Contacts of the helix formed by residues 155 - 170 (chain B) in PDB entry 1VLP
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 155 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153B TYR 3.2 0.8 + - - -
154B GLU* 1.3 79.6 - - + +
156B GLN* 1.3 57.6 + - - +
157B LEU 3.4 2.5 - - - -
158B GLU* 3.3 35.9 + - - +
159B GLN* 2.9 41.5 + - - +
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Residues in contact with GLN 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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152B ASP 4.7 0.4 + - - -
153B TYR* 3.1 27.3 + - + +
154B GLU 3.2 6.8 + - - +
155B ASN* 1.3 73.9 - - - +
157B LEU* 1.3 69.6 + - - +
158B GLU* 4.0 0.4 + - - -
159B GLN* 3.7 13.7 + - - +
160B ALA* 3.1 22.5 + - - +
187B ALA* 5.3 2.0 - - + +
190B LEU* 4.3 18.8 - - + -
191B ILE* 4.0 23.0 - - + +
357B PHE 4.6 3.5 - - - +
360B ASP 2.9 26.5 + - - +
361B PHE* 3.4 48.9 - - + +
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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
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155B ASN 3.4 0.2 - - - -
156B GLN* 1.3 80.7 - - - +
158B GLU* 1.3 75.6 + - + +
160B ALA* 3.2 0.7 + - - +
161B GLU* 2.9 31.4 + - - +
190B LEU* 3.7 26.5 + - + +
193B GLN* 3.7 34.3 - - + +
194B GLY* 3.5 24.1 - - - +
197B LYS* 3.9 27.6 - - + +
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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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155B ASN* 3.3 37.1 + - - +
156B GLN 3.3 0.2 - - - -
157B LEU* 1.3 87.5 + - + +
159B GLN* 1.3 59.9 + - - +
161B GLU* 3.5 18.8 + - - +
162B LYS* 2.9 31.0 + - - +
197B LYS* 5.8 3.1 + - - +
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Residues in contact with GLN 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 ASN* 2.9 33.8 + - - +
156B GLN* 3.7 17.3 + - - +
158B GLU* 1.3 75.8 - - - +
160B ALA* 1.3 61.7 + - - +
162B LYS* 3.3 7.1 + - - +
163B LYS* 3.2 37.8 + - - +
191B ILE* 6.2 0.2 - - - +
357B PHE 5.7 1.2 + - - -
360B ASP* 2.9 52.2 + - - +
362B ARG* 5.7 6.6 + - - +
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Residues in contact with ALA 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 GLN 3.1 15.0 + - - +
157B LEU 3.6 3.1 - - - +
159B GLN* 1.3 75.8 - - - +
161B GLU* 1.3 65.5 + - - +
162B LYS 3.2 0.2 + - - -
163B LYS* 3.3 7.8 + - - +
164B ALA* 3.0 23.2 + - - +
191B ILE* 3.5 47.1 - - + +
194B GLY* 4.4 2.2 - - - -
195B ILE 4.6 0.7 - - - +
357B PHE* 4.0 17.8 - - + +
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Residues in contact with GLU 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 LEU* 2.9 16.8 + - - +
158B GLU* 3.6 20.0 - - - +
160B ALA* 1.3 77.0 - - - +
162B LYS* 1.3 57.1 + - - +
164B ALA* 3.3 2.1 + - - +
165B GLU* 2.8 55.3 + - - +
194B GLY* 3.2 27.1 + - - +
197B LYS* 3.3 43.1 + - - +
198B ALA* 3.6 12.4 + - - +
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Residues in contact with LYS 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 GLU 2.9 18.4 + - - +
159B GLN* 3.6 7.2 - - - +
160B ALA 3.2 0.2 - - - -
161B GLU* 1.3 76.3 - - - +
163B LYS* 1.3 59.0 + - + +
165B GLU* 3.3 25.2 + - - +
166B THR* 2.9 51.0 + - - +
169B ASP* 5.6 3.0 + - - -
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Residues in contact with LYS 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 GLN* 3.2 31.8 + - + +
160B ALA* 3.6 7.8 - - - +
162B LYS* 1.3 78.4 - - + +
164B ALA* 1.3 56.7 + - - +
166B THR* 3.1 7.0 + - - -
167B LEU* 2.9 34.3 + - - +
332B VAL* 3.8 24.1 - - + +
356B ASN* 2.7 41.5 + - - +
357B PHE* 4.1 26.2 + - + +
360B ASP* 2.6 33.6 + - - +
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Residues in contact with ALA 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 ALA 3.0 16.7 + - - +
163B LYS* 1.3 75.1 - - - +
165B GLU* 1.3 62.3 + - - +
167B LEU* 3.3 3.7 + - - +
168B PHE* 2.9 38.7 + - + -
174B PHE* 4.0 21.5 - - + -
195B ILE* 4.2 17.0 - - + -
198B ALA* 3.5 21.5 - - + -
357B PHE* 4.8 1.2 - - + -
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Residues in contact with GLU 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 GLU* 2.8 42.4 + - - +
162B LYS* 3.6 33.6 + - + +
164B ALA* 1.3 70.8 - - - +
166B THR* 1.3 57.5 + - - +
168B PHE* 3.4 8.5 + - - +
169B ASP* 3.0 39.1 + - - +
198B ALA* 3.9 15.3 - - + +
205B ARG* 4.5 1.2 + - - +
206B ASN* 6.1 0.2 - - - +
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Residues in contact with THR 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 LYS* 2.9 37.2 + - - +
163B LYS* 3.1 5.8 + - - -
165B GLU* 1.3 71.9 - - - +
167B LEU* 1.3 65.1 + - - +
169B ASP* 3.3 8.1 + - - +
170B ASN* 2.8 41.2 + - - +
332B VAL* 3.5 24.7 - - + -
336B ILE* 4.2 5.2 - - + -
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Residues in contact with LEU 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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163B LYS 2.9 21.3 + - - +
164B ALA* 3.6 6.1 - - - +
166B THR* 1.3 76.5 - - - +
168B PHE* 1.3 57.3 + - - +
170B ASN* 3.1 3.2 + - - +
171B GLY 3.0 9.5 + - - -
172B ILE* 3.0 58.3 + - + +
174B PHE* 3.7 35.7 - - + -
332B VAL* 4.0 25.8 - - + +
335B ALA* 4.1 18.2 - - + -
336B ILE* 5.4 0.9 - - + -
353B ILE* 3.7 23.3 - - + -
357B PHE* 4.4 4.9 - - + -
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Residues in contact with PHE 168 (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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164B ALA* 2.9 25.5 + - + +
165B GLU* 3.7 4.7 - - - +
167B LEU* 1.3 78.0 - - - +
169B ASP* 1.3 57.4 + - - +
171B GLY* 3.0 18.9 + - - -
172B ILE 4.5 0.2 - - - -
174B PHE* 3.4 33.0 - + - -
195B ILE* 5.0 0.7 - - + -
198B ALA* 3.9 10.5 - - + -
199B VAL* 3.7 43.7 - - + -
205B ARG* 3.6 17.6 + - - +
206B ASN* 3.4 46.7 - - + +
209B LEU* 3.6 32.6 - - + +
210B LEU* 3.8 8.1 - - + -
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Residues in contact with ASP 169 (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 LYS* 5.6 2.9 + - - -
165B GLU* 3.0 27.2 + - - +
166B THR* 3.3 8.9 + - - +
168B PHE* 1.3 77.4 - - - +
170B ASN* 1.3 61.9 + - - +
171B GLY 3.2 0.8 + - - -
205B ARG* 3.0 31.2 + - - +
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Residues in contact with ASN 170 (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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166B THR* 2.8 27.2 + - - +
167B LEU 3.1 8.6 + - - +
169B ASP* 1.3 80.0 - - - +
171B GLY* 1.3 62.9 + - - +
172B ILE* 3.3 20.2 + - + +
336B ILE* 3.5 39.9 - - + +
339B SER* 5.3 1.7 + - - +
340B HIS* 5.2 3.8 + - - -
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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