Contacts of the helix formed by residues 216 - 225 (chain B) in PDB entry 2C6E
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 216 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214B LEU 4.0 1.1 + - - +
215B GLY* 1.3 75.6 - - - -
217B VAL* 1.3 64.1 + - - +
218B TYR* 3.6 11.3 + - - +
219B ARG* 3.2 32.6 + - - +
220B GLU* 3.4 13.9 + - - +
258B PRO 4.2 4.5 - - - -
259B GLU* 4.0 13.9 - - - +
261B LEU 3.4 8.7 - - - -
262B LEU* 3.4 19.7 - - + -
263B LEU* 4.5 2.1 - - - +
1388B HPM 4.0 21.3 - - + +
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Residues in contact with VAL 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B GLY 4.2 0.2 + - - -
216B THR* 1.3 70.3 - - - +
218B TYR* 1.3 66.6 + - - +
220B GLU* 3.1 8.3 + - + +
221B LEU* 2.9 22.3 + - + +
227B PHE* 4.2 14.6 - - + -
235B TYR* 4.3 5.4 - - + -
258B PRO* 3.7 11.2 - - + +
261B LEU* 2.8 30.9 + - + +
263B LEU* 4.3 12.6 - - + -
269B LEU* 3.2 32.8 - - + -
321B PHE* 3.9 30.7 - - + -
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Residues in contact with TYR 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216B THR* 3.6 9.2 - - - +
217B VAL* 1.3 74.7 - - - +
219B ARG* 1.3 65.8 + - + +
221B LEU* 3.2 11.9 + - + +
222B GLN* 3.1 61.8 + - + +
258B PRO* 3.2 33.2 + - + +
259B GLU* 3.6 39.5 - - + -
320B GLU* 6.1 1.1 - - - -
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Residues in contact with ARG 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B GLY* 6.1 0.2 - - - -
216B THR* 3.2 22.0 + - - +
217B VAL 3.3 0.2 - - - -
218B TYR* 1.3 84.2 - - + +
220B GLU* 1.3 62.1 + - + +
222B GLN* 3.3 11.7 + - - +
223B LYS* 3.2 28.2 + - + +
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Residues in contact with GLU 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214B LEU 5.3 2.9 - - - +
216B THR 3.4 5.2 + - - +
217B VAL* 3.1 11.6 + - + +
219B ARG* 1.3 77.9 - - - +
221B LEU* 1.3 63.9 + - - +
223B LYS* 3.2 23.1 + - - +
224B LEU* 3.1 35.5 + - - +
227B PHE* 4.2 11.9 - - + -
231B ARG* 3.3 28.6 + - - +
235B TYR* 5.7 0.9 - - - +
263B LEU* 3.8 27.2 - - + +
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Residues in contact with LEU 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217B VAL* 2.9 12.5 + - + +
218B TYR* 3.5 14.4 - - + +
220B GLU* 1.3 75.9 - - - +
222B GLN* 1.3 55.3 + - + +
225B SER* 2.7 45.3 + - - +
226B LYS* 3.7 26.0 - - - -
227B PHE* 3.8 25.3 - - + -
258B PRO* 5.3 9.0 - - + -
320B GLU* 4.0 44.4 - - + +
321B PHE* 4.4 7.9 - - + +
324B GLY* 4.4 9.0 - - - +
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Residues in contact with GLN 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218B TYR* 3.1 54.3 + - + +
219B ARG* 3.5 10.9 - - - +
221B LEU* 1.3 78.9 - - + +
223B LYS* 1.3 62.8 + - + +
225B SER* 3.7 6.7 + - - +
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Residues in contact with LYS 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219B ARG* 3.2 15.5 + - + +
220B GLU* 3.2 25.4 + - - +
222B GLN* 1.3 79.4 - - + +
224B LEU* 1.3 67.2 + - + +
225B SER* 5.0 0.9 - - - -
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Residues in contact with LEU 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220B GLU* 3.1 21.0 + - - +
223B LYS* 1.3 84.5 - - + +
225B SER* 1.3 66.1 + - - +
226B LYS* 2.9 22.7 + - - +
227B PHE* 4.1 17.3 - - + -
231B ARG* 3.1 35.0 - - - +
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Residues in contact with SER 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221B LEU* 2.7 26.4 + - - +
222B GLN* 3.7 5.6 + - - +
223B LYS 3.3 4.3 - - - -
224B LEU* 1.3 74.5 - - - +
226B LYS* 1.3 71.2 + - - +
323B VAL 4.6 0.3 - - - +
324B GLY* 3.6 17.8 - - - +
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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