Contacts of the helix formed by residues 221 - 235 (chain G) in PDB entry 3STJ
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 SER 221 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129G ILE* 3.7 13.3 - - - +
130G ALA 2.8 20.3 + - - -
132G SER* 3.3 12.5 + - - -
198G LEU* 3.4 30.5 + - - +
199G ILE* 3.0 17.1 + - - -
200G GLY* 4.0 3.1 - - - -
219G ILE 3.6 1.0 + - - -
220G PRO* 1.4 67.6 - - - +
222G ASN* 1.3 56.7 + - - +
224G ALA* 3.6 7.7 - - - +
225G ARG* 2.7 38.4 + - - +
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Residues in contact with ASN 222 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130G ALA 3.4 2.4 + - - -
131G ASP* 2.7 24.2 + - - +
132G SER* 3.1 32.2 + - - +
133G ASP* 3.2 22.5 - - - +
220G PRO* 5.4 0.2 - - + -
221G SER* 1.3 75.2 + - - +
223G MET* 1.4 55.7 + - - +
225G ARG* 3.2 36.7 + - - +
226G THR* 2.8 37.7 + - - +
304G ARG* 6.0 1.8 - - - +
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Residues in contact with MET 223 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111G SER* 5.0 7.4 - - - -
172G LEU* 5.1 7.2 - - - +
174G ASN* 3.6 39.5 - - + +
219G ILE* 4.0 17.7 - - + -
220G PRO* 3.1 21.9 + - + +
222G ASN* 1.4 77.3 - - - +
224G ALA* 1.4 61.9 + - - +
226G THR* 3.9 1.2 - - - -
227G LEU* 3.1 41.0 + - + +
303G SER* 3.9 26.5 - - - +
304G ARG* 4.6 5.8 - - + +
307G THR* 3.7 29.8 - - + +
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Residues in contact with ALA 224 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78G LEU* 3.9 25.3 - - + +
113G ILE* 3.7 24.0 - - + -
198G LEU* 5.5 1.8 - - + -
201G ILE* 4.0 15.0 - - + -
219G ILE* 4.3 2.2 - - + +
220G PRO 2.9 15.5 + - - +
221G SER* 3.7 8.7 - - - +
223G MET* 1.4 76.4 - - - +
225G ARG* 1.4 55.7 + - - +
227G LEU* 3.5 1.4 + - - +
228G ALA* 2.9 30.8 + - - +
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Residues in contact with ARG 225 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70G ILE* 4.8 6.9 - - + +
78G LEU* 4.8 0.4 - - - +
129G ILE* 3.6 41.6 + - + +
130G ALA 3.4 18.2 + - - -
131G ASP* 4.4 3.0 - - - +
221G SER 2.7 20.2 + - - +
222G ASN* 3.2 46.9 + - - +
224G ALA* 1.4 69.9 - - - +
226G THR* 1.3 63.7 + - - +
228G ALA* 3.3 8.2 + - - +
229G GLN* 3.0 35.8 + - + +
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Residues in contact with THR 226 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222G ASN* 2.8 17.7 + - - +
223G MET 3.9 3.4 - - - -
225G ARG* 1.3 80.6 + - - +
227G LEU* 1.3 62.6 + - - +
229G GLN* 3.3 8.9 + - - +
230G GLN* 3.1 29.3 + - - +
307G THR* 3.4 34.2 - - + +
308G THR* 4.8 5.6 - - + -
309G GLU* 5.3 1.6 - - + +
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Residues in contact with LEU 227 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108G ASP* 3.7 6.5 - - + +
111G SER* 3.3 29.8 - - - +
113G ILE* 3.8 23.6 - - + -
223G MET* 3.1 37.4 + - + +
224G ALA 3.9 3.1 - - - +
226G THR* 1.3 74.7 - - - +
228G ALA* 1.4 62.1 + - - +
230G GLN* 3.3 10.1 + - - +
231G LEU* 3.1 28.6 + - + +
237G ILE* 3.8 15.8 - - + +
239G ARG* 3.5 28.3 - - - +
307G THR* 4.0 21.1 - - + +
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Residues in contact with ALA 228 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70G ILE* 4.1 23.3 - - + -
78G LEU* 4.2 13.7 - - + -
113G ILE* 4.8 0.8 - - - +
115G LEU* 4.2 12.4 - - + +
224G ALA 2.9 19.2 + - - +
225G ARG 3.4 5.8 - - - +
227G LEU* 1.4 76.7 - - - +
229G GLN* 1.4 50.0 + - - +
231G LEU* 3.1 13.3 + - - +
232G ILE* 2.9 39.9 + - + +
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Residues in contact with GLN 229 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232D ILE* 6.1 1.2 - - - +
225G ARG* 3.0 20.7 + - + +
226G THR* 3.5 11.4 - - - +
228G ALA* 1.4 73.3 - - - +
230G GLN* 1.3 57.4 + - + +
232G ILE* 3.2 25.9 + - - +
233G ASP* 2.9 66.3 + - - +
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Residues in contact with GLN 230 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226G THR* 3.1 24.6 + - + +
227G LEU* 3.3 13.7 + - - +
229G GLN* 1.3 75.0 - - + +
231G LEU* 1.3 57.4 + - - +
233G ASP* 4.6 1.8 - - - -
234G PHE* 2.8 35.3 + - + +
236G GLU 3.0 19.0 - - - +
237G ILE* 3.5 14.6 - - + +
238G LYS 2.8 42.6 + - - +
239G ARG* 5.3 0.8 - - - +
307G THR 3.0 24.6 + - - +
309G GLU* 4.1 29.8 + - + +
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Residues in contact with LEU 231 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105G ILE* 3.4 11.8 - - + +
106G GLY* 3.6 26.5 - - - +
107G SER* 3.6 31.4 - - - +
108G ASP* 4.9 0.4 - - + +
113G ILE* 4.3 18.2 - - + +
115G LEU* 3.9 24.7 - - + +
227G LEU 3.1 18.8 + - - +
228G ALA* 3.1 8.0 + - - +
230G GLN* 1.3 75.7 - - - +
232G ILE* 1.4 61.7 + - - +
235G GLY* 3.0 25.3 + - - +
236G GLU* 3.8 27.8 - - - +
237G ILE* 4.1 10.1 - - + -
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Residues in contact with ILE 232 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233D ASP* 5.5 8.1 - - - +
70G ILE* 6.1 1.3 - - + -
71G ASN* 6.0 1.8 - - - +
74G LYS* 5.5 6.1 - - - +
76G TYR* 3.9 39.8 + - + +
105G ILE* 4.6 3.7 - - - +
115G LEU* 3.4 22.9 - - + -
228G ALA* 2.9 22.8 + - + +
229G GLN* 3.2 33.1 + - - +
231G LEU* 1.4 77.0 - - - +
233G ASP* 1.3 74.8 + - - +
235G GLY 4.8 0.3 + - - -
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Residues in contact with ASP 233 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D LYS* 5.5 4.9 + - - -
233D ASP* 5.0 6.8 - - - +
229G GLN* 2.9 42.2 + - - +
230G GLN* 4.1 1.5 + - - +
232G ILE* 1.3 87.0 - - - +
234G PHE* 1.4 90.7 + - + +
309G GLU* 5.0 4.9 - - - +
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Residues in contact with PHE 234 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230G GLN* 2.8 30.0 + - + +
233G ASP* 1.4 98.9 - - + +
235G GLY* 1.3 58.6 + - - +
236G GLU* 3.1 26.7 + - + +
238G LYS* 3.9 30.5 - - + -
309G GLU* 3.9 36.1 - - + -
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Residues in contact with GLY 235 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105G ILE* 3.8 21.3 - - - +
106G GLY* 3.9 8.8 - - - -
107G SER 5.0 0.3 + - - -
230G GLN 3.7 0.4 + - - -
231G LEU* 3.0 27.4 + - - -
232G ILE 4.7 0.6 + - - -
233G ASP 3.9 0.2 - - - -
234G PHE* 1.3 75.4 - - - +
236G GLU* 1.3 59.2 + - - +
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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