Contacts of the helix formed by residues 209 - 216 (chain H) in PDB entry 1JH0
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 SER 209 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156H CYS* 3.9 16.1 - - - +
157H ASP* 3.6 15.9 - - - -
208H LEU* 1.3 75.3 - - - +
210H SER* 1.3 70.2 + - - +
211H ASP* 3.2 18.0 + - - -
212H LEU* 3.1 35.7 + - - +
213H PHE* 3.1 13.1 - - - -
244H ALA* 4.6 1.3 - - - +
247H LYS* 3.5 19.4 - - - +
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Residues in contact with SER 210 (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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155H GLY* 4.2 0.6 - - - -
157H ASP* 2.9 32.6 + - - -
159H GLU* 3.9 27.0 - - - +
160H ILE 4.9 1.6 - - - -
161H ALA* 4.1 12.6 - - - +
209H SER* 1.3 69.5 - - - +
211H ASP* 1.3 64.6 + - - +
212H LEU 2.6 13.3 + - - -
213H PHE* 2.9 32.7 + - - +
214H ALA 4.6 0.5 + - - -
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Residues in contact with ASP 211 (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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157H ASP* 4.3 2.8 - - - +
209H SER* 3.2 18.1 + - - -
210H SER* 1.3 82.9 + - - +
212H LEU* 1.3 62.1 + - - +
213H PHE 3.5 0.2 - - - -
214H ALA* 4.7 9.4 + - - +
247H LYS* 2.6 38.3 + - - +
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Residues in contact with LEU 212 (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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105H MET* 5.2 11.9 - - + -
208H LEU* 4.1 17.3 - - + -
209H SER* 3.1 31.6 + - - +
210H SER 2.6 7.7 + - - -
211H ASP* 1.3 86.9 - - - +
213H PHE* 1.3 64.0 + - - +
214H ALA 3.2 2.9 - - - -
215H GLY* 2.9 5.3 + - - +
216H ILE* 3.6 1.8 + - - -
236H TYR* 2.8 37.2 + - + +
244H ALA* 3.8 30.3 - - + -
247H LYS* 4.3 10.8 - - + +
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Residues in contact with PHE 213 (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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153H VAL* 3.8 28.9 - - + -
154H ARG 4.2 4.7 - - - -
155H GLY* 4.0 7.0 - - - -
161H ALA* 3.5 26.0 - - + -
181H VAL* 5.5 4.3 - - + -
183H LEU* 3.9 24.2 - - + -
189H ARG* 4.1 5.5 - - - +
191H LEU* 3.9 19.7 - - + -
205H VAL* 4.0 19.5 - - + -
208H LEU* 4.1 11.4 - - + -
209H SER 3.1 34.8 - - - -
210H SER* 2.9 14.4 + - - +
212H LEU* 1.3 78.0 - - - +
214H ALA* 1.3 61.1 + - - +
216H ILE* 2.8 45.0 + - + +
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Residues in contact with ALA 214 (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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183H LEU* 4.1 11.3 - - + +
189H ARG* 3.2 28.9 + - - +
210H SER 4.6 0.8 + - - -
211H ASP 4.7 7.4 + - - +
212H LEU 3.2 1.0 - - - +
213H PHE* 1.3 77.7 - - - +
215H GLY* 1.3 61.0 + - - +
216H ILE 3.4 0.7 + - - +
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Residues in contact with GLY 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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211H ASP 5.1 0.4 + - - -
212H LEU* 2.9 7.2 + - - +
214H ALA* 1.3 77.0 - - - +
216H ILE* 1.3 69.6 + - - +
217H PRO* 3.1 7.8 - - - +
236H TYR* 3.3 24.9 - - - -
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Residues in contact with ILE 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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189H ARG* 3.0 38.0 + - + -
190H LEU 4.0 6.7 - - - +
191H LEU* 3.7 26.7 - - + -
208H LEU* 4.5 6.3 - - + -
213H PHE* 2.8 40.8 + - + +
214H ALA 3.9 0.5 - - - +
215H GLY* 1.3 72.2 - - - +
217H PRO* 1.3 84.7 - - + +
218H THR* 3.5 1.6 + - - +
233H ILE* 3.9 22.9 - - + -
236H TYR* 3.4 25.3 - - + -
237H VAL* 4.5 4.0 - - + -
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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