Contacts of the helix formed by residues 221 - 235 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129F ILE* 3.7 14.5 - - - +
130F ALA 2.8 20.1 + - - -
132F SER* 3.3 12.6 + - - -
198F LEU* 3.4 30.4 + - - +
199F ILE* 2.9 17.4 + - - -
200F GLY* 4.0 3.1 - - - -
219F ILE 3.6 0.4 + - - -
220F PRO* 1.4 66.8 - - - +
222F ASN* 1.3 56.9 + - - +
224F ALA* 3.7 7.4 - - - +
225F ARG* 2.7 37.9 + - - +
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Residues in contact with ASN 222 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130F ALA 3.4 2.8 + - - -
131F ASP* 2.7 23.5 + - - +
132F SER* 3.1 29.8 + - - +
133F ASP* 3.2 21.8 - - - +
220F PRO* 5.5 0.2 - - + -
221F SER* 1.3 74.5 + - - +
223F MET* 1.3 59.0 + - - +
225F ARG* 3.2 37.5 + - - +
226F THR* 2.8 33.5 + - - +
304F ARG* 6.1 1.6 - - - +
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Residues in contact with MET 223 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111F SER* 5.0 7.6 - - - -
132F SER* 4.8 0.2 + - - -
172F LEU* 5.1 6.5 - - - +
174F ASN* 3.6 39.0 - - + +
219F ILE* 4.0 17.5 - - + -
220F PRO* 3.1 20.8 + - + +
222F ASN* 1.3 78.4 - - - +
224F ALA* 1.4 60.8 + - - +
226F THR* 3.8 1.4 - - - -
227F LEU* 3.1 41.8 + - + +
303F SER* 4.0 28.5 - - - +
304F ARG* 4.6 5.8 - - + +
307F THR* 3.7 29.8 - - + +
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Residues in contact with ALA 224 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78F LEU* 3.9 24.9 - - + +
113F ILE* 3.7 23.8 - - + -
198F LEU* 5.5 1.6 - - + -
201F ILE* 4.2 14.6 - - + -
219F ILE* 4.2 2.4 - - + +
220F PRO 2.9 15.7 + - - +
221F SER* 3.7 9.2 - - - +
223F MET* 1.4 75.4 - - - +
225F ARG* 1.4 55.4 + - - +
227F LEU* 3.5 1.7 + - - +
228F ALA* 2.9 30.5 + - - +
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Residues in contact with ARG 225 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70F ILE* 4.8 8.2 - - + +
78F LEU* 4.8 0.4 - - - +
129F ILE* 3.6 39.8 + - + +
130F ALA 3.4 17.8 + - - -
131F ASP* 4.4 3.0 - - - +
221F SER 2.7 21.5 + - - +
222F ASN* 3.2 46.6 + - - +
224F ALA* 1.4 68.2 - - - +
226F THR* 1.3 63.1 + - - +
228F ALA* 3.3 7.4 + - - +
229F GLN* 2.9 36.5 + - + +
73J SER* 5.6 6.5 - - - -
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Residues in contact with THR 226 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222F ASN* 2.8 21.7 + - - +
223F MET 3.8 3.6 - - - -
225F ARG* 1.3 80.0 + - - +
227F LEU* 1.3 62.0 + - - +
229F GLN* 3.2 8.6 + - - +
230F GLN* 3.1 30.5 + - - +
307F THR* 3.3 33.0 - - + +
308F THR* 4.8 5.4 - - + -
309F GLU* 5.3 1.3 - - + +
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Residues in contact with LEU 227 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108F ASP* 3.7 7.9 - - + +
111F SER* 3.3 29.8 - - - +
113F ILE* 3.8 22.4 - - + -
223F MET* 3.1 37.3 + - + +
224F ALA 3.9 3.4 - - - +
226F THR* 1.3 73.6 - - - +
228F ALA* 1.4 62.1 + - - +
230F GLN* 3.2 11.0 + - - +
231F LEU* 3.1 27.5 + - - +
237F ILE* 3.8 16.7 - - + +
239F ARG* 3.6 27.1 - - - +
307F THR* 4.1 19.3 - - + +
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Residues in contact with ALA 228 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70F ILE* 4.1 23.8 - - + -
78F LEU* 4.2 14.4 - - + -
113F ILE* 4.8 0.8 - - - +
115F LEU* 4.2 11.3 - - + +
224F ALA 2.9 19.2 + - - +
225F ARG 3.3 5.8 + - - +
227F LEU* 1.4 74.3 - - - +
229F GLN* 1.4 56.0 + - - +
231F LEU* 3.1 14.0 + - - +
232F ILE* 2.9 34.4 + - + +
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Residues in contact with GLN 229 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225F ARG* 2.9 21.8 + - + +
226F THR* 3.2 11.4 + - - +
228F ALA* 1.4 74.2 - - - +
230F GLN* 1.3 57.0 + - + +
232F ILE* 3.2 23.8 + - - +
233F ASP* 2.9 56.8 + - - +
74J LYS* 2.9 36.5 + - - +
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Residues in contact with GLN 230 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226F THR* 3.1 25.9 + - + +
227F LEU* 3.5 12.8 + - - +
229F GLN* 1.3 75.2 - - + +
231F LEU* 1.3 56.1 + - - +
234F PHE* 2.8 46.4 + - + -
236F GLU 3.0 20.0 - - - +
237F ILE* 3.5 14.5 - - + +
238F LYS 2.8 41.3 + - - +
239F ARG* 5.3 0.6 - - - +
307F THR 3.1 24.0 + - - +
309F GLU* 4.2 22.7 + - + +
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Residues in contact with LEU 231 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105F ILE* 3.5 11.7 - - - +
106F GLY* 3.6 25.8 - - - +
107F SER* 3.6 28.7 - - - +
113F ILE* 4.2 18.8 - - + +
115F LEU* 3.9 25.1 - - + +
227F LEU 3.1 19.0 + - - +
228F ALA* 3.1 8.4 + - - +
230F GLN* 1.3 74.5 - - - +
232F ILE* 1.4 61.3 + - - +
235F GLY* 3.0 24.8 + - - +
236F GLU* 3.8 28.0 - - - +
237F ILE* 3.9 12.8 - - + +
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Residues in contact with ILE 232 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70F ILE* 6.0 1.3 - - + -
71F ASN* 6.0 1.8 - - - +
74F LYS* 5.5 5.6 - - - +
76F TYR* 3.9 41.4 + - + +
105F ILE* 4.6 4.1 - - - +
115F LEU* 3.4 24.5 - - + -
228F ALA* 2.9 22.8 + - + +
229F GLN* 3.2 35.4 + - - +
231F LEU* 1.4 76.6 - - - +
233F ASP* 1.4 74.6 + - - +
235F GLY 4.8 0.7 + - - -
74J LYS* 5.0 2.5 - - - +
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Residues in contact with ASP 233 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229F GLN* 2.9 42.7 + - - +
232F ILE* 1.4 86.4 - - - +
234F PHE* 1.3 88.0 + - + +
309F GLU* 5.7 0.5 - - - +
74J LYS* 4.0 16.0 + - - -
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Residues in contact with PHE 234 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230F GLN* 2.8 40.9 + - + +
233F ASP* 1.3 101.3 - - + +
235F GLY* 1.3 58.2 + - - +
236F GLU* 3.0 32.3 + - + +
238F LYS* 3.7 46.2 - - + -
309F GLU* 3.9 27.1 - - - -
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Residues in contact with GLY 235 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105F ILE* 3.8 21.6 - - - +
106F GLY* 3.9 8.5 - - - -
107F SER 5.0 0.2 + - - -
230F GLN 3.7 0.2 + - - -
231F LEU* 3.0 26.0 + - - +
232F ILE 4.7 0.8 + - - -
234F PHE* 1.3 76.3 - - - +
236F GLU* 1.3 56.7 + - - +
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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