Contacts of the helix formed by residues 227 - 237 (chain C) in PDB entry 6FQS
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 LYS 227 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210C MET* 4.8 13.7 - - + +
214C GLU* 5.1 17.3 - - - +
226C GLY* 1.3 73.4 - - - -
228C SER* 1.3 62.0 + - - +
229C GLY 3.4 2.5 - - - -
230C ILE* 4.0 16.6 + - + +
231C ARG* 3.5 22.5 + - - +
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Residues in contact with SER 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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225C LEU 5.7 0.5 + - - -
226C GLY* 3.3 5.4 - - - -
227C LYS* 1.3 78.6 - - - +
229C GLY* 1.3 62.2 + - - +
231C ARG* 4.1 5.3 - - - +
232C ARG* 3.6 27.5 + - - +
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Residues in contact with GLY 229 (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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226C GLY 4.7 1.8 + - - -
228C SER* 1.3 80.5 + - - +
230C ILE* 1.3 66.6 + - - +
231C ARG 3.3 0.4 - - - -
232C ARG* 3.9 12.6 - - - +
233C ALA* 3.2 22.3 + - - +
239C GLY* 4.1 4.5 - - - -
240C SER 3.5 26.3 - - - +
241C ILE* 4.2 4.5 - - - +
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Residues in contact with ILE 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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210C MET* 3.8 15.7 - - + -
214C GLU 4.1 5.4 - - - +
215C GLY* 4.0 17.9 - - - -
216C PRO* 3.7 18.6 - - + -
224C ILE* 4.0 25.8 - - + -
226C GLY 4.1 11.1 + - - +
227C LYS* 4.0 13.5 - - + +
229C GLY* 1.3 77.1 - - - +
231C ARG* 1.3 60.4 + - - +
233C ALA* 3.0 5.5 + - - +
234C TYR* 2.8 59.7 + - + -
241C ILE* 3.9 17.0 - - + +
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Residues in contact with ARG 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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207C ALA* 3.5 30.3 - - - +
210C MET* 3.8 29.1 - - - -
227C LYS 3.5 15.6 + - - +
228C SER* 4.3 5.8 - - - +
229C GLY 3.3 0.6 - - - -
230C ILE* 1.3 82.0 - - - +
232C ARG* 1.3 64.8 + - - +
234C TYR* 3.3 1.8 + - - +
235C GLU* 2.9 62.2 + - - +
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Residues in contact with ARG 232 (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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228C SER* 3.6 23.3 + - - +
229C GLY* 3.7 11.8 + - - +
230C ILE 3.2 0.8 - - - -
231C ARG* 1.3 78.5 - - - +
233C ALA* 1.3 54.2 + - - +
235C GLU* 4.8 3.6 - - - -
236C THR* 2.5 48.8 + - + +
238C ARG 3.7 14.1 - - - +
239C GLY* 4.8 6.3 - - - -
240C SER 5.8 0.6 - - - +
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Residues in contact with ALA 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 GLY 3.2 14.3 + - - +
230C ILE* 3.0 10.1 + - - +
232C ARG* 1.3 77.7 - - - +
234C TYR* 1.3 65.6 + - + +
237C GLY* 2.7 30.5 + - - -
238C ARG 3.8 11.2 + - - +
239C GLY 3.9 4.3 - - - +
241C ILE* 5.1 1.1 - - + -
333C VAL* 3.7 37.9 - - + -
335C MET* 3.9 5.1 - - - +
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Residues in contact with TYR 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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184C PRO* 5.7 2.7 - - + -
186C HIS* 2.5 43.0 + + - -
206C ILE* 3.1 36.1 - - + +
210C MET* 3.7 17.9 - - + -
213C ILE* 3.6 22.4 - - + -
215C GLY* 3.1 20.6 - - - -
216C PRO* 3.4 5.8 - - + +
230C ILE* 2.8 42.4 + - + +
231C ARG* 4.1 4.9 - - - +
233C ALA* 1.3 78.4 - - + +
235C GLU* 1.3 58.0 + - - +
241C ILE* 6.2 1.1 - - + -
333C VAL* 6.3 0.9 - - + -
335C MET* 4.4 11.2 - - + -
347C ASN* 3.4 0.7 - - - +
348C LEU* 3.2 38.7 + - + +
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Residues in contact with GLU 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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206C ILE* 4.1 28.5 - - + +
207C ALA 4.5 0.2 + - - -
231C ARG* 2.9 63.1 + - - +
232C ARG* 4.1 3.3 - - - +
234C TYR* 1.3 79.6 - - - +
236C THR* 1.3 68.9 + - + +
237C GLY 3.8 0.2 - - - -
347C ASN* 3.5 19.6 + - - +
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Residues in contact with THR 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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232C ARG* 2.5 30.3 + - + +
235C GLU* 1.3 86.5 - - + +
237C GLY* 1.3 59.5 + - - +
238C ARG* 3.2 19.6 + - - +
345C LEU* 3.9 19.4 - - - +
346C ILE 5.3 0.7 - - - -
347C ASN* 4.6 4.5 - - - -
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Residues in contact with GLY 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 ALA* 2.7 26.1 + - - -
235C GLU 3.8 0.6 - - - -
236C THR* 1.3 71.2 - - - +
238C ARG* 1.3 59.7 + - - +
333C VAL* 3.7 1.8 - - - +
334C ASN* 3.5 2.6 - - - -
335C MET* 2.9 35.0 + - - +
345C LEU* 4.2 5.2 - - - -
346C ILE 3.7 23.1 - - - -
347C ASN* 4.4 1.4 - - - +
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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