Contacts of the helix formed by residues 227 - 240 (chain C) in PDB entry 1SG4
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 GLN 227 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145C PHE* 3.7 26.9 - - + -
223C ARG* 2.7 39.1 + - - +
224C LEU* 2.9 1.9 + - + +
226C THR* 1.4 87.4 - - + +
228C ARG* 1.3 67.1 + - - +
229C ASP 3.3 2.7 - - - -
230C ALA* 3.1 20.1 + - + +
231C ASP* 3.0 20.5 + - - +
234C ASN* 6.0 1.6 - - - +
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Residues in contact with ARG 228 (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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84C LYS* 2.9 42.2 + - + +
87C GLN* 3.0 37.3 - - - +
88C GLU* 2.8 35.9 + - - +
91C LEU* 3.5 27.5 - - - +
224C LEU* 2.9 22.6 + - + +
225C VAL* 3.7 13.1 + - - +
226C THR 3.7 0.4 - - - -
227C GLN* 1.3 77.9 - - - +
229C ASP* 1.3 67.0 + - - +
231C ASP 3.2 1.4 + - - -
232C VAL* 3.0 19.9 + - - +
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Residues in contact with ASP 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C LYS* 4.9 15.1 + - - +
227C GLN 3.3 0.4 - - - -
228C ARG* 1.3 78.5 - - - +
230C ALA* 1.3 67.1 + - - +
232C VAL* 3.2 10.4 + - - +
233C GLN* 2.9 23.8 + - - +
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Residues in contact with ALA 230 (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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227C GLN* 3.1 28.2 + - + +
229C ASP* 1.3 79.4 - - - +
231C ASP* 1.3 55.9 + - - +
233C GLN* 3.1 20.0 + - - +
234C ASN* 2.8 41.2 + - - +
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Residues in contact with ASP 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C TRP* 2.9 25.5 + - - -
87C GLN* 2.9 13.9 - - - +
144C PRO* 4.5 6.4 - - - +
145C PHE* 3.6 23.1 + - + -
146C TRP* 2.9 26.6 + - - -
224C LEU* 4.0 8.1 - - + -
227C GLN* 3.0 11.8 + - - +
228C ARG 3.5 2.9 - - - +
230C ALA* 1.3 78.1 - - - +
232C VAL* 1.3 61.3 + - - +
234C ASN* 3.4 10.7 + - - +
235C PHE* 3.0 23.0 + - - +
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Residues in contact with VAL 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C ALA* 3.6 39.3 - - + +
83C TRP* 3.8 12.8 - - + -
84C LYS* 4.2 19.1 - - + +
87C GLN* 3.5 29.6 - - - +
228C ARG 3.0 13.0 + - - +
229C ASP* 3.2 11.6 + - - +
231C ASP* 1.3 73.3 - - - +
233C GLN* 1.3 68.7 + - - +
235C PHE* 3.2 2.8 + - - +
236C VAL* 2.9 23.5 + - + +
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Residues in contact with GLN 233 (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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229C ASP 2.9 12.4 + - - +
230C ALA* 3.1 27.0 + - - +
232C VAL* 1.3 80.5 - - - +
234C ASN* 1.3 69.5 + - - +
236C VAL* 3.2 6.2 + - - +
237C SER* 2.8 35.7 + - - +
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Residues in contact with ASN 234 (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 PHE* 6.3 1.0 - - - -
227C GLN* 6.0 2.0 - - - +
230C ALA* 2.8 29.0 + - - +
231C ASP* 3.7 11.4 + - - +
232C VAL 3.2 0.2 - - - -
233C GLN* 1.3 85.8 - - - +
235C PHE* 1.3 54.8 + - - +
237C SER* 3.9 4.7 - - - +
238C PHE* 2.9 33.3 + - - +
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Residues in contact with PHE 235 (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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71C MET* 4.0 23.1 - - + -
79C TYR* 3.6 25.8 - - + -
82C TYR* 4.8 3.1 - + - -
83C TRP* 3.4 66.6 - + + +
231C ASP 3.0 14.5 + - - +
232C VAL 3.4 6.7 - - - +
234C ASN* 1.3 73.9 - - - +
236C VAL* 1.3 69.9 + - + +
238C PHE* 3.3 7.0 + + - -
239C ILE* 2.9 65.4 + - + +
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Residues in contact with VAL 236 (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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76C PRO* 4.1 18.6 - - + +
79C TYR* 3.9 13.9 - - + -
80C ALA* 3.8 38.4 - - + +
232C VAL* 2.9 21.8 + - + +
233C GLN* 3.8 6.1 - - - +
235C PHE* 1.3 77.7 - - + +
237C SER* 1.3 65.4 + - - +
239C ILE* 4.2 6.3 - - - -
240C SER* 2.8 40.6 + - - +
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Residues in contact with SER 237 (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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233C GLN* 2.8 20.7 + - - +
234C ASN* 3.9 5.6 - - - -
236C VAL* 1.3 81.9 - - - +
238C PHE* 1.3 61.0 + - - +
240C SER* 3.6 8.3 + - - -
241C LYS* 2.8 35.3 + - - +
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Residues in contact with PHE 238 (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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207A HIS* 5.2 5.2 - + - -
208A ALA* 5.9 0.2 - - + -
211A LEU* 3.9 27.4 - - + -
140C GLY 3.8 19.7 - - - -
141C ILE* 3.7 32.8 - - + -
142C ILE* 4.1 21.5 - - + -
234C ASN 2.9 19.5 + - - +
235C PHE* 3.8 7.2 - + - +
237C SER* 1.3 77.1 - - - +
239C ILE* 1.3 70.0 + - + +
241C LYS* 3.1 37.1 + - + +
244C ILE* 3.4 25.3 - - + +
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Residues in contact with ILE 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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71C MET* 3.4 45.3 - - + +
79C TYR* 3.8 31.9 - - + -
141C ILE* 4.3 13.0 - - + -
235C PHE* 2.9 42.7 + - + +
236C VAL* 3.8 5.4 - - - +
238C PHE* 1.3 78.3 - - + +
240C SER* 1.3 59.0 + - - +
241C LYS 3.2 1.1 + - - -
244C ILE* 3.7 27.2 - - + +
245C GLN* 2.7 29.3 + - - +
248C LEU* 4.4 2.5 - - + -
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Residues in contact with SER 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C PRO* 5.7 1.0 - - - +
79C TYR* 3.4 24.9 - - - -
236C VAL* 2.8 27.0 + - - +
237C SER* 4.0 5.8 - - - -
238C PHE 3.2 0.2 - - - -
239C ILE* 1.3 77.3 - - - +
241C LYS* 1.3 65.7 + - - +
242C ASP* 3.5 5.5 + - - +
245C GLN* 4.0 12.4 - - - +
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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