Contacts of the helix formed by residues 213 - 218 (chain A) in PDB entry 6F0X
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 213 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A ALA* 4.0 8.0 - - - +
211A GLU* 3.5 24.8 + - - +
212A ILE* 1.3 69.2 - - - +
214A SER* 1.3 56.3 + - - +
215A HIS* 3.2 25.2 + - - +
216A SER* 2.5 59.5 + - - +
217A LEU* 2.8 5.4 + - - -
252A ASP* 6.1 1.6 - - - -
253A GLN* 4.3 12.4 - - - +
278B ASN* 5.6 0.3 - - - -
279B ALA* 5.2 0.4 - - - +
282B THR* 4.4 24.1 + - - +
283B GLN* 5.7 4.2 - - - +
286B GLN* 5.6 2.6 + - - +
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Residues in contact with SER 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A ILE* 2.9 13.9 + - - -
213A ASN* 1.3 70.0 + - - +
215A HIS* 1.3 62.4 + - - +
217A LEU* 2.7 38.5 + - - +
218A PHE* 3.4 15.6 + - - -
251A ILE* 5.9 3.6 - - - -
253A GLN* 4.2 13.1 + - - -
256A SER* 2.4 45.4 + - - -
257A LEU* 4.6 14.1 - - - -
278B ASN* 4.4 0.7 + - - -
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Residues in contact with HIS 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A ASN* 3.2 20.2 + - - +
214A SER* 1.3 85.7 + - - +
216A SER* 1.3 65.7 + - - +
218A PHE* 3.8 11.8 + - - +
256A SER* 4.0 1.5 + - - -
223B SER 5.7 0.3 - - - +
225B SER* 4.7 0.4 - - - -
226B GLY* 3.0 50.1 - - - -
229B VAL* 3.8 14.5 - - + +
230B THR* 4.7 8.3 - - + -
275B ARG* 3.1 32.9 - - + -
276B VAL* 4.7 2.0 - - - -
278B ASN* 3.7 16.8 - - - +
279B ALA* 3.2 30.8 - - + +
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Residues in contact with SER 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A ALA* 3.0 29.2 + - - +
213A ASN* 2.5 36.5 + - - +
215A HIS* 1.3 80.6 + - - +
217A LEU* 1.3 66.0 + - - +
218A PHE 3.9 3.8 - - - +
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Residues in contact with LEU 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A ILE* 4.5 13.9 - - + -
213A ASN 2.8 5.5 + - - +
214A SER* 2.7 30.1 + - - +
216A SER* 1.3 74.3 - - - +
218A PHE* 1.3 112.4 + - + +
219A SER* 4.2 2.1 + - - -
228A LEU* 3.0 42.3 - - + +
232A MET* 3.6 26.7 - - + -
233A PHE* 5.1 0.2 - - + -
257A LEU* 5.5 4.3 - - + -
276A VAL* 5.1 4.3 - - + -
280A VAL* 4.4 18.4 - - + -
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Residues in contact with PHE 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A SER* 3.4 21.4 + - - +
215A HIS 3.8 7.6 + - - +
216A SER 3.6 5.1 - - - +
217A LEU* 1.3 111.6 - - + +
219A SER* 1.3 65.4 + - - +
228A LEU* 3.9 5.4 - - + -
256A SER* 4.3 17.5 - - - -
257A LEU* 5.3 5.4 - - + -
259A ALA* 5.9 0.7 - - + -
272A ASP 6.0 0.4 - - - -
273A ALA* 4.4 18.2 - - + -
276A VAL* 5.2 5.8 - - + -
277A VAL* 3.6 34.5 - - + -
280A VAL* 6.1 0.4 - - + -
222B PHE* 5.5 3.4 - + + -
223B SER* 3.9 26.1 - - - +
275B ARG* 4.1 27.1 - - - +
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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