Contacts of the helix formed by residues 186 - 200 (chain X) in PDB entry 3F6E
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 186 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184X ARG* 3.4 5.3 + - - +
185X LEU* 1.3 79.2 - - - +
187X ASP* 1.3 58.2 + - - +
188X GLN* 3.2 10.7 + - - +
189X ASP* 2.9 51.1 + - - +
190X LEU* 2.9 25.6 + - - +
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Residues in contact with ASP 187 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184X ARG* 2.7 41.8 + - - +
186X ASN* 1.3 72.0 - - - +
188X GLN* 1.3 58.0 + - - +
190X LEU* 3.8 3.1 - - - +
191X ASP* 2.9 42.0 + - - +
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Residues in contact with GLN 188 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186X ASN* 3.2 9.1 + - - +
187X ASP* 1.3 80.6 - - - +
189X ASP* 1.3 72.7 + - - +
191X ASP* 3.4 8.3 + - - +
192X ILE* 3.2 30.5 + - + +
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Residues in contact with ASP 189 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185X LEU* 3.7 21.6 - - + +
186X ASN* 2.9 33.6 + - - +
188X GLN* 1.3 84.1 - - - +
190X LEU* 1.3 65.6 + - - +
192X ILE* 3.2 21.2 + - - +
193X LEU* 3.0 21.5 + - - +
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Residues in contact with LEU 190 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184X ARG* 3.7 30.3 - - - +
185X LEU* 3.7 12.0 - - + +
186X ASN 2.9 17.7 + - - +
187X ASP* 3.8 4.7 - - - +
189X ASP* 1.3 75.7 - - - +
191X ASP* 1.3 60.2 + - - +
193X LEU* 3.2 6.1 + - + +
194X VAL* 2.8 34.8 + - + +
321X MET* 4.1 23.6 - - + -
324X ALA* 4.1 12.8 - - + -
325X LEU* 3.9 27.4 - - + -
328X LEU* 3.7 28.7 - - + -
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Residues in contact with ASP 191 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187X ASP* 2.9 26.2 + - - +
188X GLN* 3.6 7.8 - - - +
190X LEU* 1.3 76.7 - - - +
192X ILE* 1.3 64.6 + - + +
194X VAL* 3.4 6.5 + - - +
195X LYS* 3.0 44.7 + - - +
328X LEU* 5.1 10.7 - - - +
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Residues in contact with ILE 192 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188X GLN* 3.2 26.3 + - + +
189X ASP* 3.2 24.0 + - - +
191X ASP* 1.3 75.1 - - + +
193X LEU* 1.3 64.2 + - - +
195X LYS* 3.3 10.3 + - + +
196X ALA* 3.0 23.1 + - + +
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Residues in contact with LEU 193 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185X LEU* 4.6 2.9 - - + -
189X ASP 3.0 13.2 + - - +
190X LEU* 3.5 10.1 - - + +
192X ILE* 1.3 79.3 - - - +
194X VAL* 1.3 63.0 + - - +
196X ALA* 3.2 4.7 + - - +
197X LEU* 3.0 32.0 + - + +
271X LEU* 4.7 3.1 - - + -
296X ILE* 3.7 38.8 - - + -
298X VAL* 4.9 3.8 - - + -
314X ILE* 3.7 25.6 - - + -
321X MET* 4.1 13.7 - - + -
325X LEU* 3.9 29.2 - - + -
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Residues in contact with VAL 194 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190X LEU* 2.8 24.8 + - + +
191X ASP* 3.8 8.3 - - - +
193X LEU* 1.3 73.4 - - - +
195X LYS* 1.3 59.1 + - + +
197X LEU* 3.2 8.9 + - - +
198X ASN* 2.8 43.7 + - - +
325X LEU* 3.9 22.4 - - + -
328X LEU* 3.8 46.2 - - + +
329X VAL* 4.1 9.6 - - + -
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Residues in contact with LYS 195 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191X ASP* 3.0 35.7 + - - +
192X ILE* 3.8 7.9 - - + +
194X VAL* 1.3 77.0 - - + +
196X ALA* 1.3 57.3 + - - +
198X ASN* 3.3 12.7 + - - +
199X SER* 2.8 37.8 + - - +
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Residues in contact with ALA 196 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192X ILE* 3.0 14.7 + - + +
193X LEU* 3.2 11.2 + - - +
195X LYS* 1.3 77.6 - - - +
197X LEU* 1.3 62.6 + - - +
199X SER* 3.4 4.9 + - - -
200X ALA* 3.2 21.7 + - - +
269X VAL* 4.5 6.6 - - + +
294X ARG* 3.4 29.2 - - - +
296X ILE* 4.8 8.3 - - + -
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Residues in contact with LEU 197 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193X LEU* 3.0 29.0 + - + +
194X VAL 3.6 5.4 - - - +
196X ALA* 1.3 76.2 - - - +
198X ASN* 1.3 62.4 + - - +
199X SER 3.2 0.7 + - - -
200X ALA* 3.2 19.0 + - - +
203X PRO* 5.0 7.3 - - + +
223X LEU* 4.9 1.1 - - + -
227X LEU* 3.9 32.8 - - + +
269X VAL* 4.2 22.2 - - + -
271X LEU* 4.1 34.5 - - + -
296X ILE* 5.0 0.4 - - + -
325X LEU* 4.0 26.0 - - + -
329X VAL* 4.0 14.8 - - + -
334X ARG* 5.2 1.6 + - - -
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Residues in contact with ASN 198 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194X VAL* 2.8 38.6 + - - +
195X LYS* 3.6 12.1 - - - +
197X LEU* 1.3 72.7 - - - +
199X SER* 1.3 61.3 + - - +
200X ALA 3.7 3.8 + - - +
227X LEU* 4.8 3.8 - - - +
328X LEU 5.0 0.8 + - - -
329X VAL* 3.6 9.5 - - - +
330X GLU* 2.8 66.5 + - - +
334X ARG* 5.2 4.0 + - - -
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Residues in contact with SER 199 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195X LYS* 2.8 23.2 + - - +
196X ALA* 3.9 6.3 - - - -
197X LEU 3.1 0.4 - - - -
198X ASN* 1.3 75.6 - - - +
200X ALA* 1.3 66.8 + - - +
201X SER* 3.5 2.9 + - - -
268X ASP* 4.6 0.5 - - - +
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Residues in contact with ALA 200 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196X ALA 3.2 12.1 + - - +
197X LEU* 3.2 14.5 + - - +
198X ASN 4.3 2.9 - - - +
199X SER* 1.3 78.7 - - - +
201X SER* 1.3 60.5 + - - +
203X PRO* 4.0 19.7 - - + -
268X ASP* 3.3 20.0 - - - +
269X VAL* 3.9 15.5 - - + -
334X ARG* 3.2 23.0 + - - -
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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