Contacts of the helix formed by residues 184 - 202 (chain A) 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 SER 184 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141A GLU* 3.3 25.1 - - - -
151A TRP* 4.9 2.1 - - - -
153A TYR* 2.6 28.8 + - - -
182A ARG* 3.2 17.8 - - - +
183A ARG* 1.3 80.9 - - - +
185A LEU* 1.3 63.8 + - - +
186A LYS* 3.4 4.1 + - - -
187A ALA* 2.9 28.2 + - - +
188A GLN 3.2 9.7 + - - -
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Residues in contact with LEU 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A VAL* 3.4 31.4 - - + +
7A LYS* 5.4 9.6 - - + -
11A ASP* 3.8 10.1 - - - +
141A GLU* 3.0 17.0 + - - +
182A ARG* 3.6 38.3 - - - +
184A SER* 1.3 71.3 - - - +
186A LYS* 1.3 63.5 + - - +
188A GLN* 3.2 5.2 + - - +
189A ASP* 3.0 22.1 + - + +
217A LEU* 5.9 4.7 - - + -
218A PHE* 3.7 23.8 - - + -
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Residues in contact with LYS 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A GLU* 5.6 0.4 + - - -
153A TYR* 3.7 45.3 - - + +
184A SER* 3.2 8.8 + - - +
185A LEU* 1.3 78.6 - - - +
187A ALA* 1.3 57.5 + - - +
189A ASP* 3.3 8.1 + - + +
190A LEU* 2.9 42.3 + - + +
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Residues in contact with ALA 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A TYR* 3.8 10.5 - - + -
156A GLN* 5.2 2.6 - - - +
183A ARG* 4.2 0.4 - - + -
184A SER* 2.9 31.2 + - - +
186A LYS* 1.3 75.6 - - - +
188A GLN* 1.3 64.2 + - - +
190A LEU* 3.3 5.0 + - - +
191A ILE* 3.1 28.9 + - + +
358A THR 3.9 17.7 - - - +
361A PHE* 3.9 23.6 - - + -
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Residues in contact with GLN 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A GLU* 3.1 33.1 + - - +
179A THR* 3.0 34.0 + - - +
182A ARG* 2.9 36.3 + - + +
184A SER 3.2 8.3 + - - +
185A LEU 3.2 6.9 + - - +
187A ALA* 1.3 80.5 - - - +
189A ASP* 1.3 55.4 + - - +
191A ILE* 3.3 11.4 + - + +
192A MSE 2.9 28.8 + - + +
215A ASN* 3.7 5.5 + - - +
218A PHE* 3.3 20.6 - - + -
358A THR* 3.9 17.0 - - + -
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Residues in contact with ASP 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A LEU* 3.0 14.6 + - + +
186A LYS* 3.5 12.4 - - + +
188A GLN* 1.3 76.8 - - - +
190A LEU* 1.3 57.7 + - - +
192A MSE 3.3 3.5 + - - +
193A GLN* 2.9 52.1 + - - +
218A PHE* 3.4 25.1 - - + -
221A LYS* 2.8 22.9 + - - -
222A TYR* 2.6 20.6 + - - -
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Residues in contact with LEU 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A TYR* 3.7 42.4 - - + +
156A GLN* 4.2 18.4 - - + -
157A LEU* 3.8 23.2 - - + +
186A LYS* 2.9 31.2 + - + +
187A ALA* 3.7 4.3 - - - +
189A ASP* 1.3 76.2 - - - +
191A ILE* 1.3 59.4 + - - +
193A GLN* 3.3 29.5 + - - +
194A GLY 3.0 21.0 + - - -
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Residues in contact with ILE 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A GLN* 3.9 24.5 - - + +
160A ALA* 3.6 23.7 - - + +
176A GLU* 3.8 31.4 - - + +
187A ALA 3.1 16.2 + - - +
188A GLN* 3.3 17.5 - - - +
190A LEU* 1.3 71.8 - - - +
192A MSE 1.3 69.3 + - + +
194A GLY* 3.1 0.9 + - - -
195A ILE* 3.0 37.3 + - + +
357A PHE* 3.3 35.2 - - + +
358A THR* 3.9 9.4 - - + -
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Residues in contact with MSE 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A GLU* 4.2 22.2 - - - +
188A GLN* 2.9 18.3 + - + +
189A ASP 3.5 8.5 - - - +
190A LEU 3.3 0.2 - - - -
191A ILE* 1.3 77.6 - - + +
193A GLN* 1.3 56.6 + - - +
195A ILE* 3.4 9.9 + - + +
196A MSE 2.9 48.2 + - - +
210A LEU* 5.9 1.3 - - + -
212A GLY 6.0 0.7 - - - -
213A THR* 4.1 35.7 - - + -
218A PHE* 3.9 27.1 - - + +
222A TYR* 3.6 40.8 - - + -
224A VAL* 4.3 9.0 - - + -
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Residues in contact with GLN 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A LEU* 3.6 24.0 - - + +
189A ASP* 2.9 33.9 + - - +
190A LEU* 3.3 27.0 - - - +
192A MSE 1.3 76.6 - - - +
194A GLY* 1.3 56.3 + - - +
196A MSE 3.4 3.6 + - - +
197A LYS* 2.9 29.8 + - - +
222A TYR* 3.3 25.2 + - + +
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Residues in contact with GLY 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A LEU* 3.4 34.5 - - - +
160A ALA* 4.3 0.2 - - - -
161A GLU* 3.3 21.2 - - - +
190A LEU 3.0 11.1 + - - -
191A ILE 3.1 3.7 + - - -
193A GLN* 1.3 72.9 - - - +
195A ILE* 1.3 60.5 + - - +
197A LYS* 3.2 1.8 + - - +
198A ALA 2.9 24.1 + - - -
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Residues in contact with ILE 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A ALA* 4.5 1.3 - - + +
164A ALA* 4.1 13.0 - - + -
168A PHE* 4.9 0.2 - - + -
174A PHE* 4.6 9.6 - - + -
176A GLU* 4.2 15.0 - - + -
191A ILE* 3.0 35.7 + - + +
192A MSE 3.7 11.0 - - + +
194A GLY* 1.3 76.3 - - - +
196A MSE 1.3 60.0 + - - +
198A ALA* 3.0 6.1 + - - +
199A VAL* 2.8 27.7 + - + +
210A LEU* 3.9 37.2 - - + -
357A PHE* 3.8 43.1 - - + -
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Residues in contact with MSE 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A MSE 2.9 26.0 + - + +
193A GLN* 3.9 4.5 - - - +
195A ILE* 1.3 79.2 - - - +
197A LYS* 1.3 60.6 + - - +
199A VAL* 3.5 19.4 - - + +
200A ASN* 3.0 44.8 + - - +
207A LYS* 5.4 3.6 - - - +
210A LEU* 3.8 24.2 - - + -
222A TYR* 3.8 39.3 - - + +
224A VAL* 3.7 26.2 - - + -
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Residues in contact with LYS 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A LEU* 4.2 14.4 - - + -
161A GLU* 3.3 33.7 - - - +
165A GLU* 4.9 0.2 - - - +
193A GLN 2.9 17.0 + - - +
194A GLY* 3.5 7.6 - - - +
195A ILE 3.2 0.2 - - - -
196A MSE 1.3 76.3 - - - +
198A ALA* 1.3 63.2 + - - +
200A ASN* 3.5 5.3 + - - +
201A GLY* 3.2 17.8 + - - -
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Residues in contact with ALA 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A GLU* 3.7 4.4 - - + +
164A ALA* 3.5 27.6 - - + -
165A GLU* 3.6 32.6 - - + +
168A PHE* 3.9 6.5 - - + -
194A GLY 2.9 10.1 + - - +
195A ILE 3.0 9.4 + - - +
197A LYS* 1.3 73.8 - - - +
199A VAL* 1.3 65.5 + - - +
201A GLY* 3.3 9.9 + - - -
206A ASN* 3.1 15.8 + - - -
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Residues in contact with VAL 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A PHE* 3.6 21.5 - - + -
195A ILE* 2.8 22.8 + - + +
196A MSE 3.2 18.4 + - + +
198A ALA* 1.3 72.1 - - - +
200A ASN* 1.3 59.9 + - - +
202A ASN 3.0 20.6 + - - +
203A PRO* 3.1 15.8 - - - +
206A ASN* 3.7 8.4 + - - +
207A LYS* 3.7 46.2 - - + +
210A LEU* 3.8 27.4 - - + -
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Residues in contact with ASN 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A MSE 3.0 37.7 + - - +
197A LYS* 3.9 6.2 - - - +
198A ALA 3.2 0.2 - - - -
199A VAL* 1.3 74.4 - - - +
201A GLY* 1.3 62.0 + - - +
202A ASN 3.3 0.4 - - - -
203A PRO* 3.6 14.7 - - - +
207A LYS* 3.1 26.6 + - - -
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Residues in contact with GLY 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A GLU* 5.8 2.5 - - - -
197A LYS 3.2 12.5 + - - -
198A ALA* 3.3 6.9 + - - -
199A VAL 3.2 1.8 - - - -
200A ASN* 1.3 78.2 - - - +
202A ASN* 1.3 62.1 + - - +
203A PRO* 3.8 1.7 - - - +
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Residues in contact with ASN 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A VAL 3.0 5.0 + - - -
201A GLY* 1.3 80.4 - - - +
203A PRO* 1.3 63.3 - - - +
204A ASP* 3.3 7.3 + - - +
205A ARG* 3.5 44.4 + - - +
206A ASN* 2.8 40.3 + - - +
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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
------------------------------------------------------------
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