Contacts of the helix formed by residues 155 - 167 (chain B) in PDB entry 1VLM
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 155 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127B ILE* 4.1 2.5 - - - -
129B ASP* 3.4 9.0 - - - -
130B ARG* 3.8 3.7 - - - +
131B GLU* 3.3 37.1 + - - -
154B PHE* 1.3 82.0 - - - +
156B THR* 1.3 63.8 + - - +
157B GLU* 3.9 6.0 + - - +
158B GLU* 2.8 42.2 + - - +
159B LEU* 3.1 18.5 + - - +
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Residues in contact with THR 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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127B ILE* 4.3 7.4 - - - +
129B ASP* 3.3 22.3 + - - +
155B SER* 1.3 74.3 - - - +
157B GLU* 1.3 58.0 + - - +
159B LEU* 3.1 4.7 + - - +
160B MSE 2.8 33.5 + - - +
173B VAL* 4.2 3.8 - - + -
194B TYR* 3.5 42.5 - - + -
200B VAL* 3.5 26.9 - - + +
202B ILE* 3.7 18.3 - - + +
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Residues in contact with GLU 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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131B GLU* 5.4 3.8 - - - +
155B SER* 3.4 5.1 + - - +
156B THR* 1.3 72.5 - - - +
158B GLU* 1.3 67.2 + - - +
160B MSE 3.8 9.2 - - - +
161B ASP* 3.0 31.1 + - - +
194B TYR* 3.2 39.9 + - + +
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Residues in contact with GLU 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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130B ARG* 2.8 31.2 + - - -
131B GLU* 5.1 1.4 - - - +
153B PHE 4.0 2.1 - - - +
154B PHE* 3.5 19.4 - - + -
155B SER* 2.8 47.9 + - - +
157B GLU* 1.3 78.6 - - + +
159B LEU* 1.3 64.1 + - - +
161B ASP* 3.3 6.0 + - - +
162B LEU* 3.1 24.3 + - - +
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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
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100B ILE* 4.1 28.7 - - + -
110B LEU* 5.0 7.6 - - + -
125B VAL* 3.4 33.0 - - + -
127B ILE* 4.0 21.1 - - + -
154B PHE* 4.4 17.7 - - + -
155B SER 3.1 14.6 + - - +
156B THR 3.1 4.0 + - - +
158B GLU* 1.3 79.8 - - - +
160B MSE 1.3 61.2 + - - +
162B LEU* 3.2 8.0 + - + +
163B MSE 3.0 33.5 + - + +
202B ILE* 3.5 22.9 - - + -
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Residues in contact with MSE 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 THR* 2.8 30.6 + - - +
157B GLU* 3.8 10.3 - - - +
159B LEU* 1.3 71.5 - - - +
161B ASP* 1.3 58.2 + - - +
163B MSE 3.2 7.0 + - - -
164B ARG* 2.8 64.6 + - - +
171B PHE* 3.4 30.2 - - + -
173B VAL* 4.2 21.1 - - - -
194B TYR* 4.7 12.1 - - - -
202B ILE* 3.8 23.8 - - + -
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Residues in contact with ASP 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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157B GLU* 3.0 21.8 + - - +
158B GLU* 3.5 7.4 - - - +
159B LEU 3.2 0.2 - - - -
160B MSE 1.3 77.0 - - - +
162B LEU* 1.3 64.0 + - + +
164B ARG* 3.3 24.9 + - - +
165B LYS* 2.9 43.6 + - + +
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Residues in contact with LEU 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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106B PRO* 4.1 20.4 - - + -
107B GLU* 4.4 21.1 - - + -
110B LEU* 3.7 18.6 - - + +
152B ARG* 4.5 10.8 - - - +
154B PHE* 3.9 27.6 - - + -
158B GLU 3.1 12.5 + - - +
159B LEU* 3.2 11.0 + - + +
161B ASP* 1.3 80.2 - - + +
163B MSE 1.3 57.7 + - - +
165B LYS* 3.4 18.0 + - + +
166B ALA* 3.0 27.2 + - - +
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Residues in contact with MSE 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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110B LEU* 4.0 22.7 - - + -
123B LEU* 3.6 42.6 - - + +
125B VAL* 4.1 12.3 - - + -
159B LEU* 3.0 35.2 + - + +
160B MSE 3.5 7.4 - - - +
162B LEU* 1.3 75.2 - - - +
164B ARG* 1.3 59.5 + - - +
166B ALA* 3.0 19.1 + - - -
167B GLY 3.1 0.9 + - - -
168B PHE* 3.1 28.2 + - + -
171B PHE* 3.6 23.1 - - + -
202B ILE* 4.1 17.5 - - - +
203B ARG 4.2 1.8 - - - -
204B GLY* 3.6 18.6 - - - +
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Residues in contact with ARG 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 MSE 2.8 55.2 + - - +
161B ASP* 3.4 24.9 + - - +
163B MSE 1.3 71.7 - - - +
165B LYS* 1.3 60.5 + - + +
167B GLY* 3.0 19.9 + - - -
168B PHE 3.4 17.8 + - - +
169B GLU* 6.2 0.7 - - + -
171B PHE* 3.6 14.4 - - + -
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Residues in contact with LYS 165 (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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161B ASP* 2.9 34.2 + - + +
162B LEU* 3.7 19.3 - - + +
164B ARG* 1.3 76.7 - - + +
166B ALA* 1.3 60.0 + - - +
167B GLY 3.7 0.2 + - - -
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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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107B GLU* 5.0 2.7 - - - +
110B LEU* 3.6 36.3 - - + -
111B LYS* 4.2 6.7 - - + +
114B TYR* 3.6 22.5 - - - +
162B LEU 3.0 13.9 + - - +
163B MSE 3.0 10.2 + - - +
165B LYS* 1.3 77.3 - - - +
167B GLY* 1.3 54.7 + - - +
168B PHE* 3.7 9.0 - - + -
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Residues in contact with GLY 167 (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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114B TYR* 3.7 25.4 + - - -
164B ARG 3.0 10.6 + - - -
165B LYS 3.3 1.2 - - - -
166B ALA* 1.3 78.9 - - - +
168B PHE* 1.3 61.9 + - - +
169B GLU* 4.0 12.7 + - - +
205B THR 4.1 3.8 - - - +
206B LYS* 4.6 2.1 - - - -
207B LYS 4.9 1.9 + - - -
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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