Contacts of the helix formed by residues 212 - 228 (chain H) in PDB entry 6ALG
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 212 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21H SER* 4.9 7.2 - - - +
211H ILE* 1.3 79.1 - - - +
213H PRO* 1.3 69.7 - - + +
214H GLU* 4.4 11.7 - - + +
215H GLU* 3.1 45.1 + - - +
216H ALA 3.4 6.9 + - - -
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Residues in contact with PRO 213 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18H GLN* 5.6 3.4 - - - +
21H SER 3.3 17.9 - - - +
22H THR 3.3 30.1 - - - +
23H HIS 4.2 6.5 - - - +
24H ALA* 3.6 22.6 - - + +
26H VAL* 5.3 0.5 - - - +
205H MET* 3.2 37.6 - - + +
207H THR* 3.8 13.9 - - + +
211H ILE 4.0 2.0 - - - +
212H ASP* 1.3 84.8 - - + +
214H GLU* 1.3 62.3 + - - +
215H GLU 3.2 0.2 - - - -
216H ALA 4.0 2.1 + - - +
217H ILE* 4.0 11.1 - - - +
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Residues in contact with GLU 214 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13H LEU* 6.5 0.2 - - + -
16H ILE* 3.9 35.1 - - + +
18H GLN* 5.7 7.7 + - - +
212H ASP* 3.2 12.7 - - + +
213H PRO* 1.3 80.2 - - - +
215H GLU* 1.3 58.4 + - - +
217H ILE* 4.3 4.2 + - - +
218H ARG* 3.5 41.7 + - - +
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Residues in contact with GLU 215 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211H ILE* 3.3 11.2 - - + +
212H ASP* 3.1 29.7 + - - +
214H GLU* 1.3 79.4 - - - +
216H ALA* 1.3 59.7 + - - +
217H ILE 3.2 2.0 - - - -
218H ARG* 2.9 13.0 + - + +
219H ARG* 2.8 63.8 + - + +
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Residues in contact with ALA 216 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47H LEU* 3.3 19.6 - - + +
51H MET* 4.2 7.9 - - + +
179H PRO* 5.7 1.1 - - + -
180H VAL* 4.7 4.5 - - + -
205H MET* 3.7 22.4 - - + -
207H THR* 4.7 4.9 - - + -
211H ILE* 4.1 23.0 - - + +
212H ASP 3.4 5.2 + - - +
213H PRO* 4.0 1.5 + - + -
214H GLU 3.6 0.4 - - - -
215H GLU* 1.3 74.1 - - - +
217H ILE* 1.3 64.2 + - - +
219H ARG* 3.4 11.2 + - - +
220H ALA 3.1 15.4 + - - -
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Residues in contact with ILE 217 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231G PHE* 3.6 32.8 - - + -
24H ALA* 6.1 0.4 - - + -
26H VAL* 3.7 34.5 - - + -
43H LEU* 3.9 12.3 - - + -
47H LEU* 4.5 6.5 - - + -
203H ILE* 3.8 25.6 - - + -
205H MET* 3.7 23.2 - - + +
213H PRO 4.0 12.7 + - - +
214H GLU* 4.5 4.5 - - - +
215H GLU 3.2 0.2 - - - -
216H ALA* 1.3 77.6 - - - +
218H ARG* 1.3 58.4 + - + +
219H ARG 3.1 0.2 - - - -
220H ALA* 2.8 23.1 + - - +
221H ALA 3.1 11.3 + - - -
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Residues in contact with ARG 218 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230G ALA 5.4 0.6 + - - -
231G PHE* 2.7 57.4 + - + +
232G VAL* 4.4 8.5 - - + +
13H LEU* 4.0 25.2 - - - +
214H GLU* 3.5 36.5 + - - +
215H GLU* 2.9 18.1 + - + +
217H ILE* 1.3 76.9 - - + +
219H ARG* 1.3 51.4 + - - +
221H ALA* 4.8 1.6 - - - +
222H THR* 2.3 30.5 + - - -
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Residues in contact with ARG 219 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51H MET* 4.2 20.2 - - + -
52H PRO* 5.8 7.0 - - + -
211H ILE* 3.4 28.6 - - - +
215H GLU* 2.8 54.7 + - + +
216H ALA* 3.9 7.2 - - - +
217H ILE 3.1 0.2 - - - -
218H ARG* 1.3 77.5 - - - +
220H ALA* 1.3 64.0 + - - +
221H ALA 3.4 0.4 - - - -
222H THR* 3.5 10.1 - - + +
223H ILE* 3.1 30.3 + - + +
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Residues in contact with ALA 220 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43H LEU* 4.3 18.4 - - + +
46H ILE* 3.9 19.9 - - + +
47H LEU* 3.7 25.6 - - + -
51H MET* 4.9 1.8 - - - -
216H ALA 3.1 13.1 + - - +
217H ILE* 2.8 14.8 + - - +
219H ARG* 1.3 75.4 - - - +
221H ALA* 1.3 63.3 + - - +
223H ILE* 3.5 4.3 + - - +
224H LEU* 3.2 21.1 + - - +
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Residues in contact with ALA 221 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228G LEU* 3.7 24.5 - - + +
231G PHE* 3.7 30.4 - - + -
232G VAL* 3.8 22.6 - - + +
43H LEU* 5.2 2.9 - - + +
217H ILE 3.1 6.5 + - - +
218H ARG 5.1 0.9 - - - +
220H ALA* 1.3 74.3 - - - +
222H THR* 1.3 59.1 + - - +
224H LEU* 4.4 0.7 - - - -
225H ALA* 2.9 33.6 + - - +
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Residues in contact with THR 222 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232G VAL* 3.9 15.3 - - + +
218H ARG 2.3 29.4 + - - -
219H ARG* 3.4 13.5 + - + +
220H ALA 3.2 0.6 - - - -
221H ALA* 1.3 75.4 - - - +
223H ILE* 1.3 65.1 + - + +
225H ALA* 4.4 2.9 - - - +
226H GLU* 3.4 29.3 + - + +
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Residues in contact with ILE 223 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8G PHE* 4.1 23.1 - - + -
35G PHE* 3.6 33.2 - - + -
46H ILE* 4.3 7.6 - - + -
50H SER 3.8 20.6 - - - +
51H MET* 3.9 15.5 - - - -
52H PRO* 4.0 17.3 - - + -
219H ARG* 3.1 19.5 + - + +
220H ALA 3.9 4.3 - - - +
222H THR* 1.3 76.9 - - + +
224H LEU* 1.3 63.4 + - - +
226H GLU* 3.4 7.9 + - - +
227H GLN* 3.2 22.0 + - + +
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Residues in contact with LEU 224 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35G PHE* 5.2 1.6 - - + -
38G THR* 4.8 5.8 - - + -
39G LEU* 4.4 24.5 - - + -
224G LEU* 3.9 20.9 - - + -
228G LEU* 3.8 23.3 - - + -
39H LEU* 5.7 0.2 - - + -
42H ALA* 4.2 22.7 - - + +
43H LEU* 5.1 6.5 - - + -
46H ILE* 3.7 22.9 - - + -
220H ALA 3.2 14.3 + - - +
221H ALA 3.3 3.8 + - - +
223H ILE* 1.3 78.9 - - - +
225H ALA* 1.3 60.6 + - - +
227H GLN* 3.0 26.0 + - + +
228H LEU* 3.3 15.4 + - + +
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Residues in contact with ALA 225 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225G ALA* 5.6 8.9 - - + +
228G LEU* 4.3 11.8 - - + +
232G VAL* 5.1 8.7 - - + -
221H ALA 2.9 18.7 + - - +
222H THR* 4.5 3.8 - - - +
224H LEU* 1.3 77.1 - - - +
226H GLU* 1.3 63.0 + - + +
228H LEU* 3.5 15.9 + - - +
229H GLU* 3.7 17.3 + - - +
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Residues in contact with GLU 226 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10G LYS* 3.4 45.3 + - - +
222H THR* 3.4 18.6 + - + +
223H ILE* 3.4 10.6 + - - +
224H LEU 3.2 0.4 - - - -
225H ALA* 1.3 78.8 - - - +
227H GLN* 1.3 62.3 + - + +
229H GLU* 3.3 31.2 + - - +
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Residues in contact with GLN 227 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8G PHE* 3.5 23.8 - - - +
9G LEU 3.1 21.7 + - - +
10G LYS* 4.3 7.0 - - - +
11G PRO* 3.3 50.1 - - + +
31G LEU* 4.4 9.4 - - - +
32G GLU* 5.2 2.9 + - - +
35G PHE* 4.1 35.1 - - + +
39G LEU* 4.8 9.8 - - + +
223H ILE 3.2 15.5 + - - +
224H LEU* 3.0 18.4 + - + +
226H GLU* 1.3 76.5 - - - +
228H LEU* 1.3 63.0 + - + +
229H GLU 3.3 1.5 + - - -
230H ALA 4.9 0.5 + - - -
231H PHE* 4.8 1.6 - - - -
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Residues in contact with LEU 228 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39G LEU* 4.0 25.1 - - + -
43G LEU* 5.7 4.0 - - + -
221G ALA* 3.8 15.3 - - + +
224G LEU* 3.7 40.6 - - + -
225G ALA* 4.3 20.6 - - + +
228G LEU* 5.9 0.4 - - + -
224H LEU* 3.3 20.3 + - + +
225H ALA* 3.5 7.6 + - - +
226H GLU 3.2 1.0 - - - -
227H GLN* 1.3 78.5 - - - +
229H GLU* 1.3 61.0 + - - +
230H ALA 3.4 2.7 - - - -
231H PHE* 3.4 38.2 + - + +
232H VAL* 3.6 16.9 + - - +
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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
------------------------------------------------------------
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