Contacts of the helix formed by residues 221 - 235 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129H ILE* 3.7 14.0 - - - +
130H ALA 2.9 20.1 + - - -
132H SER* 3.3 12.5 + - - -
198H LEU* 3.4 30.4 + - - +
199H ILE* 3.0 16.8 + - - -
200H GLY* 4.0 3.1 - - - -
219H ILE 3.5 1.0 + - - -
220H PRO* 1.4 69.8 - - - +
222H ASN* 1.4 53.6 + - - +
224H ALA* 3.6 7.5 - - - +
225H ARG* 2.7 38.6 + - - +
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Residues in contact with ASN 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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130H ALA 3.5 2.0 + - - -
131H ASP* 2.7 23.8 - - - +
132H SER* 3.2 33.7 + - - +
133H ASP* 3.3 20.0 - - - +
220H PRO* 5.4 0.2 - - + -
221H SER* 1.4 74.0 + - - +
223H MET* 1.3 59.4 + - - +
225H ARG* 3.2 37.0 + - - +
226H THR* 2.8 34.4 + - - +
304H ARG* 6.1 1.3 - - - +
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Residues in contact with MET 223 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111H SER* 5.0 8.3 - - - +
172H LEU* 5.2 7.6 - - - +
174H ASN* 3.6 38.6 - - + +
219H ILE* 4.0 18.4 - - + -
220H PRO* 3.1 21.5 + - + +
222H ASN* 1.3 77.5 - - - +
224H ALA* 1.3 61.3 + - - +
226H THR* 3.9 1.2 - - - -
227H LEU* 3.1 40.6 + - + +
303H SER* 3.9 27.1 - - - +
304H ARG* 4.7 5.8 - - + +
307H THR* 3.7 29.6 - - + +
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Residues in contact with ALA 224 (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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78H LEU* 3.8 13.0 - - + +
113H ILE* 3.7 23.3 - - + +
198H LEU* 5.5 0.7 - - + -
201H ILE* 3.7 30.1 - - + -
219H ILE* 4.2 3.5 - - + +
220H PRO 2.9 15.6 + - - +
221H SER* 3.7 6.3 - - - +
223H MET* 1.3 76.7 - - - +
225H ARG* 1.4 55.3 + - - +
227H LEU* 3.9 1.2 - - - +
228H ALA* 2.9 31.2 + - - +
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Residues in contact with ARG 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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70H ILE* 4.8 7.6 - - + -
78H LEU* 4.8 0.4 - - - +
129H ILE* 3.5 39.5 + - + +
130H ALA 3.4 17.8 + - - -
131H ASP* 4.4 3.2 - - - +
221H SER 2.7 20.6 + - - +
222H ASN* 3.2 47.9 + - - +
224H ALA* 1.4 69.0 - - - +
226H THR* 1.4 63.3 + - - +
228H ALA* 3.3 7.6 + - - +
229H GLN* 2.9 34.4 + - + +
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Residues in contact with THR 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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222H ASN* 2.8 20.2 + - - +
223H MET 3.9 3.4 - - - -
225H ARG* 1.4 79.1 + - - +
227H LEU* 1.3 62.6 + - - +
229H GLN* 3.2 9.7 + - - +
230H GLN* 3.1 33.6 + - + +
307H THR* 3.4 33.6 - - + +
308H THR* 5.0 4.3 - - + -
309H GLU* 5.4 1.3 - - + +
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Residues in contact with LEU 227 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108H ASP* 3.8 5.6 - - + +
111H SER* 3.3 29.2 - - - +
113H ILE* 3.8 25.4 - - + -
223H MET* 3.1 35.3 + - + +
224H ALA 3.9 2.9 - - - +
226H THR* 1.3 73.4 - - - +
228H ALA* 1.3 62.1 + - - +
230H GLN* 3.2 14.5 + - - +
231H LEU* 3.1 28.0 + - + +
237H ILE* 3.8 14.7 - - + +
239H ARG* 3.6 27.6 - - - +
307H THR* 4.1 20.2 - - + +
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Residues in contact with ALA 228 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70H ILE* 4.2 18.6 - - + -
78H LEU* 4.2 8.7 - - + -
113H ILE* 4.8 0.8 - - - +
115H LEU* 4.1 22.1 - - + +
224H ALA 2.9 18.8 + - - +
225H ARG 3.5 4.7 - - - +
226H THR 3.3 0.2 - - - -
227H LEU* 1.3 75.2 - - - +
229H GLN* 1.4 50.9 + - - +
231H LEU* 3.1 14.4 + - - +
232H ILE* 2.9 39.2 + - + +
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Residues in contact with GLN 229 (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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225H ARG* 2.9 22.1 + - + +
226H THR* 3.2 11.2 + - - +
228H ALA* 1.4 70.2 - - - +
230H GLN* 1.3 62.3 + - + +
232H ILE* 3.2 26.4 + - - +
233H ASP* 2.9 66.8 + - - +
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Residues in contact with GLN 230 (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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226H THR* 3.1 23.5 + - + +
227H LEU* 3.2 12.4 + - - +
229H GLN* 1.3 74.0 - - + +
231H LEU* 1.4 52.8 + - - +
233H ASP* 4.5 0.7 - - - -
234H PHE* 2.8 57.6 + - + -
236H GLU 3.2 13.3 - - - +
237H ILE* 3.6 14.5 - - - +
238H LYS 3.0 36.5 + - - +
239H ARG* 5.4 0.6 - - - +
307H THR 3.0 25.1 + - - +
309H GLU* 4.0 21.0 + - + +
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Residues in contact with LEU 231 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105H ILE* 3.5 11.4 - - + +
106H GLY* 3.6 27.6 - - - +
107H SER* 3.6 30.1 - - - +
108H ASP* 4.9 0.4 - - + +
113H ILE* 4.2 18.2 - - + +
115H LEU* 3.9 24.2 - - + +
227H LEU 3.1 17.9 + - - +
228H ALA* 3.1 8.7 + - - +
230H GLN* 1.4 74.2 - - - +
232H ILE* 1.4 60.1 + - - +
235H GLY* 2.9 26.4 + - - +
236H GLU* 3.8 28.7 - - - +
237H ILE* 4.0 10.1 - - + +
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Residues in contact with ILE 232 (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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70H ILE* 6.2 1.1 - - + -
71H ASN* 6.2 0.9 - - - +
74H LYS* 5.5 6.1 - - - +
76H TYR* 3.9 39.7 + - + +
105H ILE* 4.6 4.7 - - - +
115H LEU* 3.5 22.9 - - + -
228H ALA* 2.9 22.9 + - + +
229H GLN* 3.2 37.7 + - - +
231H LEU* 1.4 77.5 - - - +
233H ASP* 1.4 72.1 + - - +
235H GLY 4.7 0.7 + - - -
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Residues in contact with ASP 233 (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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229H GLN* 2.9 41.3 + - - +
230H GLN* 4.0 2.8 - - - +
232H ILE* 1.4 84.7 - - - +
234H PHE* 1.4 86.3 + - + +
309H GLU* 5.3 2.4 - - - +
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Residues in contact with PHE 234 (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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230H GLN* 2.8 41.2 + - + +
233H ASP* 1.4 100.1 - - + +
235H GLY* 1.3 57.4 + - - +
236H GLU* 3.1 31.8 + - + +
238H LYS* 3.6 46.0 - - + -
309H GLU* 3.9 28.3 - - - -
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Residues in contact with GLY 235 (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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105H ILE* 3.9 21.0 - - - +
106H GLY* 4.0 7.1 - - - -
230H GLN 3.7 0.4 + - - -
231H LEU* 2.9 27.4 + - - -
232H ILE 4.7 0.6 + - - -
233H ASP 4.0 0.2 - - - -
234H PHE* 1.3 75.9 - - - +
236H GLU* 1.3 59.1 + - - +
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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