Contacts of the helix formed by residues 198 - 212 (chain B) in PDB entry 3SZ9
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 PRO 198 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37B PHE* 4.3 5.8 - - + -
39B THR* 3.5 14.4 - - - +
51B VAL* 3.9 36.6 - - + -
109B ASP* 3.1 14.6 - - - +
193B VAL* 3.8 17.3 - - + +
194B ALA 3.2 7.6 - - - +
195B GLU 3.6 12.3 - - - +
197B THR* 1.3 92.3 - - - +
199B LEU* 1.3 64.6 + - + +
200B THR 3.5 0.7 - - - -
201B ALA* 3.5 6.6 + - - +
202B LEU* 3.3 25.4 + - + +
222B PRO* 4.3 5.8 - - + -
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Residues in contact with LEU 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B VAL* 3.9 21.8 - - + -
19B CYS 4.3 10.0 - - - +
20B ASN* 4.8 1.1 - - + -
39B THR* 3.8 9.4 - - + -
48B ILE* 3.7 31.2 - - + -
49B CYS* 3.7 11.9 - - - -
51B VAL* 3.7 30.7 - - + -
105B LEU* 3.9 29.2 - - + +
109B ASP* 3.4 23.3 + - + +
197B THR 3.5 1.8 - - - -
198B PRO* 1.3 76.7 - - + +
200B THR* 1.3 66.1 + - - +
202B LEU* 3.4 7.6 + - + +
203B TYR* 3.1 17.5 + - - +
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Residues in contact with THR 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B LEU* 4.0 10.2 - - + +
105B LEU* 3.7 21.1 - - + +
106B GLU* 2.8 53.2 + - + +
109B ASP* 4.9 3.0 + - + -
171B PRO* 3.8 11.8 - - - +
172B LEU* 3.4 23.5 + - + +
197B THR* 4.7 1.9 + - - -
199B LEU* 1.3 77.1 - - - +
201B ALA* 1.3 63.3 + - - +
203B TYR* 3.3 4.3 + - - +
204B VAL* 3.1 26.0 + - - +
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Residues in contact with ALA 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B ILE* 5.2 1.3 - - + -
171B PRO* 5.4 4.9 - - + +
172B LEU* 4.3 1.1 - - - +
175B GLN* 3.2 42.6 + - + +
193B VAL* 3.5 31.0 - - + -
197B THR 5.1 2.2 - - - +
198B PRO 3.5 7.5 + - - +
199B LEU 3.3 0.6 - - - -
200B THR* 1.3 77.6 + - - +
202B LEU* 1.3 60.7 + - - +
204B VAL 3.4 0.3 + - - -
205B ALA 3.1 21.3 + - - -
220B ILE* 3.4 7.2 - - + +
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Residues in contact with LEU 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B CYS* 3.9 18.4 - - + +
20B ASN* 3.8 23.6 - - - -
21B GLN 3.7 25.8 - - - +
28B TRP* 3.4 15.2 - - + -
51B VAL* 4.2 15.3 - - + -
193B VAL* 5.0 0.7 - - + -
198B PRO* 3.3 20.1 + - + +
199B LEU* 3.7 8.1 - - + +
200B THR 3.3 0.4 - - - -
201B ALA* 1.3 75.1 - - - +
203B TYR* 1.3 67.7 + - - +
205B ALA* 3.1 17.0 + - - +
206B ASN 3.3 4.0 + - - -
220B ILE* 3.8 32.3 - - + +
222B PRO* 4.2 10.1 - - + -
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Residues in contact with TYR 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B PHE* 4.1 21.8 - + + -
19B CYS* 4.2 20.9 - - + +
97B ARG* 4.4 2.3 + - - -
98B ASP* 2.5 35.1 + - + -
101B TYR* 3.8 35.8 - + + +
102B LEU* 3.8 22.4 - - + -
105B LEU* 4.6 4.5 - - + -
199B LEU 3.1 13.6 + - - +
200B THR 3.3 7.6 + - - +
202B LEU* 1.3 76.6 - - - +
204B VAL* 1.3 62.1 + - - +
206B ASN* 2.9 31.2 + - + +
207B LEU* 3.1 28.4 + - + +
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Residues in contact with VAL 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B LEU* 4.3 16.2 - - + -
95B ILE* 4.3 16.4 - - + -
102B LEU* 4.3 15.3 - - + -
129B LEU* 6.1 0.2 - - + -
172B LEU* 3.4 33.2 - - + -
175B GLN* 3.4 24.7 - - - +
179B LEU* 5.0 2.0 - - + -
200B THR 3.1 5.3 + - - +
201B ALA 3.6 2.7 - - - +
202B LEU 3.3 0.2 - - - -
203B TYR* 1.3 74.5 - - - +
205B ALA* 1.3 57.4 + - - +
207B LEU* 2.8 12.3 + - - +
208B ILE* 2.8 39.7 + - + +
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Residues in contact with ALA 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B PHE* 3.3 41.7 - - + -
28B TRP* 4.0 3.4 - - + -
201B ALA 3.1 6.5 + - - -
202B LEU* 3.2 11.7 - - - +
204B VAL* 1.3 75.0 - - - +
206B ASN* 1.3 62.0 + - - +
208B ILE* 3.2 14.5 + - + +
209B LYS 3.1 18.7 + - - -
220B ILE* 3.6 25.8 - - + +
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Residues in contact with ASN 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B PHE* 5.6 3.0 - - - +
19B CYS* 3.8 27.9 - - - -
23B PHE* 4.7 0.4 - - - -
28B TRP* 3.1 23.4 + - - +
202B LEU 3.3 2.0 + - - -
203B TYR* 2.9 24.9 + - + +
205B ALA* 1.3 78.0 - - - +
207B LEU* 1.3 59.3 + - + +
209B LYS* 3.5 17.5 + - - +
210B GLU* 3.0 26.5 + - - +
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Residues in contact with LEU 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B LEU* 3.8 14.4 - - + -
94B LEU* 3.3 20.2 - - + +
95B ILE* 3.9 35.7 - - + +
97B ARG* 3.6 15.0 - - - +
98B ASP* 3.8 5.2 - - - +
102B LEU* 4.4 4.5 - - + -
203B TYR* 3.1 37.9 + - + +
204B VAL* 2.8 18.2 + - - +
206B ASN* 1.3 72.5 - - + +
208B ILE* 1.3 52.1 + - - -
210B GLU* 3.3 23.5 + - - +
211B ALA* 2.7 31.4 + - - +
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Residues in contact with ILE 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B PHE* 4.9 2.0 - - + -
26B ASN* 4.9 7.2 - - - +
91B LEU* 3.9 22.0 - - + -
175B GLN* 5.2 2.2 - - - +
179B LEU* 3.9 20.9 - - + -
183B LEU* 5.6 1.1 - - + -
204B VAL* 2.8 24.5 + - + +
205B ALA* 3.3 17.5 - - - +
207B LEU* 1.3 69.6 - - - +
209B LYS* 1.3 66.3 + - - +
211B ALA* 3.2 9.6 + - - -
212B GLY 3.2 0.3 + - - -
213B PHE* 3.2 51.1 + - + -
218B VAL* 3.8 41.7 - - + +
220B ILE* 5.3 0.2 - - + -
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Residues in contact with LYS 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B PHE* 4.0 11.0 - - + -
26B ASN* 3.2 51.2 + - + +
27B GLU* 3.9 17.1 + - - +
28B TRP* 5.5 6.2 - - - +
205B ALA 3.1 11.9 + - - +
206B ASN* 3.6 20.7 + - - +
208B ILE* 1.3 77.2 - - - +
210B GLU* 1.3 61.7 - - - +
212B GLY* 3.1 14.2 + - - -
213B PHE 4.9 0.4 - - - -
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Residues in contact with GLU 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B ARG* 4.7 9.4 + - - +
94B LEU* 3.6 14.6 - - + +
97B ARG* 2.9 43.4 + - - -
206B ASN 3.0 14.6 + - - +
207B LEU* 3.3 18.9 + - - +
209B LYS* 1.3 75.6 - - - +
211B ALA* 1.3 63.2 + - - +
212B GLY* 3.1 2.1 + - - -
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Residues in contact with ALA 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B LEU* 3.3 16.6 - - - +
90B ARG* 3.8 21.4 - - + +
91B LEU* 3.9 27.1 - - - +
94B LEU* 3.9 2.7 - - + -
207B LEU 2.7 21.1 + - - +
208B ILE* 3.5 7.9 - - - +
209B LYS 3.2 0.2 - - - -
210B GLU* 1.3 73.7 - - - +
212B GLY* 1.3 59.2 + - - +
213B PHE* 3.9 17.7 - - + -
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Residues in contact with GLY 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B MET* 5.6 0.5 - - - +
87B LEU* 3.8 11.8 - - - +
209B LYS 3.1 9.4 + - - -
210B GLU 3.0 4.5 - - - -
211B ALA* 1.3 81.0 - - - +
213B PHE* 1.3 68.3 + - - +
214B PRO* 3.4 6.2 - - - +
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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