.7 + - - +
143B HIS 5.2 0.8 + - - -
144B ASP* 5.0 10.9 + - - +
149B PRO* 4.2 20.0 - - - +
153B GLU* 2.5 50.8 + - - +
154B MET* 3.2 6.7 + - - +
156B SER* 1.4 75.7 - - - +
158B LEU* 1.4 70.0 + - - +
160B LYS* 3.0 18.4 + - - +
161B MET* 3.1 23.1 + - + +
171B ILE* 4.0 15.2 - - + +
173B VAL* 6.1 0.4 - - - +
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Residues in contact with LEU 158 (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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154B MET* 3.0 24.8 + - + +
155B VAL* 3.9 1.3 - - - +
157B ARG* 1.4 80.7 - - - +
159B ARG* 1.3 61.7 + - - +
161B MET* 3.4 10.7 + - + +
162B GLN* 3.3 17.7 + - - +
169B PRO* 3.8 28.8 - - + +
170B LYS* 3.9 14.8 - - - +
171B ILE* 3.9 33.9 - - + -
187B ALA* 5.4 5.2 - - + +
188B THR* 5.7 0.7 - - - -
191B MET* 3.8 34.1 - - + +
200B VAL* 4.3 12.3 - - + -
202B THR* 4.2 13.7 - - + -
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Residues in contact with ARG 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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155B VAL* 2.8 42.5 + - - +
156B SER* 3.6 11.8 + - - +
158B LEU* 1.3 71.4 - - - +
160B LYS* 1.3 60.0 + - - +
162B GLN* 3.2 10.2 + - - +
163B ALA* 2.9 28.2 + - - +
191B MET* 4.1 6.5 - - + -
195B TYR* 3.2 52.4 + - + +
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Residues in contact with LYS 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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117B LEU* 4.2 25.1 - - + -
118B PHE* 5.7 4.9 - - + -
121B ASP* 3.0 41.3 + - - -
156B SER 2.7 20.7 + - - +
157B ARG* 3.0 11.4 + - - +
159B ARG* 1.3 71.8 - - - +
161B MET* 1.3 52.2 + - - +
163B ALA* 3.2 8.8 + - + +
164B LEU* 3.1 41.8 + - + +
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Residues in contact with MET 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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117B LEU* 3.8 13.5 - - + -
140B MET* 3.2 50.9 - - + +
141B SER 3.9 5.8 - - - +
142B ASN* 3.5 25.4 - - + -
157B ARG* 3.1 22.1 + - + +
158B LEU* 3.7 15.7 - - + +
160B LYS* 1.3 71.5 - - - +
162B GLN* 1.3 62.7 + - - +
164B LEU* 3.5 3.5 + - - +
165B GLY 3.4 3.5 + - - -
166B ALA* 2.9 33.7 + - + +
169B PRO* 3.9 12.8 - - + -
170B LYS 3.3 30.5 - - - +
171B ILE* 4.8 1.3 - - + -
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Residues in contact with GLN 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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158B LEU 3.3 6.7 + - - +
159B ARG* 3.2 12.0 + - - +
161B MET* 1.3 77.4 - - - +
163B ALA* 1.4 67.1 + - - +
164B LEU 3.2 0.2 - - - -
165B GLY* 3.1 11.1 + - - -
169B PRO* 4.4 6.7 - - + +
191B MET* 3.8 16.3 - - - +
195B TYR* 3.3 16.8 - - - +
196B ALA* 3.2 9.1 - - - +
197B ASP* 2.9 39.2 + - - +
198B ARG* 3.0 55.8 + - - +
200B VAL* 5.0 0.6 - - - +
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Residues in contact with ALA 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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125B LYS* 4.4 5.2 + - - +
159B ARG 2.9 12.9 + - - +
160B LYS* 3.2 13.9 + - + +
162B GLN* 1.4 78.8 - - - +
164B LEU* 1.3 60.8 + - + +
165B GLY* 3.3 1.6 + - - -
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Residues in contact with LEU 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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117B LEU* 3.6 32.1 - - + -
121B ASP* 3.9 22.4 - - + +
124B VAL* 4.1 12.8 - - + -
125B LYS* 2.6 53.4 + - + +
128B VAL* 3.8 8.5 - - + +
140B MET* 4.4 11.7 - - + -
160B LYS* 3.1 32.6 + - + +
161B MET 4.0 5.2 - - - +
162B GLN 3.2 1.0 - - - -
163B ALA* 1.3 78.7 - - + +
165B GLY* 1.3 57.2 + - - +
166B ALA 3.5 1.1 - - - -
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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