Contacts of the helix formed by residues 223 - 235 (chain C) in PDB entry 6S6A
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 HIS 223 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222C ASP* 1.3 75.9 + - - +
224C SER* 1.3 66.2 + - - +
225C ILE 2.9 4.8 + - - -
226C PHE* 2.9 41.5 + + + +
227C GLU* 3.0 21.4 + - + +
282C TYR* 4.9 3.6 - + + -
283C GLU* 3.3 53.0 + - + -
286C CYS* 3.5 32.3 - - - +
287C ASP* 3.3 21.9 + - - -
290C ASP* 5.9 0.4 + - - -
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Residues in contact with SER 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C VAL* 5.7 0.7 - - - +
217C LEU 3.3 25.5 - - - +
218C THR* 3.6 3.3 - - - -
219C SER 3.2 16.6 + - - -
222C ASP* 3.1 29.6 + - - +
223C HIS* 1.3 73.6 - - - +
225C ILE* 1.3 50.0 + - - +
227C GLU* 3.3 19.4 + - - +
228C ALA* 2.7 37.8 + - - +
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Residues in contact with ILE 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C ILE* 3.8 31.0 - - + -
80C VAL* 4.4 11.7 - - + -
81C VAL* 4.1 17.0 - - + -
176C PHE* 3.6 35.9 - - + -
178C HIS* 4.9 0.7 - - - +
218C THR* 3.9 13.5 - - - -
219C SER 3.5 24.2 - - - +
220C ILE* 4.6 1.8 - - + -
222C ASP 3.6 11.4 - - - +
223C HIS 2.9 1.0 + - - -
224C SER* 1.3 80.8 + - - +
226C PHE* 1.3 71.1 + - + +
228C ALA* 3.6 3.5 - - - +
229C PHE* 2.9 35.6 + - + -
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Residues in contact with PHE 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C VAL* 3.7 35.9 - - + -
81C VAL* 4.2 13.0 - - + -
220C ILE 5.6 0.2 - - - -
222C ASP 4.1 6.5 - - - -
223C HIS* 2.9 40.0 + + + +
225C ILE* 1.3 89.4 - - + +
227C GLU* 1.3 54.8 + - - +
229C PHE* 3.2 5.4 + - - +
230C SER* 2.7 38.5 + - - -
266C SER 3.3 26.9 - - - -
267C LYS* 4.2 27.4 - - + -
268C ILE* 4.8 2.5 - - + +
282C TYR* 3.5 20.6 + - + +
286C CYS* 5.1 0.9 - - - -
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Residues in contact with GLU 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223C HIS* 3.0 24.2 + - + +
224C SER* 3.5 16.6 - - - +
226C PHE* 1.3 73.9 - - - +
228C ALA* 1.3 58.3 + - - +
230C SER* 3.2 3.9 + - - -
231C LYS* 3.0 45.7 + - - +
269C TYR* 5.7 1.5 - - - -
279C MET* 3.1 48.9 - - + +
282C TYR* 3.9 19.7 - - + -
283C GLU* 5.0 2.9 - - - +
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Residues in contact with ALA 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C PHE* 3.8 18.2 - - + -
216C TYR* 3.9 24.8 - - + -
217C LEU 5.7 0.2 - - - +
218C THR* 3.9 17.5 - - + -
224C SER 2.7 21.4 + - - +
225C ILE 3.6 4.9 - - - +
227C GLU* 1.3 72.4 - - - +
229C PHE* 1.3 57.3 + - - +
231C LYS* 3.2 6.2 + - - +
232C VAL* 3.0 33.0 + - - +
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Residues in contact with PHE 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C ILE* 3.9 22.7 - - + -
66C LEU* 4.2 2.5 - - + -
77C ILE* 3.9 20.0 - - + -
81C VAL* 4.3 11.4 - - + -
82C PHE* 4.1 11.9 - + - -
112C PHE* 3.6 32.8 - + - -
141C ILE* 3.8 20.6 - - + -
176C PHE* 3.7 20.4 - + - -
225C ILE* 2.9 30.9 + - + +
226C PHE* 3.7 4.3 - - - +
228C ALA* 1.3 72.1 - - - +
230C SER* 1.3 61.0 + - - +
232C VAL* 3.2 6.7 + - + +
233C VAL* 2.8 35.1 + - - +
268C ILE* 3.8 29.6 - - + -
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Residues in contact with SER 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226C PHE 2.7 17.5 + - - -
227C GLU* 3.5 5.8 - - - -
229C PHE* 1.3 71.9 - - - +
231C LYS* 1.3 61.4 + - - +
233C VAL* 4.1 0.7 - - - +
234C GLN* 3.1 33.3 + - - +
268C ILE* 3.3 12.5 - - - +
269C TYR* 2.8 53.2 + - - +
282C TYR* 2.8 17.4 + - - -
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Residues in contact with LYS 231 (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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216C TYR* 4.1 32.6 - - + +
227C GLU* 3.0 25.6 + - - +
228C ALA* 3.6 8.0 - - - +
230C SER* 1.3 73.1 - - - +
232C VAL* 1.3 67.2 + - - +
234C GLN* 3.1 19.9 + - - +
235C LYS* 3.5 16.7 + - + +
269C TYR* 5.6 5.4 - - + +
279C MET* 5.0 16.8 - - - -
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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
----------------------------------------------------------
64C ILE* 4.5 9.9 - - + -
139C ALA* 3.9 26.9 - - + -
141C ILE* 4.1 14.4 - - + -
172C ASN* 4.8 0.2 + - - -
174C GLU* 3.8 40.5 - - + +
176C PHE* 4.0 19.1 - - + -
216C TYR* 4.1 6.3 + - - +
228C ALA 3.0 15.6 + - - +
229C PHE* 3.6 8.3 - - - +
231C LYS* 1.3 76.2 - - - +
233C VAL* 1.3 65.2 + - + +
234C GLN 3.2 0.2 + - - -
235C LYS* 3.3 16.1 + - - +
236C LEU* 3.8 8.4 - - + +
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Residues in contact with VAL 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C PRO* 4.8 8.7 - - + -
64C ILE* 3.7 22.4 - - + -
109C PHE* 4.7 2.7 - - + -
110C VAL* 3.4 34.5 - - + -
229C PHE* 2.8 24.2 + - + +
230C SER 4.3 0.4 - - - +
232C VAL* 1.3 71.1 - - - +
234C GLN* 1.3 62.7 + - + +
236C LEU* 3.0 20.7 + - - +
237C ILE* 3.6 22.7 - - + +
268C ILE* 4.2 27.1 - - + -
270C ILE* 4.6 6.1 - - + -
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Residues in contact with GLN 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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230C SER 3.1 22.9 + - - +
231C LYS* 3.1 11.5 + - - +
233C VAL* 1.3 76.3 - - - +
235C LYS* 1.3 62.4 + - + +
236C LEU 3.3 1.2 + - - -
237C ILE* 3.4 17.3 + - - +
240C LEU* 3.3 32.4 - - + +
269C TYR* 2.9 57.7 + - - +
270C ILE* 3.3 26.4 - - - +
271C ALA* 4.5 3.5 - - - -
272C THR* 5.2 1.2 + - - +
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Residues in contact with LYS 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172C ASN* 3.7 22.3 + - - +
174C GLU* 3.0 40.7 + - - -
212C HIS* 5.1 4.0 - - - -
214C SER* 3.3 17.6 + - - -
216C TYR* 4.0 7.1 + - - -
231C LYS* 3.6 15.0 - - + +
232C VAL 3.3 4.5 + - - +
233C VAL 3.2 0.8 - - - -
234C GLN* 1.3 78.3 - - + +
236C LEU* 1.3 61.2 + - - +
237C ILE 3.4 3.4 + - - +
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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