Contacts of the helix formed by residues 155 - 170 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153C TYR 3.3 0.6 + - - -
154C GLU* 1.3 100.1 + - - +
156C GLN* 1.3 58.1 + - - +
157C LEU 3.4 2.9 - - - -
158C GLU* 3.4 11.8 + - + +
159C GLN* 2.8 37.4 + - + +
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Residues in contact with GLN 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C TYR* 3.1 28.9 + - + +
154C GLU 3.1 6.9 + - - -
155C ASN* 1.3 76.0 - - - +
157C LEU* 1.3 64.0 + - - +
159C GLN* 3.8 13.4 + - - +
160C ALA* 3.1 24.8 + - - +
187C ALA* 5.3 1.4 - - + +
190C LEU* 4.1 17.9 - - + -
191C ILE* 3.8 23.6 - - + +
357C PHE 4.7 3.3 - - - +
360C ASP 3.0 26.5 + - - +
361C PHE* 3.3 48.0 - - + +
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Residues in contact with LEU 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C TYR 4.8 0.4 + - - -
155C ASN 3.4 0.2 - - - -
156C GLN* 1.3 79.1 - - - +
158C GLU* 1.3 80.6 + - + +
160C ALA 3.4 0.2 + - - -
161C GLU* 2.9 24.2 + - + +
190C LEU* 4.0 25.1 - - + +
193C GLN* 3.7 37.2 - - + +
194C GLY* 3.6 21.8 - - - +
197C LYS* 4.0 15.7 - - + +
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Residues in contact with GLU 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155C ASN* 3.4 13.8 + - + +
156C GLN 3.3 0.2 - - - -
157C LEU* 1.3 90.0 - - + +
159C GLN* 1.3 57.3 + - - +
161C GLU* 3.2 17.0 + - - +
162C LYS* 2.9 31.3 + - - +
197C LYS* 3.5 29.9 + - - -
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Residues in contact with GLN 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155C ASN* 2.8 24.4 + - + +
156C GLN* 3.8 18.0 + - - +
158C GLU* 1.3 76.5 - - - +
160C ALA* 1.3 61.9 + - - +
162C LYS* 3.4 7.0 + - - +
163C LYS* 3.1 40.5 + - + +
191C ILE* 6.2 0.4 - - - +
357C PHE 5.6 1.2 + - - -
360C ASP* 2.9 50.1 + - - +
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Residues in contact with ALA 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156C GLN 3.1 17.4 + - - +
157C LEU 3.7 4.0 - - - +
159C GLN* 1.3 73.5 - - - +
161C GLU* 1.3 67.0 + - - +
163C LYS* 3.4 6.8 + - - +
164C ALA* 3.0 23.4 + - - +
191C ILE* 3.7 43.5 - - + +
194C GLY* 4.2 3.9 - - - -
195C ILE* 4.6 0.4 - - - +
357C PHE* 4.0 18.0 - - + -
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Residues in contact with GLU 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157C LEU* 2.9 18.1 + - + +
158C GLU* 3.4 23.1 - - - +
160C ALA* 1.3 75.1 - - - +
162C LYS* 1.3 64.3 + - - +
164C ALA 3.3 1.0 + - - -
165C GLU* 2.8 50.5 + - - +
194C GLY* 3.4 24.8 + - - +
197C LYS* 4.1 20.6 - - + +
198C ALA* 3.4 26.2 - - - +
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Residues in contact with LYS 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158C GLU 2.9 16.8 + - - +
159C GLN* 3.8 6.3 - - - +
160C ALA 3.3 0.2 - - - -
161C GLU* 1.3 86.5 + - - +
163C LYS* 1.3 56.0 + - + +
165C GLU* 3.5 7.3 + - + +
166C THR* 2.8 44.0 + - - +
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Residues in contact with LYS 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159C GLN* 3.1 33.9 + - + +
160C ALA* 3.5 7.6 - - - +
162C LYS* 1.3 76.3 - - + +
164C ALA* 1.3 62.7 - - - +
166C THR* 3.3 5.9 + - - -
167C LEU* 3.0 29.1 + - - +
332C VAL* 3.9 22.7 - - + +
356C ASN* 2.8 41.9 + - - +
357C PHE* 3.9 27.3 + - + +
360C ASP* 2.7 32.4 + - - +
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Residues in contact with ALA 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160C ALA 3.0 13.1 + - - +
163C LYS* 1.3 77.7 - - - +
165C GLU* 1.3 59.4 + - - +
167C LEU* 3.1 4.2 + - - +
168C PHE* 2.9 44.4 + - + -
174C PHE* 4.0 21.1 - - + -
195C ILE* 4.2 15.7 - - + -
198C ALA* 3.6 20.2 - - + -
357C PHE* 4.6 1.0 - - + -
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Residues in contact with GLU 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161C GLU* 2.8 46.2 + - - +
162C LYS* 3.8 7.4 - - - +
164C ALA* 1.3 72.5 - - - +
166C THR* 1.3 58.4 + - - +
168C PHE* 3.3 11.7 + - + +
169C ASP* 2.8 48.1 + - - +
198C ALA* 3.8 3.7 - - + +
205C ARG* 5.8 1.1 - - - +
206C ASN* 6.0 0.2 - - - +
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Residues in contact with THR 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162C LYS* 2.8 30.3 + - - +
163C LYS* 3.3 5.4 + - - -
165C GLU* 1.3 76.3 - - - +
167C LEU* 1.3 62.2 + - - +
169C ASP* 3.3 7.0 + - - +
170C ASN* 2.8 42.8 + - - +
332C VAL* 3.7 25.1 - - + -
336C ILE* 4.3 5.4 - - + -
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Residues in contact with LEU 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163C LYS 3.0 21.6 + - - +
164C ALA* 3.5 6.1 - - - +
166C THR* 1.3 75.1 - - - +
168C PHE* 1.3 64.3 + - - +
170C ASN* 3.0 13.6 + - - -
172C ILE* 3.0 40.7 + - + +
174C PHE* 3.8 35.0 - - + -
332C VAL* 4.0 24.9 - - + +
335C ALA* 3.8 29.4 - - + -
336C ILE* 5.2 0.7 - - + -
353C ILE* 3.6 25.8 - - + -
357C PHE* 4.5 4.0 - - + -
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Residues in contact with PHE 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164C ALA* 2.9 25.1 + - + +
165C GLU* 3.6 7.2 - - - +
167C LEU* 1.3 75.3 - - - +
169C ASP* 1.3 56.2 + - - +
171C GLY* 2.9 19.4 + - - -
172C ILE 4.4 0.2 - - - -
174C PHE* 3.3 33.7 - + - -
195C ILE* 4.9 0.9 - - + -
198C ALA* 3.8 11.7 - - + -
199C VAL* 3.7 43.1 - - + -
205C ARG* 3.5 19.6 + - - +
206C ASN* 3.4 34.8 - - + +
209C LEU* 3.6 36.2 - - + +
210C LEU* 3.8 11.4 - - + -
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Residues in contact with ASP 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165C GLU* 2.8 39.8 + - - +
166C THR* 3.6 9.0 - - - +
167C LEU 3.3 0.2 - - - -
168C PHE* 1.3 73.6 - - - +
170C ASN* 1.3 63.1 - - - +
171C GLY 3.6 0.3 + - - -
205C ARG* 3.1 30.3 + - - +
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Residues in contact with ASN 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166C THR* 2.8 31.8 + - - +
167C LEU 3.0 5.6 + - - +
169C ASP* 1.3 81.7 - - - +
171C GLY* 1.3 61.8 + - - +
172C ILE* 3.2 23.6 + - + +
336C ILE* 3.9 33.4 - - + +
339C SER* 5.3 1.0 + - - -
343C LYS* 4.8 11.3 + - - -
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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