Contacts of the helix formed by residues 203 - 216 (chain C) in PDB entry 1AX4
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 MET 203 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163C TRP* 5.4 0.2 - - - -
202C SER* 1.3 74.3 - - - +
204C SER* 1.3 58.4 + - - +
206C LEU* 3.4 5.7 + - - +
207C LYS* 2.9 28.3 + - + +
234C ILE* 3.9 14.6 - - + +
238C ASP* 4.2 10.4 + - - +
240C LYS* 5.2 3.1 - - - +
241C TYR* 3.5 39.3 - - + +
249C VAL* 3.5 23.3 - - + +
252C ASP* 3.4 24.0 - - + -
253C MET* 3.7 32.1 - - + +
256C TYR* 3.9 20.9 - - + +
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Residues in contact with SER 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202C SER* 3.4 10.3 + - - -
203C MET* 1.3 77.8 - - - +
205C ASN* 1.3 61.3 + - - +
207C LYS* 3.4 9.0 + - - +
208C GLU* 2.9 30.6 + - - +
238C ASP* 5.2 3.2 + - - -
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Residues in contact with ASN 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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166C ASP* 3.4 27.5 + - - +
167C PHE* 2.8 51.9 + - - +
169C ILE* 3.7 21.0 - - - +
201C VAL* 3.4 10.4 - - + +
202C SER* 3.1 18.4 + - - +
204C SER* 1.3 79.0 + - - +
206C LEU* 1.4 65.6 + - - +
208C GLU* 3.2 4.8 + - - +
209C VAL* 2.9 28.8 + - - +
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Residues in contact with LEU 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167C PHE* 5.2 1.8 - - + -
189C SER* 4.0 28.8 + - - +
191C VAL* 4.1 19.3 - - + -
201C VAL* 3.7 24.9 - - + +
202C SER 3.0 18.8 + - - +
203C MET* 3.7 13.7 - - - +
205C ASN* 1.4 76.4 - - - +
207C LYS* 1.3 62.7 + - - +
209C VAL* 3.6 5.3 + - - +
210C TYR* 3.1 23.7 + - - +
222C MET* 4.2 9.9 - - + -
230C ASN* 4.7 0.2 - - - +
234C ILE* 4.7 0.4 - - + -
253C MET* 3.9 33.2 - - + -
256C TYR* 3.6 19.5 - - + +
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Residues in contact with LYS 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203C MET* 2.9 19.9 + - + +
204C SER* 3.6 9.2 - - - +
205C ASN 3.2 0.2 - - - -
206C LEU* 1.3 76.8 - - - +
208C GLU* 1.3 57.5 + - - +
210C TYR* 3.2 2.9 + - - +
211C GLU* 2.9 62.3 + - - +
240C LYS* 6.4 0.2 - - - +
256C TYR* 3.4 43.5 - - + +
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Residues in contact with GLU 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169C ILE* 3.9 36.5 - - + +
173C LYS* 4.8 6.4 + - - -
204C SER 2.9 21.1 + - - +
205C ASN* 3.9 4.8 + - - +
207C LYS* 1.3 69.7 - - - +
209C VAL* 1.3 66.8 + - - +
211C GLU* 3.7 12.3 - - + +
212C ILE* 3.0 36.1 + - + +
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Residues in contact with VAL 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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167C PHE* 3.5 42.4 - - + -
169C ILE* 3.6 17.9 - - + -
172C LEU* 4.3 17.5 - - + +
187C ILE* 3.9 29.6 - - + +
189C SER* 4.4 6.3 - - - +
205C ASN* 2.9 21.3 + - - +
206C LEU* 3.8 4.3 - - - +
208C GLU* 1.3 75.2 - - - +
210C TYR* 1.3 59.3 + - - +
212C ILE* 3.5 3.1 + - - +
213C ALA* 3.0 26.2 + - - +
220C VAL* 5.3 3.6 - - + -
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Residues in contact with TYR 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 LEU 3.1 18.1 + - - +
207C LYS 3.2 4.5 + - - +
209C VAL* 1.3 77.1 - - - +
211C GLU* 1.3 64.8 + - + +
213C ALA* 3.3 4.6 + - - +
214C LYS* 2.9 64.5 + - + +
220C VAL* 3.8 12.8 - - + -
255C LYS 3.7 15.9 - - - -
256C TYR* 3.4 34.3 - + + +
257C ALA* 3.7 13.0 - - - -
258C ASP* 2.8 29.4 + - - -
279C ARG* 3.4 17.6 + - - -
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Residues in contact with GLU 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 LYS* 2.9 56.3 + - + +
208C GLU* 3.7 14.2 - - + +
210C TYR* 1.3 77.1 - - + +
212C ILE* 1.3 66.8 - - + +
214C LYS* 3.3 6.7 + - - +
215C GLN* 3.0 29.7 + - + +
256C TYR* 6.2 0.9 - - + -
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Residues in contact with ILE 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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169C ILE* 3.9 27.6 - - + -
172C LEU* 4.0 18.8 - - + -
173C LYS* 4.2 25.8 - - + +
176C ILE* 3.7 27.8 - - + -
208C GLU* 3.0 28.8 + - + +
209C VAL 3.7 3.1 - - - +
211C GLU* 1.3 77.7 - - + +
213C ALA* 1.3 63.3 + - - +
215C GLN* 3.1 16.3 + - - +
216C HIS* 3.0 32.1 + - + +
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Residues in contact with ALA 213 (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 ILE* 3.8 17.2 - - + +
209C VAL 3.0 16.2 + - - +
210C TYR 3.3 3.1 + - - +
212C ILE* 1.3 77.1 - - - +
214C LYS* 1.3 55.4 + - - +
216C HIS 3.2 3.3 + - - -
217C GLY 2.9 7.8 + - - -
218C ILE* 2.7 43.5 + - + +
220C VAL* 3.4 33.0 - - + -
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Residues in contact with LYS 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210C TYR* 2.9 62.2 + - + +
211C GLU* 3.8 5.8 - - - +
213C ALA* 1.3 73.9 - - - +
215C GLN* 1.3 64.4 + - + +
216C HIS 3.1 1.2 + - - -
217C GLY* 3.4 12.0 + - - +
218C ILE 2.7 31.9 + - - +
219C PHE* 4.0 2.2 - - - +
258C ASP* 2.7 27.4 + - - +
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Residues in contact with GLN 215 (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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211C GLU* 3.0 18.6 + - + +
212C ILE* 3.1 16.5 + - - +
214C LYS* 1.3 76.5 - - - +
216C HIS* 1.3 74.7 + - + +
217C GLY 3.6 0.4 + - - -
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Residues in contact with HIS 216 (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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115C LYS* 5.3 1.0 + - - -
176C ILE* 4.2 23.6 - - + +
181C ALA* 3.7 24.5 - - + +
212C ILE* 3.0 33.1 + - + +
213C ALA 3.2 2.2 + - - +
214C LYS 3.1 0.4 - - - -
215C GLN* 1.3 95.7 + - + +
217C GLY* 1.3 62.3 + - - +
218C ILE* 3.3 22.1 + - + +
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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