Contacts of the helix formed by residues 181 - 196 (chain M) 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 M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180M THR* 1.3 73.8 - - - +
182M SER* 1.3 61.1 + - - +
183M ASN* 3.3 7.5 + - - +
184M ILE* 3.3 21.9 + - - +
185M ASP* 3.3 14.8 + - - -
341M ARG* 5.1 1.1 - - - -
343M PRO 3.5 16.6 + - - -
346M GLY* 3.6 21.3 - - - -
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Residues in contact with SER 182 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169M ASN* 2.7 24.2 + - - -
171M VAL* 4.1 3.4 - - - -
179M ARG* 2.9 50.5 + - - -
180M THR 3.3 3.8 + - - -
181M GLY* 1.3 73.8 - - - +
183M ASN* 1.3 56.5 + - - +
184M ILE 3.2 0.7 - - - -
185M ASP* 3.3 10.8 + - - +
186M CYS* 2.8 34.1 + - - +
235M LEU* 3.5 9.2 - - - +
341M ARG* 4.8 3.0 - - - +
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Residues in contact with ASN 183 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169M ASN* 3.5 19.2 - - - +
171M VAL* 4.0 23.2 - - - +
180M THR* 5.9 0.3 - - - -
181M GLY* 3.3 3.8 + - - +
182M SER* 1.3 77.5 - - - +
184M ILE* 1.3 58.3 + - + +
186M CYS* 3.9 1.5 - - - +
187M GLU* 3.2 32.9 + - - +
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Residues in contact with ILE 184 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181M GLY* 3.3 16.8 + - - +
182M SER 3.2 0.4 - - - -
183M ASN* 1.3 76.7 - - + +
185M ASP* 1.3 59.6 + - - +
187M GLU* 3.5 3.9 + - - +
188M LYS* 2.9 48.0 + - + +
343M PRO 5.4 0.2 - - - +
344M LYS 3.1 28.3 - - - +
345M SER* 3.6 16.4 - - - +
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Residues in contact with ASP 185 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179M ARG* 5.4 1.2 + - - -
181M GLY 3.3 9.5 + - - +
182M SER* 3.3 15.5 + - - +
184M ILE* 1.3 78.6 - - - +
186M CYS* 1.3 60.5 + - - +
188M LYS* 3.5 8.9 + - - +
189M LEU* 3.1 29.5 + - - +
235M LEU* 3.8 13.4 - - + +
283M GLN* 5.3 1.2 - - - +
341M ARG* 4.9 1.6 - - - -
345M SER 4.4 2.4 - - - +
346M GLY* 3.6 7.3 - - - -
347M SER* 2.8 44.0 + - - +
350M VAL* 3.5 28.5 - - + +
351M GLU* 4.4 2.9 + - - +
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Residues in contact with CYS 186 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167M ILE* 3.7 20.3 - - - +
169M ASN* 3.4 23.6 - - - +
182M SER 2.8 20.8 + - - +
183M ASN* 3.9 5.4 - - - +
184M ILE 3.3 0.2 - - - -
185M ASP* 1.3 73.8 - - - +
187M GLU* 1.3 56.3 + - + +
189M LEU* 3.3 5.2 + - - +
190M ARG* 2.8 35.0 + - - +
202M VAL* 3.4 37.7 - - - -
235M LEU* 3.8 7.4 - - + +
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Residues in contact with GLU 187 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183M ASN 3.2 18.5 + - - +
184M ILE* 4.1 3.6 - - - +
186M CYS* 1.3 78.6 - - + +
188M LYS* 1.3 64.4 + - - +
190M ARG* 3.2 41.1 + - - +
191M ARG* 3.2 50.5 + - - +
202M VAL* 5.1 4.9 - - - +
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Residues in contact with LYS 188 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184M ILE* 2.9 37.8 + - + +
185M ASP* 3.6 13.2 + - - +
186M CYS 3.3 0.2 - - - -
187M GLU* 1.3 78.0 - - - +
189M LEU* 1.3 56.8 + - - +
191M ARG* 3.9 11.0 - - - +
192M ARG* 3.0 27.2 + - - +
345M SER 4.7 8.3 + - - -
350M VAL* 4.9 6.1 - - + +
351M GLU* 3.9 32.9 + - - +
354M ASP* 3.6 36.1 + - + +
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Residues in contact with LEU 189 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167M ILE* 4.1 13.0 - - + -
185M ASP 3.1 18.1 + - - +
186M CYS* 3.8 3.6 - - - +
188M LYS* 1.3 77.6 - - - +
190M ARG* 1.3 60.7 + - - +
192M ARG* 4.0 8.5 - - + -
193M PHE* 2.9 55.1 + - + +
233M VAL* 3.6 29.8 - - + -
235M LEU* 4.2 13.0 - - + -
281M PHE* 6.1 1.8 - - + -
350M VAL* 3.8 24.7 - - + +
353M LEU* 4.2 27.4 - - + -
354M ASP* 5.5 4.5 - - + -
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Residues in contact with ARG 190 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D GLU* 5.7 4.4 + - - -
167M ILE* 4.0 1.9 - - - +
186M CYS 2.8 21.6 + - - +
187M GLU* 3.2 35.0 + - - +
188M LYS 3.4 0.2 - - - -
189M LEU* 1.3 73.0 - - - +
191M ARG* 1.3 76.5 + - - +
194M SER* 2.7 47.6 + - - -
200M VAL* 3.6 29.3 - - + +
202M VAL* 3.8 24.5 - - + -
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Residues in contact with ARG 191 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187M GLU* 3.2 41.1 + - - +
188M LYS* 4.0 10.7 - - - +
190M ARG* 1.3 99.2 - - - +
192M ARG* 1.3 62.9 + - - +
194M SER* 3.9 5.8 - - - -
195M SER* 3.2 21.7 + - - -
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Residues in contact with ARG 192 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188M LYS 3.0 17.4 + - - +
189M LEU* 3.2 16.5 + - + +
191M ARG* 1.3 75.6 - - - +
193M PHE* 1.3 66.5 + - + +
195M SER* 3.1 29.8 + - - -
196M LEU* 3.2 25.0 + - + +
353M LEU* 5.6 0.9 - - + -
354M ASP* 3.0 30.5 + - - +
357M PHE* 3.9 35.0 + - + -
358M GLU* 2.8 59.0 + - - +
361M ALA* 5.9 0.2 - - - +
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Residues in contact with PHE 193 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165M CYS* 3.6 21.1 - - - -
167M ILE* 4.7 1.1 - - + -
189M LEU* 2.9 49.5 + - + +
192M ARG* 1.3 73.9 - - + +
194M SER* 1.3 62.6 + - - +
196M LEU* 3.3 27.4 + - + +
197M HIS 3.4 0.5 + - - -
198M PHE* 3.1 38.8 + + + +
200M VAL* 3.6 19.7 - - + -
231M VAL* 3.9 17.9 - - + -
233M VAL* 3.7 21.8 - - + -
281M PHE* 3.7 29.8 - + - -
353M LEU* 5.5 2.5 - - + -
357M PHE* 4.8 11.4 - + - -
400M PHE* 4.8 5.4 - + - -
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Residues in contact with SER 194 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190M ARG* 2.7 36.8 + - - -
191M ARG* 3.9 7.4 - - - -
193M PHE* 1.3 77.0 - - - +
195M SER* 1.3 60.5 + - - +
197M HIS* 3.3 15.8 + - - -
198M PHE 4.0 11.3 + - - +
200M VAL* 3.5 13.3 - - - +
403M SER* 5.3 0.2 + - - -
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Residues in contact with SER 195 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191M ARG 3.2 11.9 + - - -
192M ARG* 3.1 24.6 + - - -
194M SER* 1.3 78.4 - - - +
196M LEU* 1.3 61.0 + - - +
197M HIS* 3.3 3.8 + - - -
401M LYS 4.0 1.4 - - - +
402M THR* 4.3 0.9 - - - -
403M SER* 2.7 49.3 + - - -
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Residues in contact with LEU 196 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162M CYS* 3.9 7.1 + - - -
192M ARG* 3.2 22.7 + - + +
193M PHE* 3.3 26.7 + - + +
194M SER 3.2 0.6 - - - -
195M SER* 1.3 78.2 - - - +
197M HIS* 1.3 71.5 + - - +
198M PHE* 3.2 21.8 - - + -
357M PHE* 4.1 22.2 - - + -
361M ALA* 4.6 6.3 - - + -
400M PHE* 3.6 39.5 - - + -
401M LYS 3.7 9.3 + - - +
402M THR* 3.8 28.3 - - + -
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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