Contacts of the helix formed by residues 202 - 213 (chain X) in PDB entry 5A31
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 ALA 202 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195X VAL* 4.4 11.0 - - + +
196X LEU* 3.4 11.2 - - + +
199X CYS* 3.1 18.9 + - + +
200X PRO 3.2 1.0 - - - -
201X LEU* 1.3 70.3 - - - +
203X LEU* 1.3 63.4 + - - +
204X ASP 3.3 2.5 - - - -
205X ALA* 3.2 17.7 + - + -
206X ILE* 3.4 10.3 + - - +
44Y MET* 3.7 17.5 - - + +
49Y LEU* 5.3 3.4 - - + -
52Y ASN* 3.6 20.9 - - - +
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Residues in contact with LEU 203 (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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201X LEU 2.5 12.9 + - - +
202X ALA* 1.3 72.5 - - - +
204X ASP* 1.3 58.5 + - - +
206X ILE* 3.1 15.6 + - + +
207X LEU* 2.8 26.3 + - + -
235X TRP* 5.1 0.4 - - + -
236X LEU* 4.9 12.6 - - + -
239X TRP* 3.2 53.2 - - + -
44Y MET* 4.8 1.8 - - - +
52Y ASN* 4.8 2.3 + - - +
55Y LEU* 3.2 42.0 - - + -
56Y LEU* 4.9 18.8 - - + +
59Y LEU* 4.4 15.3 - - + -
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Residues in contact with ASP 204 (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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173X MET* 5.5 1.3 - - + -
180X LYS* 5.6 0.3 + - - -
192X TYR* 4.5 4.4 + - - -
202X ALA 3.3 0.8 - - - -
203X LEU* 1.3 75.9 - - - +
205X ALA* 1.3 57.1 + - - +
207X LEU* 3.7 8.3 - - - +
208X GLY* 2.8 26.7 + - - -
51Y SER* 2.8 47.6 + - - +
52Y ASN* 3.2 25.2 - - - +
55Y LEU* 3.4 29.7 - - - +
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Residues in contact with ALA 205 (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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173X MET* 5.6 1.1 - - + +
192X TYR* 3.4 19.3 - - + +
195X VAL* 3.2 34.1 - - + -
196X LEU* 3.5 12.3 - - + -
202X ALA* 3.2 15.7 + - + +
203X LEU 3.2 0.2 - - - -
204X ASP* 1.3 76.4 - - - +
206X ILE* 1.3 58.5 + - - +
208X GLY* 3.3 1.7 + - - -
209X LEU* 2.9 33.7 + - - +
52Y ASN* 4.3 4.6 - - - +
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Residues in contact with ILE 206 (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 LEU* 3.4 23.1 - - + +
200X PRO 3.8 6.3 - - - +
201X LEU* 5.0 1.6 - - - +
202X ALA 3.5 2.2 - - - +
203X LEU* 3.1 26.2 + - + +
205X ALA* 1.3 75.5 - - - +
207X LEU* 1.3 58.3 + - - +
209X LEU* 3.0 8.6 + - - +
210X LEU* 2.9 48.8 + - + +
218X GLU* 5.1 4.5 - - + -
222X MET* 3.5 44.6 - - + -
236X LEU* 5.1 7.6 - - + -
239X TRP* 5.0 5.2 - - + -
240X ILE* 4.3 21.1 - - + -
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Residues in contact with LEU 207 (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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203X LEU 2.8 19.9 + - - +
204X ASP* 3.7 7.2 - - - +
206X ILE* 1.3 73.4 - - - +
208X GLY* 1.3 56.1 + - - +
210X LEU* 3.4 6.9 + - - +
211X SER* 3.0 26.5 + - - -
239X TRP* 4.2 12.5 - - + -
243X TYR* 3.6 40.2 - - + -
247X HIS* 3.9 14.8 - - + +
306X LYS* 5.8 4.5 - - - +
55Y LEU* 3.7 28.3 - - + -
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Residues in contact with GLY 208 (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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180X LYS* 4.2 17.5 - - - -
192X TYR* 4.4 6.7 - - - -
204X ASP 2.8 16.9 + - - -
205X ALA 3.6 2.2 - - - -
207X LEU* 1.3 73.6 - - - +
209X LEU* 1.3 58.3 + - - +
211X SER* 2.5 26.1 + - - -
212X LEU* 2.8 24.1 + - - +
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Residues in contact with LEU 209 (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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189X VAL* 4.0 26.9 - - + +
192X TYR* 3.4 29.8 - - + -
193X LYS* 4.6 13.0 - - + +
196X LEU* 3.4 34.1 - - + -
205X ALA 2.9 18.1 + - - +
206X ILE* 3.0 8.5 + - - +
208X GLY* 1.3 70.1 - - - +
210X LEU* 1.3 59.1 + - - +
212X LEU* 3.1 8.1 + - + +
213X SER 2.8 36.1 + - - +
218X GLU* 4.3 22.2 - - + -
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Residues in contact with LEU 210 (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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206X ILE* 2.9 27.5 + - + +
207X LEU* 3.7 11.0 - - - +
208X GLY 3.2 0.2 - - - -
209X LEU* 1.3 74.8 - - - +
211X SER* 1.3 61.6 + - - +
213X SER* 3.2 15.0 + - - +
215X LYS* 3.7 37.7 - - + +
218X GLU* 4.1 14.8 - - + -
239X TRP* 5.0 2.2 - - + -
240X ILE* 3.5 30.7 - - + +
243X TYR* 3.4 31.9 - - + +
244X ALA* 3.7 4.4 - - + +
247X HIS* 3.5 27.4 - - + +
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Residues in contact with SER 211 (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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180X LYS* 4.5 9.9 + - - +
185X GLU* 5.3 0.5 - - - +
207X LEU 3.0 11.6 + - - -
208X GLY* 2.5 27.0 + - - -
210X LEU* 1.3 77.6 - - - +
212X LEU* 1.3 63.0 + - - +
213X SER* 5.0 0.7 - - - -
247X HIS* 3.4 29.8 + - - +
404X PRO* 5.9 2.6 - - - +
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Residues in contact with LEU 212 (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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180X LYS* 4.0 25.6 - - + -
185X GLU* 4.0 39.1 - - + +
188X SER* 3.8 11.7 - - - -
189X VAL* 3.6 32.1 - - + -
192X TYR* 3.6 33.0 - - + -
208X GLY 2.8 18.8 + - - +
209X LEU* 3.5 10.3 - - + +
211X SER* 1.3 74.8 - - - +
213X SER* 1.3 73.5 + - - +
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Residues in contact with SER 213 (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 GLU* 5.1 1.4 + - - -
189X VAL* 5.6 2.8 - - - +
209X LEU* 2.8 18.6 + - - +
210X LEU 3.2 12.6 + - - -
211X SER 5.0 0.7 - - - -
212X LEU* 1.3 87.5 + - - +
214X VAL* 1.3 82.1 + - - +
215X LYS* 3.3 3.4 - - - +
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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