Contacts of the helix formed by residues 221 - 235 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129I ILE* 3.7 13.8 - - - +
130I ALA 2.8 20.6 + - - -
132I SER* 3.3 12.6 + - - -
198I LEU* 3.3 30.2 + - - +
199I ILE* 3.0 17.3 + - - -
200I GLY* 4.0 3.4 - - - -
219I ILE 3.6 1.0 + - - -
220I PRO* 1.4 71.6 - - - +
222I ASN* 1.3 53.1 + - - +
224I ALA* 3.7 7.4 - - - +
225I ARG* 2.7 38.8 + - - +
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Residues in contact with ASN 222 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130I ALA 3.4 2.4 + - - -
131I ASP* 2.8 23.6 + - - +
132I SER* 3.1 33.0 + - - +
133I ASP* 3.2 20.3 - - - +
220I PRO* 5.4 0.7 - - + -
221I SER* 1.3 73.5 + - - +
223I MET* 1.3 58.4 + - - +
225I ARG* 3.2 36.6 + - - +
226I THR* 2.8 33.9 + - - +
304I ARG* 6.2 0.7 - - - +
307I THR* 5.6 0.2 - - - -
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Residues in contact with MET 223 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111I SER* 5.0 8.3 - - - -
172I LEU* 5.2 7.6 - - - +
174I ASN* 3.6 38.8 - - + +
219I ILE* 4.0 18.2 - - + -
220I PRO* 3.1 22.4 + - + +
222I ASN* 1.3 78.6 - - - +
224I ALA* 1.3 61.7 + - - +
226I THR* 3.9 1.0 - - - -
227I LEU* 3.1 41.0 + - + +
303I SER* 3.8 27.4 - - - +
304I ARG* 4.6 6.3 - - + +
307I THR* 3.7 29.4 - - + +
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Residues in contact with ALA 224 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78I LEU* 3.8 25.3 - - + +
113I ILE* 3.7 24.2 - - + +
198I LEU* 5.5 1.1 - - + -
201I ILE* 4.4 12.1 - - + -
219I ILE* 4.2 5.3 - - + +
220I PRO 3.0 15.9 + - - +
221I SER* 3.7 8.7 - - - +
223I MET* 1.3 75.6 - - - +
225I ARG* 1.4 56.9 + - - +
227I LEU* 3.9 1.4 - - - +
228I ALA* 2.9 30.7 + - - +
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Residues in contact with ARG 225 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70I ILE* 4.8 7.4 - - + +
78I LEU* 4.8 0.4 - - - +
129I ILE* 3.6 39.9 + - + +
130I ALA 3.4 17.8 + - - -
131I ASP* 4.4 3.0 - - - +
221I SER 2.7 20.9 + - - +
222I ASN* 3.2 46.5 + - - +
224I ALA* 1.4 72.4 - - - +
226I THR* 1.4 61.0 + - - +
228I ALA* 3.3 7.7 + - - +
229I GLN* 3.0 35.6 + - + +
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Residues in contact with THR 226 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222I ASN* 2.8 18.5 + - - +
223I MET 3.9 3.1 - - - -
225I ARG* 1.4 77.2 + - - +
227I LEU* 1.3 66.1 + - - +
229I GLN* 3.3 8.6 + - - +
230I GLN* 3.2 43.1 + - - +
307I THR* 3.4 24.0 - - + +
308I THR* 4.8 6.1 - - + +
309I GLU* 5.2 2.2 - - + +
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Residues in contact with LEU 227 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108I ASP* 3.7 5.6 - - + +
111I SER* 3.3 29.2 - - - +
113I ILE* 3.8 22.7 - - + -
223I MET* 3.1 37.8 + - + +
224I ALA 3.9 2.9 - - - +
226I THR* 1.3 73.5 - - - +
228I ALA* 1.4 62.7 + - - +
230I GLN* 3.2 15.8 + - - +
231I LEU* 3.0 28.2 + - - +
237I ILE* 3.7 15.3 - - + +
239I ARG* 3.5 28.5 - - - +
307I THR* 4.0 16.4 - - + +
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Residues in contact with ALA 228 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70I ILE* 4.1 23.6 - - + -
78I LEU* 4.3 13.2 - - + -
113I ILE* 4.8 0.8 - - - +
115I LEU* 4.2 12.9 - - + +
224I ALA 2.9 19.0 + - - +
225I ARG 3.4 5.4 - - - +
227I LEU* 1.4 75.7 - - - +
229I GLN* 1.4 57.0 + - - +
231I LEU* 3.1 13.6 + - - +
232I ILE* 2.9 34.7 + - + +
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Residues in contact with GLN 229 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225I ARG* 3.0 19.8 + - + +
226I THR* 3.3 11.4 + - - +
228I ALA* 1.4 71.2 - - - +
230I GLN* 1.3 66.1 + - + +
232I ILE* 3.2 25.1 + - - +
233I ASP* 3.0 61.1 + - - +
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Residues in contact with GLN 230 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226I THR* 3.2 30.4 + - - +
227I LEU* 3.2 10.9 + - - +
229I GLN* 1.3 73.9 - - + +
231I LEU* 1.3 59.2 + - - +
234I PHE* 2.9 51.7 + - + -
236I GLU 3.2 18.4 - - - +
237I ILE* 3.5 14.4 - - - +
238I LYS 2.9 40.5 + - - +
239I ARG* 5.3 0.8 - - - +
307I THR 3.3 21.5 + - - +
309I GLU* 4.3 20.7 + - + +
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Residues in contact with LEU 231 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105I ILE* 3.5 11.0 - - - +
106I GLY* 3.7 24.7 - - - +
107I SER* 3.6 30.5 - - - +
108I ASP 4.8 0.2 - - - +
113I ILE* 4.1 22.0 - - + +
115I LEU* 4.0 22.4 - - + +
227I LEU 3.0 19.8 + - - +
228I ALA* 3.1 7.6 + - - +
230I GLN* 1.3 76.4 - - - +
232I ILE* 1.4 56.9 + - - +
235I GLY* 2.9 27.2 + - - +
236I GLU* 3.8 28.3 - - - +
237I ILE* 3.9 11.9 - - + +
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Residues in contact with ILE 232 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70I ILE* 6.0 1.3 - - + -
71I ASN* 5.9 2.5 - - - +
74I LYS* 5.5 5.8 - - - +
76I TYR* 3.8 41.4 + - + +
105I ILE* 4.6 4.4 - - - +
115I LEU* 3.5 24.0 - - + -
228I ALA* 2.9 22.4 + - + +
229I GLN* 3.2 39.2 + - - +
231I LEU* 1.4 76.9 - - - +
233I ASP* 1.3 74.7 + - - +
235I GLY 4.7 0.7 + - - -
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Residues in contact with ASP 233 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229I GLN* 3.0 42.8 + - - +
232I ILE* 1.3 86.4 - - - +
234I PHE* 1.4 89.4 + - + +
309I GLU* 5.4 1.4 - - - +
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Residues in contact with PHE 234 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230I GLN* 2.9 46.1 + - + +
233I ASP* 1.4 94.9 - - + +
235I GLY* 1.3 59.1 + - - +
236I GLU* 3.0 31.6 + - + +
238I LYS* 3.6 46.4 - - + -
309I GLU* 3.9 20.6 - - - -
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Residues in contact with GLY 235 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105I ILE* 3.7 21.1 - - - +
106I GLY* 3.8 8.3 - - - -
107I SER 5.0 0.2 + - - -
230I GLN 3.7 0.4 + - - -
231I LEU* 2.9 26.7 + - - -
232I ILE 4.6 0.4 + - - -
233I ASP 3.9 0.6 - - - -
234I PHE* 1.3 75.7 - - - +
236I GLU* 1.3 58.1 + - - +
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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