Contacts of the helix formed by residues 221 - 235 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129L ILE* 3.8 11.9 - - - +
130L ALA 2.8 23.4 + - - -
132L SER* 3.4 6.4 - - - -
198L LEU* 3.1 31.0 + - - +
199L ILE* 2.8 22.4 + - - -
200L GLY* 3.9 2.7 - - - -
219L ILE 3.6 1.4 + - - -
220L PRO* 1.4 70.5 - - - +
222L ASN* 1.4 54.8 + - - +
224L ALA* 3.5 9.3 - - - +
225L ARG* 2.7 37.5 + - - +
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Residues in contact with ASN 222 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130L ALA 3.4 2.6 + - - -
131L ASP* 2.8 24.0 + - - +
132L SER* 3.1 30.9 + - - +
133L ASP* 3.2 21.6 - - - +
220L PRO* 5.5 0.4 - - + -
221L SER* 1.4 75.6 + - - +
223L MET* 1.3 58.7 - - - +
225L ARG* 3.2 36.0 + - - +
226L THR* 2.8 34.7 + - - +
304L ARG* 5.9 2.5 - - - +
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Residues in contact with MET 223 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111L SER* 5.0 7.6 - - - -
172L LEU* 5.2 7.6 - - - +
174L ASN* 3.6 39.0 - - + +
219L ILE* 4.0 17.3 - - + -
220L PRO* 3.1 20.9 + - + +
222L ASN* 1.3 78.1 - - - +
224L ALA* 1.3 62.7 + - - +
226L THR* 3.8 1.2 - - - -
227L LEU* 3.2 40.4 + - + +
303L SER* 3.6 27.8 - - - +
304L ARG* 4.5 5.6 - - + +
307L THR* 3.7 30.5 - - + +
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Residues in contact with ALA 224 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78L LEU* 3.9 24.8 - - + +
113L ILE* 3.7 19.0 - - + +
198L LEU* 5.4 2.2 - - + -
201L ILE* 4.2 15.9 - - + -
219L ILE* 4.2 2.7 - - + +
220L PRO 2.9 16.6 + - - +
221L SER* 3.5 11.2 - - - +
223L MET* 1.3 77.2 - - - +
225L ARG* 1.4 55.1 + - - +
227L LEU* 4.0 1.7 - - - +
228L ALA* 3.0 29.5 + - - +
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Residues in contact with ARG 225 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70L ILE* 4.8 6.7 - - + -
78L LEU* 4.8 0.2 - - - +
129L ILE* 3.6 41.2 + - + +
130L ALA 3.4 17.4 + - - -
131L ASP* 4.5 3.0 - - - +
221L SER 2.7 22.1 + - - +
222L ASN* 3.2 46.6 + - - +
224L ALA* 1.4 69.4 - - - +
226L THR* 1.3 62.9 + - - +
228L ALA* 3.2 8.6 + - - +
229L GLN* 2.9 33.5 + - + +
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Residues in contact with THR 226 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222L ASN* 2.8 17.8 + - - +
223L MET 3.8 3.8 - - - -
224L ALA 3.5 0.2 - - - -
225L ARG* 1.3 81.4 + - - +
227L LEU* 1.3 60.8 + - - +
229L GLN* 3.2 10.5 + - - +
230L GLN* 3.1 31.4 + - - +
307L THR* 3.4 33.2 - - + +
308L THR* 4.9 5.4 - - + -
309L GLU* 5.3 2.0 - - + +
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Residues in contact with LEU 227 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108L ASP* 3.8 1.6 - - + +
111L SER* 3.2 29.8 - - - +
113L ILE* 3.8 26.2 - - + -
223L MET* 3.2 29.5 + - + +
224L ALA 4.0 2.9 - - - +
226L THR* 1.3 70.4 - - - +
228L ALA* 1.4 66.1 + - - +
230L GLN* 3.0 27.9 + - - +
231L LEU* 3.0 18.5 + - - +
237L ILE* 3.7 18.8 - - + -
239L ARG* 3.6 27.1 - - - +
307L THR* 4.1 15.3 - - + +
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Residues in contact with ALA 228 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70L ILE* 3.9 25.4 - - + -
78L LEU* 4.2 13.5 - - + -
113L ILE* 4.7 1.0 - - - +
115L LEU* 4.1 13.9 - - + +
224L ALA 3.0 20.0 + - - +
225L ARG 3.2 5.6 + - - +
227L LEU* 1.4 75.0 - - - +
229L GLN* 1.4 55.9 + - - +
231L LEU* 3.5 9.4 + - - +
232L ILE* 3.1 34.8 + - + +
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Residues in contact with GLN 229 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225L ARG* 2.9 17.5 + - + +
226L THR* 3.4 12.3 - - - +
227L LEU 3.2 0.2 - - - -
228L ALA* 1.4 73.8 - - - +
230L GLN* 1.4 64.6 + - - +
232L ILE* 3.1 25.2 + - - +
233L ASP* 3.0 64.9 + - - +
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Residues in contact with GLN 230 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226L THR* 3.1 27.3 + - - +
227L LEU* 3.0 15.8 + - - +
229L GLN* 1.4 74.8 - - - +
231L LEU* 1.3 56.7 + - - +
234L PHE* 3.0 42.8 + - + -
236L GLU 3.0 15.2 - - - +
237L ILE* 3.8 20.3 - - + +
238L LYS* 2.9 49.6 + - + +
306L ALA 4.9 1.4 + - - -
307L THR 3.5 23.9 + - - +
309L GLU* 4.7 14.5 + - + +
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Residues in contact with LEU 231 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105L ILE* 3.5 11.7 - - + +
106L GLY* 3.6 24.2 - - - +
107L SER* 3.7 28.0 - - - +
108L ASP 4.8 0.4 - - - +
113L ILE* 4.2 18.8 - - + +
115L LEU* 4.0 24.7 - - + +
227L LEU 3.0 19.4 + - - +
228L ALA* 3.9 4.3 - - - +
230L GLN* 1.3 75.9 - - - +
232L ILE* 1.4 61.1 + - - +
235L GLY* 3.0 26.4 + - - +
236L GLU* 3.7 30.3 - - - +
237L ILE* 3.8 14.1 - - + +
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Residues in contact with ILE 232 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70L ILE* 6.1 1.1 - - + -
71L ASN* 6.0 1.8 - - - +
74L LYS* 5.5 5.8 - - - +
76L TYR* 3.8 41.3 + - + +
105L ILE* 4.6 4.6 - - - +
115L LEU* 3.4 22.4 - - + -
228L ALA* 3.1 18.3 + - + +
229L GLN* 3.1 31.8 + - - +
231L LEU* 1.4 75.3 - - - +
233L ASP* 1.3 77.1 + - - +
235L GLY 4.7 0.7 + - - -
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Residues in contact with ASP 233 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229L GLN* 3.0 41.8 + - - +
232L ILE* 1.3 87.1 - - - +
234L PHE* 1.4 90.8 + - + +
309L GLU* 5.2 2.9 - - - +
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Residues in contact with PHE 234 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230L GLN* 3.0 29.7 + - + -
233L ASP* 1.4 103.5 - - + +
235L GLY* 1.3 59.8 + - - +
236L GLU* 3.1 34.2 + - + +
238L LYS* 3.6 46.9 - - + -
309L GLU* 3.9 28.0 - - - -
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Residues in contact with GLY 235 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105L ILE* 3.8 21.3 - - - +
106L GLY* 3.9 8.8 - - - -
107L SER 4.9 0.2 + - - -
231L LEU* 3.0 26.8 + - - -
232L ILE 4.7 0.6 + - - -
233L ASP 3.9 0.6 - - - -
234L PHE* 1.3 76.5 - - - +
236L GLU* 1.3 57.9 + - - +
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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
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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