Contacts of the helix formed by residues 222 - 234 (chain C) in PDB entry 1FVU
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 ASN 222 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221C MET* 1.3 77.0 - - - +
223C TRP* 1.3 64.8 + - - +
224C ALA* 3.3 8.5 + - - +
225C ASP* 2.7 56.3 + - - +
226C ALA* 2.9 19.9 + - - +
320C CYS 3.6 9.4 - - - +
321C ALA* 3.8 14.6 + - - +
322C GLN 3.1 17.9 - - - +
323C LYS* 3.6 17.9 - - + +
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Residues in contact with TRP 223 (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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222C ASN* 1.3 72.9 - - - +
224C ALA* 1.3 84.7 + - + +
226C ALA* 3.2 3.5 + - - +
227C GLU* 3.0 26.3 + - + +
239C LEU* 3.5 13.7 - - + +
268C TRP* 3.3 40.5 - + + +
269C ILE 3.0 22.6 + - - -
270C GLY 4.1 8.7 - - - -
271C LEU 3.9 6.8 + - - -
272C ARG* 3.6 36.6 - - + -
303C CYS* 3.3 37.7 - - + -
304C PHE 4.3 0.7 - - - -
320C CYS* 3.3 12.0 + - + +
680D THR* 3.4 34.8 - - + -
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Residues in contact with ALA 224 (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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222C ASN* 3.3 8.1 + - - +
223C TRP* 1.3 93.9 - - + +
225C ASP* 1.3 65.6 + - - +
227C GLU* 3.4 6.2 + - - +
228C ARG* 3.1 27.3 + - - +
320C CYS* 4.8 1.2 + - - +
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Residues in contact with ASP 225 (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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221C MET* 3.7 26.1 - - + +
222C ASN* 2.7 46.7 + - - +
224C ALA* 1.3 75.2 - - - +
226C ALA* 1.3 57.6 + - - +
228C ARG* 2.7 39.8 + - - +
229C PHE* 2.9 27.7 + - - +
323C LYS* 5.2 5.0 + - - -
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Residues in contact with ALA 226 (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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221C MET* 4.1 6.3 - - + +
222C ASN 2.9 17.1 + - - +
223C TRP 3.5 5.2 - - - +
225C ASP* 1.3 74.3 - - - +
227C GLU* 1.3 64.8 + - - +
229C PHE* 3.2 8.3 + - - +
230C CYS* 2.9 28.2 + - - -
239C LEU* 4.0 12.1 - - + -
268C TRP* 4.1 10.3 - - + -
326C PHE* 3.8 32.4 - - + -
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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
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223C TRP* 3.0 18.5 + - + +
224C ALA* 3.6 11.2 - - - +
226C ALA* 1.3 78.4 - - - +
228C ARG* 1.3 62.9 + - - +
230C CYS* 3.3 3.7 + - - +
231C SER* 3.1 22.5 + - - -
237C GLY 4.6 0.3 - - - +
238C HIS* 2.8 29.1 + - - -
239C LEU* 2.9 33.8 + - + +
680D THR* 2.8 40.5 + - + +
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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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221C MET* 5.4 3.0 - - - +
224C ALA* 3.1 13.5 + - - +
225C ASP* 2.7 44.9 + - - +
226C ALA 3.2 0.2 - - - -
227C GLU* 1.3 79.5 - - - +
229C PHE* 1.3 61.9 + - - +
231C SER* 2.6 27.4 + - - +
232C GLU* 3.0 33.4 + - + +
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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
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217C PHE* 3.4 27.1 - + - -
219C GLN* 3.2 35.4 - - - -
221C MET* 3.9 24.0 - - + -
225C ASP 2.9 18.2 + - - +
226C ALA* 3.2 6.3 + - - +
228C ARG* 1.3 76.5 - - - +
230C CYS* 1.3 62.1 + - - +
232C GLU* 3.0 17.6 + - - +
233C GLN* 3.0 63.0 + - + +
326C PHE* 3.5 18.6 - + - -
328C CYS* 4.3 0.7 - - - -
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Residues in contact with CYS 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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206C TRP* 5.4 0.3 - - - -
226C ALA 2.9 17.4 + - - -
227C GLU 3.6 6.3 - - - +
228C ARG 3.2 0.2 - - - -
229C PHE* 1.3 76.9 - - - +
231C SER* 1.3 62.3 + - - +
232C GLU 3.2 0.7 + - - -
233C GLN* 3.2 12.2 + - - +
234C ALA 3.6 4.9 + - - -
237C GLY* 3.4 15.3 - - - -
238C HIS 3.5 27.8 - - - +
239C LEU* 3.9 7.6 - - - -
326C PHE* 3.9 10.1 - - - -
328C CYS* 2.0 57.8 - - + +
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Residues in contact with SER 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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227C GLU* 3.1 14.2 + - - -
228C ARG* 2.6 27.9 + - - +
230C CYS* 1.3 76.2 - - - +
232C GLU* 1.3 59.7 + - - +
233C GLN 3.5 0.2 - - - -
234C ALA 3.3 15.2 - - - +
235C LYS* 4.7 3.3 - - - +
236C GLY 5.2 0.5 + - - -
237C GLY 3.2 21.0 + - - +
238C HIS* 5.5 2.7 - - - -
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Residues in contact with GLU 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 ARG* 3.0 39.8 + - + +
229C PHE* 3.0 19.9 + - - +
231C SER* 1.3 82.5 - - - +
233C GLN* 1.3 68.2 + - - +
234C ALA* 3.3 2.2 + - - -
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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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203C PRO* 6.2 0.2 - - - +
206C TRP* 4.0 24.3 + - + -
215C LYS* 5.4 0.9 + - - -
217C PHE* 4.0 15.8 - - + -
229C PHE* 3.0 61.8 + - + +
230C CYS* 3.2 8.2 + - - +
232C GLU* 1.3 83.4 + - - +
234C ALA* 1.3 60.9 + - - +
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Residues in contact with ALA 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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203C PRO* 5.8 5.8 - - + -
206C TRP* 4.6 11.7 - - + -
230C CYS 3.6 1.8 + - - -
231C SER 3.3 13.0 - - - +
232C GLU 3.3 2.1 - - - -
233C GLN* 1.3 81.0 - - - +
235C LYS* 1.3 62.6 + - - +
237C GLY* 2.9 20.6 + - - +
330C SER* 3.9 27.8 - - - +
331C PRO 5.7 0.7 - - - +
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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