Contacts of the helix formed by residues 214 - 220 (chain H) in PDB entry 1R4N
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 PRO 214 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263G GLU* 6.0 2.7 - - - +
212H ASN 3.6 8.1 - - - +
213H PHE* 1.3 81.3 - - + +
215H MET* 1.3 68.1 + - - +
216H ALA* 2.7 11.0 + - + +
217H THR* 3.0 36.6 + - + +
218H ILE* 3.5 1.8 + - - +
227H HIS* 6.3 0.4 - - - +
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Residues in contact with MET 215 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213H PHE 3.2 5.7 + - - -
214H PRO* 1.3 69.7 - - - +
216H ALA* 1.3 68.4 + - - +
218H ILE* 3.0 24.6 + - + +
219H ALA* 3.1 16.3 + - + +
234H MET* 5.2 10.5 - - - +
235H LEU* 4.4 33.2 - - + -
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Residues in contact with ALA 216 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214H PRO* 2.7 12.2 + - + +
215H MET* 1.3 78.0 - - - +
217H THR* 1.3 55.9 + - + +
219H ALA* 3.8 0.8 - - - +
220H SER* 2.7 45.8 + - - +
221H MET* 4.9 7.4 - - + -
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Residues in contact with THR 217 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333G ILE* 5.2 6.5 - - + -
213H PHE* 4.9 0.3 - - - +
214H PRO* 3.0 30.6 + - + +
216H ALA* 1.3 77.7 - - + +
218H ILE* 1.3 68.3 + - - +
221H MET* 2.8 56.9 + - + -
222H PRO* 3.1 6.2 - - - +
223H ARG* 3.0 34.4 + - - +
227H HIS* 4.8 8.8 + - - -
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Residues in contact with ILE 218 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213H PHE* 3.3 46.4 - - + +
214H PRO 3.7 6.5 - - - +
215H MET* 3.0 18.1 + - + +
217H THR* 1.3 83.9 + - - +
219H ALA* 1.3 58.0 + - - +
222H PRO* 4.3 1.0 - - - +
227H HIS* 3.7 17.4 - - + +
230H GLU* 3.8 16.6 - - + +
231H TYR* 3.4 37.7 - - + +
234H MET* 4.3 14.1 - - + -
235H LEU* 5.0 6.1 - - + -
267H ARG* 2.9 22.0 + - - -
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Residues in contact with ALA 219 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215H MET* 3.1 18.9 + - + +
216H ALA* 4.1 1.3 - - - +
218H ILE* 1.3 78.0 - - - +
220H SER* 1.3 65.6 + - - +
231H TYR* 4.3 6.9 - - + -
235H LEU* 4.4 19.3 - - + -
267H ARG* 3.6 15.9 + - - +
271H TYR* 4.0 8.8 + - - -
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Residues in contact with SER 220 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211G HIS* 5.8 1.6 - - - -
336G SER* 4.7 2.8 - - - -
216H ALA* 2.7 24.1 + - - +
219H ALA* 1.3 78.9 - - - +
221H MET* 1.3 77.2 + - - +
222H PRO* 3.8 7.4 - - - +
271H TYR* 3.9 11.3 + - - -
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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