Contacts of the helix formed by residues 197 - 212 (chain C) in PDB entry 5AJI
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 ASP 197 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195C ASP 3.8 1.2 + - - -
196C SER* 1.3 71.3 - - - +
198C ILE* 1.3 65.9 + - - +
199C ASP* 3.0 22.0 + - - +
200C GLN* 3.7 32.6 + - + +
201C VAL* 3.0 26.8 + - - +
266C ILE* 6.1 0.2 - - - +
259D ARG* 5.0 4.5 + - - -
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Residues in contact with ILE 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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196C SER* 3.9 11.4 - - - +
197C ASP* 1.3 74.4 + - - +
199C ASP* 1.3 62.7 + - - +
201C VAL* 3.6 1.7 + - - +
202C LYS* 3.2 34.8 + - + +
225C LEU* 4.4 18.8 - - + -
233C ILE* 5.8 3.8 - - + -
235C PHE* 4.2 23.5 - - + -
255D GLU* 3.8 22.7 - - + +
258D LYS* 4.0 31.0 - - + +
259D ARG* 3.7 33.4 - - + +
262D ASP* 5.4 0.2 - - - +
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Residues in contact with ASP 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197C ASP* 3.0 14.7 + - - +
198C ILE* 1.3 77.2 - - - +
200C GLN* 1.3 58.3 + - - +
202C LYS* 3.5 10.6 + - - +
203C GLN* 3.0 29.7 + - - +
255D GLU* 4.3 2.3 - - - +
259D ARG* 2.6 34.3 + - - -
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Residues in contact with GLN 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197C ASP* 3.2 30.7 + - + +
199C ASP* 1.3 75.9 - - - +
201C VAL* 1.3 67.5 + - - +
203C GLN* 3.1 7.1 + - + +
204C ILE* 2.9 35.9 + - + +
264C ALA* 3.9 27.0 + - - +
266C ILE* 4.0 20.4 - - + +
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Residues in contact with VAL 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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192C VAL* 4.3 4.9 - - + -
196C SER* 3.8 21.5 - - - -
197C ASP 3.0 21.1 + - - +
198C ILE 3.8 3.8 - - - +
200C GLN* 1.3 78.0 - - - +
202C LYS* 1.3 63.0 + - - +
204C ILE* 3.4 2.3 + - - +
205C LEU* 3.0 33.3 + - + +
235C PHE* 3.4 42.4 - - + -
261C PHE* 4.0 13.4 - - + -
266C ILE* 3.8 26.5 - - + -
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Residues in contact with LYS 202 (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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198C ILE* 3.2 29.1 + - + +
199C ASP* 3.7 11.3 + - - +
201C VAL* 1.3 80.6 - - - +
203C GLN* 1.3 56.6 + - - +
205C LEU* 3.4 1.9 + - - +
206C THR* 2.8 36.2 + - - +
223C VAL* 4.0 34.9 - - + +
224C ARG* 4.5 11.8 - - - +
225C LEU 4.5 11.0 - - - +
235C PHE* 4.1 11.7 - - + -
255D GLU* 2.9 33.4 + - - -
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Residues in contact with GLN 203 (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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199C ASP 3.0 18.8 + - - +
200C GLN* 3.1 8.9 + - + +
202C LYS* 1.3 77.0 - - - +
204C ILE* 1.3 59.3 + - + +
206C THR* 3.2 10.6 + - - +
207C ASN* 2.8 51.9 + - - +
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Residues in contact with ILE 204 (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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200C GLN* 2.9 26.2 + - + +
201C VAL 3.7 3.6 - - - +
203C GLN* 1.3 78.1 - - + +
205C LEU* 1.3 64.1 + - - +
207C ASN* 3.1 12.9 + - + +
208C ILE* 3.0 26.9 + - + +
260C GLU* 3.8 27.6 - - + +
261C PHE* 3.6 18.2 - - + -
264C ALA* 3.6 23.6 - - + -
266C ILE* 3.4 32.1 - - + -
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Residues in contact with LEU 205 (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 ILE* 4.8 6.1 - - + -
201C VAL* 3.0 33.2 + - + +
202C LYS 3.8 3.8 - - - +
204C ILE* 1.3 78.9 - - - +
206C THR* 1.3 62.3 + - - +
208C ILE* 3.2 7.6 + - + +
209C ILE* 3.1 28.2 + - + +
223C VAL* 3.8 20.0 - - + -
235C PHE* 4.2 13.0 - - + -
237C VAL* 3.8 28.0 - - + -
257C ILE* 3.7 37.9 - - + -
261C PHE* 3.8 18.4 - - + -
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Residues in contact with THR 206 (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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202C LYS* 2.8 22.5 + - - +
203C GLN* 3.6 14.1 - - - +
205C LEU* 1.3 76.4 - - - +
207C ASN* 1.3 57.9 + - - +
209C ILE* 3.3 12.4 - - + +
210C GLN* 2.9 54.9 + - + +
223C VAL* 3.8 17.4 - - - +
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Residues in contact with ASN 207 (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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203C GLN* 2.8 47.5 + - - +
204C ILE* 3.5 11.2 - - - +
206C THR* 1.3 78.6 - - - +
208C ILE* 1.3 64.2 + - + +
210C GLN* 3.4 8.0 + - - +
211C SER* 3.1 26.2 + - - -
256C ARG* 4.4 2.4 + - - +
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Residues in contact with ILE 208 (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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204C ILE* 3.0 29.7 + - + +
205C LEU* 3.2 11.2 + - + +
207C ASN* 1.3 77.3 - - + +
209C ILE* 1.3 62.1 + - + +
211C SER* 3.1 15.8 + - - -
212C GLU* 3.3 8.3 + - - +
253C VAL* 4.0 29.6 - - + +
256C ARG* 3.3 44.4 + - + +
257C ILE* 3.9 28.7 - - + +
260C GLU* 3.7 29.8 - - + +
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Residues in contact with ILE 209 (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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205C LEU* 3.1 11.9 + - + +
206C THR* 3.3 18.2 - - + +
208C ILE* 1.3 79.8 - - + +
210C GLN* 1.3 64.1 + - + +
212C GLU* 3.7 7.6 - - - +
215C ILE* 3.8 30.7 - - + +
217C LYS* 3.3 16.8 - - - +
221C MET* 4.1 23.0 - - + +
223C VAL* 3.6 28.0 - - + -
237C VAL* 4.1 18.4 - - + -
239C VAL* 3.7 20.9 - - + -
253C VAL* 4.7 9.2 - - + -
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Residues in contact with GLN 210 (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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206C THR* 2.9 41.5 + - + +
207C ASN* 3.7 9.4 - - - +
209C ILE* 1.3 79.2 - - + +
211C SER* 1.3 58.0 + - - +
213C ASP* 4.9 1.0 - - - +
217C LYS* 3.0 37.9 + - - +
221C MET* 3.7 26.9 - - - +
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Residues in contact with SER 211 (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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207C ASN 3.1 10.8 + - - -
208C ILE 3.1 1.7 + - - -
210C GLN* 1.3 74.4 - - - +
212C GLU* 1.3 59.4 + - - +
213C ASP* 3.2 16.4 + - - +
256C ARG* 2.7 44.6 + - - -
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Residues in contact with GLU 212 (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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208C ILE 3.3 16.5 + - - +
209C ILE 4.1 0.2 - - - +
210C GLN 3.3 1.2 - - - -
211C SER* 1.3 75.9 - - - +
213C ASP* 1.3 61.0 + - - +
214C ARG* 2.9 52.6 + - + +
215C ILE* 3.3 40.2 + - + +
217C LYS* 3.1 19.4 + - - -
249C VAL* 4.3 10.5 - - + -
252C ASP* 4.6 8.3 - - - +
253C VAL* 4.4 10.1 - - + +
256C ARG* 4.5 12.5 + - - +
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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