Contacts of the helix formed by residues 181 - 196 (chain C) in PDB entry 3V3K
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 GLY 181 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180C THR* 1.3 72.8 - - - +
182C SER* 1.3 62.6 + - - +
183C ASN* 3.3 8.3 - - - +
184C ILE* 3.4 23.5 + - - +
185C ASP* 3.6 4.1 + - - -
341C ARG* 4.8 2.5 - - - -
343C PRO* 3.7 20.4 + - - -
346C GLY* 3.4 24.6 - - - -
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Residues in contact with SER 182 (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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169C ASN* 2.8 23.0 + - - +
171C VAL* 3.9 4.9 - - - -
179C ARG* 2.8 58.2 + - - +
180C THR 3.3 1.0 + - - -
181C GLY* 1.3 75.3 - - - +
183C ASN* 1.3 59.8 + - - +
184C ILE 3.2 0.7 - - - -
185C ASP* 3.2 12.1 + - - +
186C CYS* 2.9 28.1 + - - +
235C LEU* 3.6 6.9 - - - +
341C ARG* 4.6 2.8 - - - +
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Residues in contact with ASN 183 (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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169C ASN* 3.4 16.3 + - - -
171C VAL* 3.7 20.2 - - - +
172C ASN* 6.1 0.6 - - - +
179C ARG 4.9 0.4 + - - -
180C THR* 6.2 0.6 - - - +
181C GLY* 3.3 4.9 - - - +
182C SER* 1.3 75.4 - - - +
184C ILE* 1.3 59.3 + - + +
186C CYS* 3.8 5.3 - - - +
187C GLU* 3.1 36.7 + - + +
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Residues in contact with ILE 184 (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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181C GLY* 3.4 19.5 - - - +
182C SER 3.2 0.4 - - - -
183C ASN* 1.3 78.2 - - + +
185C ASP* 1.3 58.0 + - - +
187C GLU* 4.0 3.1 - - - +
188C LYS* 3.1 47.0 + - + +
343C PRO 4.2 3.1 - - - +
344C LYS* 3.5 32.8 - - - +
345C SER* 4.0 15.3 - - - +
346C GLY* 3.8 9.6 - - - +
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Residues in contact with ASP 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179C ARG* 5.0 1.6 + - - -
181C GLY 3.9 7.8 - - - +
182C SER* 3.2 14.5 + - - +
184C ILE* 1.3 77.6 - - - +
186C CYS* 1.3 59.3 + - - +
188C LYS* 3.3 5.7 + - - +
189C LEU* 3.0 34.8 + - - +
235C LEU* 4.0 12.7 - - + +
283C GLN* 4.9 3.1 - - - +
341C ARG* 5.4 0.9 - - - -
345C SER 4.7 1.0 - - - +
346C GLY* 3.6 6.1 - - - -
347C SER* 3.1 42.7 + - - +
350C VAL* 3.5 34.1 - - + +
351C GLU* 4.4 2.4 + - - -
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Residues in contact with CYS 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167C ILE* 4.3 7.8 - - - +
169C ASN* 3.4 35.2 - - - +
182C SER 2.9 9.4 + - - +
183C ASN* 3.8 6.1 - - - +
184C ILE 3.4 0.2 - - - -
185C ASP* 1.3 77.6 - - - +
187C GLU* 1.3 64.7 + - + +
189C LEU* 3.4 3.4 + - - +
190C ARG* 2.9 30.7 + - - +
202C VAL* 3.4 42.4 - - - -
235C LEU* 3.7 8.2 - - + +
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Residues in contact with GLU 187 (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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183C ASN* 3.1 19.7 + - + +
184C ILE* 4.3 3.1 - - - +
186C CYS* 1.3 85.0 - - + +
188C LYS* 1.3 63.8 + - - +
190C ARG* 3.8 35.9 + - - +
191C ARG* 3.5 39.4 + - - +
202C VAL* 5.4 1.0 - - - +
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Residues in contact with LYS 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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184C ILE* 3.1 39.1 + - + +
185C ASP* 3.5 9.9 - - - +
186C CYS 3.2 0.2 - - - -
187C GLU* 1.3 77.2 - - - +
189C LEU* 1.3 59.0 + - - +
191C ARG* 3.5 5.2 + - - +
192C ARG* 2.9 29.6 + - - +
345C SER 4.5 6.1 + - - -
350C VAL* 4.9 3.6 - - + +
351C GLU* 3.5 42.0 + - - +
354C ASP* 3.3 36.3 + - + +
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Residues in contact with LEU 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167C ILE* 4.0 14.4 - - + -
185C ASP 3.0 17.9 + - - +
186C CYS* 4.0 2.9 - - - +
188C LYS* 1.3 74.7 - - - +
190C ARG* 1.3 60.5 + - - +
192C ARG* 3.9 9.9 - - + -
193C PHE* 2.9 54.6 + - + +
233C VAL* 3.6 31.2 - - + -
235C LEU* 4.3 11.9 - - + -
281C PHE* 6.0 0.9 - - + -
350C VAL* 3.7 30.7 - - + +
353C LEU* 4.3 25.4 - - + -
354C ASP* 5.2 4.3 - - + -
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Residues in contact with ARG 190 (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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167C ILE* 4.0 1.9 - - - +
186C CYS 2.9 19.0 + - - +
187C GLU* 3.8 34.5 + - - +
189C LEU* 1.3 76.4 - - - +
191C ARG* 1.3 64.7 + - + +
194C SER* 3.3 25.0 + - - -
200C VAL* 3.9 29.4 + - + +
201C GLU* 6.1 0.2 - - - +
202C VAL* 3.8 29.3 - - + +
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Residues in contact with ARG 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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187C GLU* 3.5 28.9 + - - +
188C LYS* 3.5 4.6 + - - +
189C LEU 3.3 0.2 - - - -
190C ARG* 1.3 81.7 - - + +
192C ARG* 1.3 59.7 + - - +
194C SER* 3.9 4.4 - - - -
195C SER* 3.0 28.1 + - - -
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Residues in contact with ARG 192 (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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188C LYS 2.9 18.3 + - - +
189C LEU* 3.2 15.9 + - + +
191C ARG* 1.3 76.4 - - - +
193C PHE* 1.3 62.8 - - + +
195C SER* 3.3 20.2 + - - -
196C LEU* 3.1 33.2 + - + +
353C LEU* 5.7 0.4 - - + -
354C ASP* 2.7 34.1 + - - +
357C PHE* 3.9 37.0 + - + -
358C GLU* 3.1 55.0 + - - +
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Residues in contact with PHE 193 (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 CYS* 3.8 17.5 - - - -
167C ILE* 4.5 1.1 - - + -
189C LEU* 2.9 52.2 + - + +
192C ARG* 1.3 73.3 - - + +
194C SER* 1.3 61.9 + - - +
196C LEU* 3.1 31.0 + - + +
197C HIS 3.3 0.5 + - - -
198C PHE* 3.1 38.6 + + + +
200C VAL* 3.8 16.6 - - + -
231C VAL* 3.9 18.4 - - + -
233C VAL* 3.7 21.5 - - + -
281C PHE* 3.8 32.5 - + - -
353C LEU* 5.3 2.5 - - + -
357C PHE* 4.7 9.2 - + - -
400C PHE* 4.7 6.5 - + - -
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Residues in contact with SER 194 (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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190C ARG* 3.3 22.0 + - - -
191C ARG* 4.0 5.6 - - - -
193C PHE* 1.3 76.5 - - - +
195C SER* 1.3 61.5 + - - +
197C HIS* 3.2 16.3 + - - -
198C PHE 3.9 14.2 + - - +
200C VAL* 3.5 9.6 + - - +
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Residues in contact with SER 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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191C ARG 3.0 19.6 + - - -
192C ARG* 3.3 24.9 + - - -
193C PHE 3.2 0.2 - - - -
194C SER* 1.3 75.8 - - - +
196C LEU* 1.3 59.5 + - - +
197C HIS* 3.2 6.5 + - - -
402C THR* 4.4 0.2 - - - -
403C SER* 3.5 40.6 + - - +
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Residues in contact with LEU 196 (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 CYS* 4.3 4.7 + - - -
192C ARG* 3.1 20.6 + - + +
193C PHE* 3.1 25.6 + - + +
195C SER* 1.3 77.9 - - - +
197C HIS* 1.3 69.4 + - - +
198C PHE* 3.5 18.1 - - + -
357C PHE* 3.9 26.9 - - + +
361C ALA* 4.6 8.3 - - + -
400C PHE* 3.6 40.3 - - + -
401C LYS* 3.5 14.6 + - - +
402C THR* 3.8 23.6 - - + -
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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
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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