Contacts of the helix formed by residues 184 - 202 (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 SER 184 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141C GLU* 3.3 24.7 - - - -
151C TRP* 4.6 4.9 - - - -
153C TYR* 2.7 27.9 + - - -
182C ARG* 3.2 15.8 - - - +
183C ARG* 1.3 79.9 - - - +
185C LEU* 1.3 64.2 + - - +
186C LYS* 3.4 3.6 + - - -
187C ALA* 2.9 27.6 + - - +
188C GLN 3.3 9.5 + - - -
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Residues in contact with LEU 185 (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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5C VAL* 3.5 30.1 - - + +
7C LYS* 5.2 11.2 - - + -
11C ASP* 3.7 11.2 - - - +
141C GLU* 2.9 17.3 + - - +
182C ARG* 3.5 37.0 - - - +
184C SER* 1.3 70.3 - - - +
186C LYS* 1.3 64.2 + - - +
188C GLN* 3.2 6.1 + - - +
189C ASP* 3.0 21.1 + - + +
217C LEU* 6.0 3.6 - - + -
218C PHE* 3.7 21.3 - - + -
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Residues in contact with LYS 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C GLU* 5.6 0.2 + - - -
153C TYR* 3.5 53.3 - - + +
184C SER* 3.2 2.0 - - - +
185C LEU* 1.3 78.1 - - - +
187C ALA* 1.3 63.1 + - - +
189C ASP* 3.2 9.2 + - + +
190C LEU* 2.9 35.6 + - + +
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Residues in contact with ALA 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153C TYR* 3.7 17.9 - - + -
156C GLN* 5.5 2.0 - - - +
183C ARG* 4.2 0.4 - - + -
184C SER* 2.9 30.4 + - - +
186C LYS* 1.3 77.9 - - - +
188C GLN* 1.3 61.8 + - - +
190C LEU* 3.3 4.5 + - - +
191C ILE* 3.1 29.1 + - + +
358C THR 4.1 13.7 - - - +
361C PHE* 4.0 20.2 - - + -
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Residues in contact with GLN 188 (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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176C GLU* 3.1 32.7 + - - +
179C THR* 3.0 33.9 + - - +
182C ARG* 3.0 40.4 + - + +
184C SER 3.3 1.8 + - - -
185C LEU 3.2 8.1 + - - +
187C ALA* 1.3 78.0 - - - +
189C ASP* 1.3 63.0 + - - +
191C ILE* 3.3 8.6 + - + +
192C MSE 3.0 23.8 + - + +
215C ASN* 4.0 4.8 - - - +
218C PHE* 3.3 21.7 - - + -
358C THR* 3.9 16.1 - - + -
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Residues in contact with ASP 189 (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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185C LEU* 3.0 13.0 + - + +
186C LYS* 3.2 11.8 + - + +
188C GLN* 1.3 74.8 - - - +
190C LEU* 1.3 57.9 + - - +
192C MSE 3.3 4.4 + - - +
193C GLN* 2.9 53.2 + - - +
218C PHE* 3.4 24.7 - - + -
221C LYS* 2.9 25.1 + - - -
222C TYR* 2.7 20.1 + - - -
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Residues in contact with LEU 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153C TYR* 3.8 42.2 - - + +
156C GLN* 4.1 17.9 - - + -
157C LEU* 4.0 24.6 - - + +
186C LYS* 2.9 27.9 + - + +
187C ALA* 3.7 4.5 - - - +
188C GLN 3.2 0.4 - - - -
189C ASP* 1.3 78.8 - - - +
191C ILE* 1.3 57.9 + - - +
193C GLN* 3.2 28.9 + - - +
194C GLY* 3.0 23.6 + - - -
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Residues in contact with ILE 191 (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* 3.8 24.2 - - + +
160C ALA* 3.7 23.2 - - + +
176C GLU* 3.8 30.1 - - + +
187C ALA* 3.1 16.0 + - + +
188C GLN* 3.4 17.7 - - - +
190C LEU* 1.3 75.8 - - - +
192C MSE 1.3 64.3 + - + +
194C GLY* 3.2 0.9 + - - -
195C ILE* 2.9 39.9 + - + +
357C PHE* 3.3 38.8 - - + +
358C THR* 4.0 8.7 - - + -
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Residues in contact with MSE 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C GLU* 4.3 20.4 - - - +
188C GLN* 3.0 20.3 + - + +
189C ASP 3.3 7.6 + - - +
191C ILE* 1.3 75.8 - - + +
193C GLN* 1.3 63.7 + - - +
195C ILE* 3.2 10.3 + - + +
196C MSE 2.9 39.3 + - - +
210C LEU* 5.7 3.1 - - + -
212C GLY 5.8 0.9 - - - -
213C THR* 3.9 39.3 - - + -
218C PHE* 4.1 23.3 - - + +
222C TYR* 3.6 41.5 - - + -
224C VAL* 4.2 9.0 - - + -
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Residues in contact with GLN 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157C LEU* 3.7 21.5 - - + +
189C ASP* 2.9 30.9 + - - +
190C LEU* 3.3 28.9 - - - +
192C MSE 1.3 76.7 - - - +
194C GLY* 1.3 56.5 + - - +
196C MSE 3.3 4.0 + - - +
197C LYS* 2.9 28.8 + - - +
222C TYR* 3.2 26.6 + - + +
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Residues in contact with GLY 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157C LEU* 3.6 34.1 - - - -
160C ALA* 4.2 0.7 - - - -
161C GLU* 3.4 19.2 - - - -
190C LEU 3.0 11.6 + - - -
191C ILE 3.2 3.5 + - - -
193C GLN* 1.3 74.9 - - - +
195C ILE* 1.3 64.2 + - - +
197C LYS* 3.3 3.6 + - - +
198C ALA* 3.1 16.6 + - - +
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Residues in contact with ILE 195 (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 4.6 1.8 - - - +
164C ALA* 4.2 11.9 - - + -
168C PHE* 4.5 0.4 - - + -
174C PHE* 4.4 11.0 - - + -
176C GLU* 4.2 17.7 - - + -
191C ILE* 2.9 35.7 + - + +
192C MSE 3.7 13.2 - - + +
194C GLY* 1.3 76.2 - - - +
196C MSE 1.3 60.1 + - - +
198C ALA* 3.1 5.2 + - - +
199C VAL* 2.9 27.2 + - + +
210C LEU* 3.8 36.6 - - + -
357C PHE* 3.9 37.7 - - + -
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Residues in contact with MSE 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192C MSE 2.9 26.2 + - + +
193C GLN* 3.8 4.7 - - - +
195C ILE* 1.3 78.8 - - - +
197C LYS* 1.3 56.2 + - - +
199C VAL* 3.3 19.0 + - + +
200C ASN* 2.9 49.1 + - - +
210C LEU* 3.8 23.3 - - + -
222C TYR* 3.7 40.6 - - + +
224C VAL* 3.6 26.2 - - + -
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Residues in contact with LYS 197 (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* 4.0 12.3 - - + +
158C GLU* 3.5 29.2 + - - +
161C GLU* 4.1 13.8 - - + +
193C GLN 2.9 14.0 + - - +
194C GLY* 3.5 10.8 - - - +
195C ILE 3.2 0.2 - - - -
196C MSE 1.3 76.4 - - - +
198C ALA* 1.3 61.1 + - - +
200C ASN* 3.4 5.5 + - - +
201C GLY* 3.1 18.7 + - - -
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Residues in contact with ALA 198 (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* 3.4 28.6 - - - +
164C ALA* 3.6 27.4 - - + -
165C GLU* 3.8 8.6 - - - +
168C PHE* 3.8 6.5 - - + -
194C GLY 3.1 6.7 + - - +
195C ILE 3.1 9.1 + - - +
197C LYS* 1.3 76.0 - - - +
199C VAL* 1.3 65.8 + - - +
201C GLY* 3.3 10.3 + - - -
206C ASN* 3.0 15.9 + - - -
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Residues in contact with VAL 199 (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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168C PHE* 3.7 19.7 - - + -
195C ILE 2.9 18.4 + - - +
196C MSE 3.3 21.5 + - + +
198C ALA* 1.3 75.4 - - - +
200C ASN* 1.3 69.2 + - - +
202C ASN 3.0 21.1 + - - +
203C PRO* 3.1 12.7 - - + -
206C ASN* 3.5 9.0 + - + +
207C LYS* 3.8 35.9 - - + +
210C LEU* 3.8 27.4 - - + -
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Residues in contact with ASN 200 (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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196C MSE 2.9 38.8 + - - +
197C LYS* 3.4 5.8 + - - +
198C ALA 3.2 0.2 - - - -
199C VAL* 1.3 83.0 - - - +
201C GLY* 1.3 62.8 + - - +
202C ASN 3.2 1.5 + - - -
203C PRO* 3.5 23.7 - - + +
207C LYS* 5.6 1.0 - - - +
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Residues in contact with GLY 201 (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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197C LYS 3.1 12.4 + - - -
198C ALA* 3.3 7.1 + - - -
199C VAL 3.2 1.4 - - - -
200C ASN* 1.3 77.8 - - - +
202C ASN* 1.3 61.7 + - - +
203C PRO* 4.0 0.6 - - - +
206C ASN* 4.7 0.4 - - - -
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Residues in contact with ASN 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199C VAL 3.0 5.0 + - - -
201C GLY* 1.3 80.8 - - - +
203C PRO* 1.3 63.8 - - - +
204C ASP* 3.9 7.6 + - - +
205C ARG* 3.5 41.6 + - - +
206C ASN* 2.8 39.6 + - - +
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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