Contacts of the helix formed by residues 221 - 226 (chain C) in PDB entry 6CAJ
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 ALA 221 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217C MET* 3.7 26.7 - - + -
218C THR* 3.7 10.0 + - - +
219C ASP 3.3 1.0 - - - -
220C ALA* 1.3 79.5 - - - +
222C ILE* 1.3 58.1 + - - +
223C PHE 3.6 1.3 - - - -
224C ALA* 3.7 7.9 - - + -
225C VAL* 2.9 31.5 + - - +
418F VAL* 3.9 17.3 - - + -
486F ASN* 6.3 0.2 - - - -
487F LEU* 4.5 17.5 - - + +
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Residues in contact with ILE 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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166C MET* 3.8 20.5 - - + +
168C ILE* 5.0 6.7 - - + -
192C ALA* 4.9 1.3 - - + -
218C THR 4.2 3.4 - - - +
219C ASP* 3.3 42.4 - - + +
220C ALA 3.5 2.4 - - - -
221C ALA* 1.3 79.0 - - - +
223C PHE* 1.3 60.4 + - - +
225C VAL* 3.4 4.0 - - - +
226C MET* 2.9 28.6 + - - +
250C GLY* 4.3 17.9 - - - +
253C THR* 4.8 2.5 - - + +
254C LEU* 3.8 41.3 - - + +
257C ALA* 4.6 7.6 - - + -
388F ILE* 5.6 0.4 - - + -
422F GLN* 3.4 16.6 + - - +
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Residues in contact with PHE 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 ILE* 1.3 77.8 - - - +
224C ALA* 1.3 65.1 + - - +
226C MET* 3.5 11.7 + - - +
227C SER* 4.3 4.5 + - - -
257C ALA* 3.8 15.7 - - + -
260C HIS* 3.8 17.9 - + - -
261C HIS* 3.3 32.8 + + - -
421F ALA* 3.6 36.3 - - + -
422F GLN* 3.7 29.7 + - + +
425F LEU* 3.6 30.1 - - + -
490F ASP* 6.0 0.2 - - - +
491F VAL 5.0 2.5 - - - -
493F PRO* 4.2 20.9 - - + -
496F LEU* 4.7 4.7 - - + -
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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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220C ALA 5.3 0.6 + - - -
221C ALA* 3.4 19.2 + - - +
222C ILE 3.2 0.4 - - - -
223C PHE* 1.3 81.8 - - - +
225C VAL* 1.3 57.6 + - - +
226C MET 3.5 0.2 - - - -
227C SER* 4.2 2.4 + - - -
418F VAL* 4.2 11.0 + - + +
422F GLN* 5.6 0.4 - - - +
451F ALA* 4.3 8.2 + - + +
452F PHE* 3.2 24.8 - - - -
487F LEU* 4.4 13.7 - - + -
490F ASP* 4.0 31.4 + - + +
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Residues in contact with VAL 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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166C MET* 3.9 21.3 - - + -
190C ILE* 3.8 5.6 - - + -
217C MET* 3.7 21.3 - - + -
221C ALA* 2.9 20.4 + - + +
222C ILE 3.4 6.1 - - - +
224C ALA* 1.3 74.5 - - + +
226C MET* 1.3 61.0 + - - +
227C SER 3.2 3.1 - - - -
228C ARG* 3.0 20.1 + - - +
229C VAL* 3.4 8.9 + - + +
401C C7B 3.1 46.2 - - + -
452F PHE* 3.8 11.7 - - + -
487F LEU* 5.6 4.0 - - + -
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Residues in contact with MET 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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166C MET* 4.3 2.5 - - - +
222C ILE 2.9 15.5 + - - +
223C PHE* 3.5 11.6 + - - +
224C ALA 3.5 1.4 - - - -
225C VAL* 1.3 76.5 - - - +
227C SER* 1.3 60.1 + - - +
228C ARG 3.1 2.3 + - - -
229C VAL* 3.4 42.6 + - + +
232C VAL* 3.7 17.5 - - + -
254C LEU* 4.0 22.7 - - - -
257C ALA* 3.7 16.6 - - + +
258C ALA* 3.7 11.7 - - - -
261C HIS* 3.5 32.4 - - + +
263C THR* 3.3 31.0 - - + +
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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