Contacts of the helix formed by residues 217 - 226 (chain C) in PDB entry 3H0Z
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 THR 217 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1C 45B 3.5 61.9 + - + +
215C LEU 4.6 0.3 - - - +
216C GLY* 1.3 75.7 - - - -
218C VAL* 1.3 63.2 + - - +
219C TYR* 3.6 3.8 - - - +
220C ARG* 3.2 28.4 + - - +
221C GLU* 3.6 14.0 + - - +
259C PRO 4.1 3.6 - - - -
260C GLU 4.3 2.7 - - - +
262C LEU 3.3 10.5 - - - +
263C LEU* 3.4 20.2 - - + -
264C LEU* 4.4 1.1 - - - +
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Residues in contact with VAL 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217C THR* 1.3 71.2 - - - +
219C TYR* 1.3 64.7 + - - +
221C GLU* 3.3 6.4 + - + +
222C LEU* 3.1 22.3 + - + +
228C PHE* 4.1 24.7 - - + -
236C TYR* 4.6 9.9 - - + +
259C PRO* 3.9 5.8 - - + +
262C LEU* 2.8 45.3 + - + +
263C LEU 4.0 0.7 - - - +
264C LEU* 3.9 19.1 - - + -
270C LEU* 3.7 15.9 - - + -
322C PHE* 4.2 21.5 - - + -
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Residues in contact with TYR 219 (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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204A THR* 3.8 20.7 - - + +
1C 45B 3.7 30.8 - + + -
217C THR* 3.6 8.1 - - - +
218C VAL* 1.3 76.1 - - - +
220C ARG* 1.3 71.0 + - + +
222C LEU* 3.3 7.9 + - - +
223C GLN* 3.3 49.6 + - + +
259C PRO* 3.0 31.9 + - + +
260C GLU* 3.8 33.2 - - + +
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Residues in contact with ARG 220 (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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1C 45B 3.7 34.9 - - + +
217C THR* 3.2 19.3 + - - +
218C VAL 3.3 0.4 - - - -
219C TYR* 1.3 87.6 - - + +
221C GLU* 1.3 64.5 + - + +
223C GLN* 3.2 33.4 + - - +
224C LYS* 3.2 54.2 + - - +
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Residues in contact with GLU 221 (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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1C 45B 5.3 8.3 - - - +
215C LEU 4.8 6.4 - - - +
217C THR 3.6 5.7 + - - +
218C VAL* 3.3 9.9 + - - +
220C ARG* 1.3 80.1 - - + +
222C LEU* 1.3 57.1 + - - +
224C LYS* 3.5 25.3 + - - +
225C LEU* 3.0 49.0 + - - +
228C PHE* 3.7 14.3 - - + -
232C ARG* 3.5 21.6 + - - +
236C TYR* 5.2 0.4 - - - +
264C LEU* 3.7 28.5 - - + -
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Residues in contact with LEU 222 (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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218C VAL* 3.1 12.2 + - + +
219C TYR* 3.6 9.4 - - - +
220C ARG 3.2 0.2 - - - -
221C GLU* 1.3 74.6 - - - +
223C GLN* 1.3 60.6 + - - +
225C LEU 4.6 0.2 - - - +
226C SER* 2.8 36.7 + - - +
227C LYS* 4.0 20.4 - - - -
228C PHE* 3.4 34.7 - - + -
259C PRO* 5.0 8.3 - - + -
321C GLU* 3.7 40.8 - - + +
322C PHE* 4.1 14.6 - - + +
325C GLY* 4.5 8.1 - - - +
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Residues in contact with GLN 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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167A ALA* 3.6 29.3 - - - +
204A THR* 4.7 8.7 - - - +
219C TYR* 3.3 46.6 + - + +
220C ARG* 3.2 29.6 + - - +
222C LEU* 1.3 77.1 - - - +
224C LYS* 1.3 67.1 + - - +
226C SER* 3.6 8.7 + - - -
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Residues in contact with LYS 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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250B LYS* 3.8 14.9 + - - -
1C 45B 4.3 24.4 - - - +
220C ARG* 3.2 44.9 + - - +
221C GLU* 3.6 26.1 + - - +
222C LEU 3.4 0.2 - - - -
223C GLN* 1.3 83.6 - - - +
225C LEU* 1.3 75.0 + - + +
226C SER* 3.4 0.9 + - - -
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Residues in contact with LEU 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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250B LYS* 4.1 9.6 - - - +
221C GLU* 3.0 32.3 + - - +
224C LYS* 1.3 91.8 - - + +
226C SER* 1.3 58.9 + - - +
227C LYS* 2.8 30.3 + - - +
228C PHE* 3.5 16.4 - - + -
232C ARG* 3.5 38.1 - - - +
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Residues in contact with SER 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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171A LYS* 3.4 26.5 + - - +
249B SER* 4.7 6.3 - - - -
250B LYS* 3.5 18.7 + - - -
222C LEU* 2.8 24.2 + - - +
223C GLN 3.6 6.4 + - - -
224C LYS 3.3 3.7 + - - -
225C LEU* 1.3 77.8 - - - +
227C LYS* 1.3 59.9 + - - +
325C GLY* 3.2 24.9 - - - +
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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