Contacts of the helix formed by residues 238 - 252 (chain C) in PDB entry 1SOZ
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 PHE 238 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143C ILE* 4.2 21.1 - - + -
144C ASN 3.3 29.4 - - - -
145C ALA* 4.0 11.0 - - + -
147C ARG 3.9 15.5 - - - -
149C PRO* 4.2 14.4 - - + -
212C LEU* 3.2 44.5 - - + +
213C MET* 2.9 30.6 + - + +
214C GLY* 4.3 1.3 - - - -
236C ILE 3.3 2.5 + - - -
237C PRO* 1.3 70.8 - - + +
239C GLN* 1.3 94.4 + - - +
241C ALA* 3.6 10.8 - - - +
242C THR* 3.2 28.3 + - - -
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Residues in contact with GLN 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145C ALA* 3.3 27.2 - - - +
147C ARG 4.6 3.4 + - - +
149C PRO* 5.4 2.4 - - - +
237C PRO* 2.8 8.0 + - + +
238C PHE* 1.3 120.9 - - - +
240C LEU* 1.3 65.2 + - - +
242C THR* 3.2 6.1 + - - -
243C LYS* 3.1 22.4 + - - +
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Residues in contact with LEU 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125C THR* 3.6 31.9 - - + -
127C LEU* 4.5 0.9 - - + -
187C GLN* 5.2 14.8 - - + -
188C ASN* 5.3 8.7 - - - +
236C ILE* 3.6 22.0 - - + -
237C PRO* 3.0 19.6 + - + +
239C GLN* 1.3 74.9 - - - +
241C ALA* 1.3 66.9 + - - +
242C THR 3.0 0.2 + - - -
243C LYS* 3.1 22.1 + - - +
244C ILE* 3.0 41.1 + - + +
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Residues in contact with ALA 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C MET* 5.7 0.4 - - + -
92C ILE* 3.7 14.4 - - + +
127C LEU* 3.5 21.4 - - + +
212C LEU* 5.5 1.3 - - + -
215C ILE* 3.9 27.8 - - + -
236C ILE* 3.9 5.4 - - + +
237C PRO 3.0 12.4 + - - +
238C PHE* 3.6 13.9 - - + +
239C GLN 3.2 0.2 - - - -
240C LEU* 1.3 78.6 - - - +
242C THR* 1.3 56.6 + - - +
245C MET* 3.1 26.0 + - - +
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Residues in contact with THR 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C MET* 4.2 16.2 - - - +
92C ILE* 5.2 1.3 - - - -
143C ILE* 4.6 8.5 - - - +
238C PHE* 3.2 18.2 + - - -
239C GLN* 3.2 7.6 + - - -
240C LEU 3.1 0.6 - - - -
241C ALA* 1.3 76.6 - - - +
243C LYS* 1.3 66.7 + - - +
245C MET* 3.6 8.0 - - + +
246C ASP* 3.1 40.8 + - - +
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Residues in contact with LYS 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239C GLN 3.1 13.3 + - - +
240C LEU* 3.7 25.4 - - - +
242C THR* 1.3 78.6 - - - +
244C ILE* 1.3 68.3 + - + +
246C ASP* 4.1 4.7 - - - +
247C LYS* 3.2 41.9 + - + +
320C ASP* 5.1 8.3 + - - -
324C GLU* 3.4 25.5 + - - +
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Residues in contact with ILE 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C ASP* 4.2 2.0 - - + +
125C THR* 3.9 24.9 - - + +
127C LEU* 3.6 20.6 - - + -
240C LEU* 3.0 43.7 + - + +
243C LYS* 1.3 79.8 - - + +
245C MET* 1.3 65.5 + - - +
247C LYS* 3.7 10.2 - - + +
248C LEU* 2.9 41.6 + - + +
254C VAL* 4.1 18.4 - - + -
256C ARG* 4.0 15.0 - - - +
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Residues in contact with MET 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C MET* 3.4 44.4 - - + -
86C ASP* 4.4 12.6 - - - +
88C ARG* 4.9 1.8 - - - +
90C TYR* 4.5 7.9 - - + -
92C ILE* 3.6 14.1 - - + -
127C LEU* 5.2 0.4 - - - +
129C VAL* 3.8 24.5 - - + -
241C ALA 3.1 21.3 + - - +
242C THR* 3.2 11.4 + - + +
244C ILE* 1.3 75.3 - - - +
246C ASP* 1.3 66.1 + - - +
248C LEU* 2.8 24.8 + - - +
249C ILE* 2.8 38.4 + - + +
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Residues in contact with ASP 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C ARG* 5.2 4.0 + - - -
242C THR* 3.1 31.7 + - - +
243C LYS* 4.1 4.9 - - - +
245C MET* 1.3 94.3 - - - +
247C LYS* 1.3 56.4 - - + +
249C ILE* 3.5 11.1 + - - +
250C ARG* 3.1 29.7 + - - +
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Residues in contact with LYS 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243C LYS* 3.2 39.4 + - + +
244C ILE* 3.7 13.0 - - + +
245C MET 3.0 0.8 - - - -
246C ASP* 1.3 74.9 - - + +
248C LEU* 1.3 66.8 + - - +
250C ARG* 3.2 24.4 + - - +
251C ASP* 3.0 26.9 + - - +
253C ARG 3.2 13.6 - - - +
254C VAL* 4.7 22.4 - - + -
255C ILE* 4.4 17.4 + - - +
324C GLU* 3.3 37.6 + - - -
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Residues in contact with LEU 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C VAL* 4.0 6.8 - - - +
120C GLY* 3.7 9.4 - - - +
121C SER* 3.6 37.2 - - - +
122C ASP 4.4 0.7 - - - +
127C LEU* 4.5 0.9 - - + +
128C ALA* 4.2 5.2 - - - +
129C VAL* 3.5 28.7 - - + +
244C ILE* 2.9 33.3 + - + +
245C MET 2.8 7.0 + - - +
247C LYS* 1.3 77.7 - - - +
249C ILE* 1.3 58.3 + - - +
252C GLY* 3.1 29.8 + - - -
253C ARG* 3.3 32.5 - - - +
254C VAL* 3.5 14.6 - - + +
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Residues in contact with ILE 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C ARG* 4.0 17.0 - - - +
90C TYR* 3.5 60.6 - - + +
119C VAL* 4.3 7.4 - - + +
129C VAL* 4.3 9.4 - - + -
245C MET* 2.8 38.1 + - + +
246C ASP* 3.8 10.3 - - - +
247C LYS 3.2 0.2 - - - -
248C LEU* 1.3 78.8 - - - +
250C ARG* 1.3 62.1 + - + +
252C GLY* 4.3 2.1 + - - -
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Residues in contact with ARG 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246C ASP 3.1 17.1 + - - +
247C LYS* 3.2 24.8 + - - +
249C ILE* 1.3 82.8 - - + +
251C ASP* 1.3 104.0 + - - +
252C GLY 3.2 4.0 + - - -
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Residues in contact with ASP 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247C LYS* 3.0 11.3 + - - +
250C ARG* 1.3 117.7 + - - +
252C GLY* 1.3 52.8 + - - +
253C ARG* 2.6 44.9 + - - +
255C ILE* 3.1 43.8 + - + +
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Residues in contact with GLY 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C VAL* 3.5 19.2 - - - +
120C GLY* 3.8 7.0 - - - -
248C LEU 3.1 17.6 + - - -
249C ILE 4.3 1.7 + - - -
250C ARG 3.2 5.7 + - - -
251C ASP* 1.3 73.9 - - - +
253C ARG* 1.3 63.8 + - - +
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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