Contacts of the helix formed by residues 213 - 226 (chain H) in PDB entry 6V96
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 213 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121H ILE* 4.1 22.4 - - + -
122H GLU* 6.2 1.8 - - + -
125H ALA* 5.7 0.9 - - - -
126H PRO* 2.7 32.5 + - + +
127H GLU* 3.0 15.5 + - - -
128H TYR 3.2 13.5 + - - -
129H MET* 3.5 22.5 - - + +
211H PHE 3.6 1.2 + - - -
212H HIS* 1.3 71.7 - - - +
214H LYS* 1.3 65.1 + - - +
216H LEU* 3.1 2.7 + - - +
217H MET* 2.9 37.6 + - + +
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Residues in contact with LYS 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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212H HIS* 3.3 35.8 + - + +
213H THR* 1.3 78.9 - - - +
215H PHE* 1.3 89.7 + - - +
217H MET* 3.5 7.8 + - - +
218H GLU* 3.3 21.1 + - - +
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Residues in contact with PHE 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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155H ASP* 3.6 55.9 - - + +
211H PHE* 4.0 8.3 - + - -
212H HIS* 3.1 10.9 + - + +
214H LYS* 1.3 105.3 - - - +
216H LEU* 1.3 58.4 + - - +
218H GLU* 3.3 6.3 + - - +
219H ALA* 2.9 28.8 + - + +
222H ARG* 3.9 31.6 - - - -
241H ILE* 3.8 29.4 - - + -
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Residues in contact with LEU 216 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114H VAL* 4.7 1.8 - - + -
129H MET* 3.8 26.2 - - + -
131H ILE* 3.9 15.7 - - + -
211H PHE* 3.7 42.4 - - + -
212H HIS 3.0 6.4 + - - +
213H THR* 3.7 7.2 - - - +
215H PHE* 1.3 79.5 - - - +
217H MET* 1.3 63.7 + - + +
219H ALA* 3.0 3.7 + - + +
220H LEU* 2.7 59.6 + - + +
233H PHE* 3.8 25.1 - - + -
237H ILE* 4.8 6.1 - - + -
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Residues in contact with MET 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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118H ILE* 3.7 33.2 - - - +
121H ILE* 4.2 26.0 - - + -
122H GLU* 4.7 11.0 - - + +
129H MET* 4.4 2.7 - - + -
213H THR* 2.9 40.6 + - + +
214H LYS* 3.8 7.4 - - - +
216H LEU* 1.3 98.5 - - + +
218H GLU* 1.3 58.2 + - - +
220H LEU* 3.5 14.7 + - + +
221H ARG* 3.1 51.3 + - - +
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Residues in contact with GLU 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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214H LYS 3.3 10.8 + - - +
215H PHE* 3.7 9.0 - - - +
216H LEU 3.2 0.6 - - - -
217H MET* 1.3 77.0 - - - +
219H ALA* 1.3 59.9 + - - +
221H ARG* 3.4 8.9 + - - +
222H ARG* 3.0 50.1 + - - +
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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 PHE* 2.9 27.4 + - + +
216H LEU* 3.0 9.8 + - + +
218H GLU* 1.3 76.9 - - - +
220H LEU* 1.3 59.4 + - - +
222H ARG* 3.6 28.4 + - - +
223H ASP* 3.1 27.2 + - - +
237H ILE* 4.2 22.2 - - + +
240H TYR* 6.3 0.7 - - + -
241H ILE* 5.1 2.5 - - + -
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Residues in contact with LEU 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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111H ALA* 3.6 37.5 - - + +
114H VAL* 3.6 31.0 - - + +
115H TYR* 3.8 26.1 - - + +
118H ILE* 4.6 1.3 - - + -
216H LEU* 2.7 45.6 + - + +
217H MET* 3.8 18.2 - - + +
219H ALA* 1.3 70.8 - - - +
221H ARG* 1.3 60.4 + - - +
223H ASP* 3.1 5.4 + - - +
224H ALA* 2.8 30.3 + - - +
233H PHE* 4.2 6.7 - - + -
237H ILE* 4.3 6.5 - - + -
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Residues in contact with ARG 221 (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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115H TYR* 4.0 21.2 + - + +
118H ILE* 3.5 22.6 - - + +
122H GLU* 3.0 31.5 + - - -
217H MET* 3.1 35.8 + - - +
218H GLU* 3.8 7.5 - - - +
220H LEU* 1.3 73.2 - - - +
222H ARG* 1.3 67.6 + - - +
223H ASP 3.3 0.2 + - - -
224H ALA* 3.3 9.5 + - - +
225H ALA* 3.4 12.6 + - - +
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Residues in contact with ARG 222 (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 PHE* 3.9 30.7 - - - -
218H GLU* 3.0 41.5 + - - +
219H ALA* 3.6 26.9 - - - +
221H ARG* 1.3 74.9 - - - +
223H ASP* 1.3 64.2 + - - +
225H ALA* 3.1 17.5 + - - +
226H ASP* 3.1 14.4 + - - +
240H TYR* 4.0 36.3 - - + +
241H ILE* 5.4 1.6 - - - +
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Residues in contact with ASP 223 (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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111H ALA* 3.7 10.3 - - - +
219H ALA 3.1 14.8 + - - +
220H LEU* 3.1 6.3 + - - +
222H ARG* 1.3 80.8 - - - +
224H ALA* 1.3 61.9 + - - +
225H ALA 3.0 1.1 + - - -
226H ASP* 3.3 23.7 + - - +
229H SER* 2.6 26.0 + - - -
231H ARG* 2.9 38.3 + - - -
236H ASP* 3.6 13.7 - - - +
237H ILE* 3.5 21.7 - - + +
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Residues in contact with ALA 224 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115H TYR* 3.4 42.2 - - + +
220H LEU 2.8 12.5 + - - +
221H ARG 3.3 4.4 + - - +
223H ASP* 1.3 76.7 + - - +
225H ALA* 1.3 58.4 + - - +
226H ASP 5.0 0.6 - - - +
231H ARG* 3.6 23.4 + - - +
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Residues in contact with ALA 225 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221H ARG 3.4 8.6 + - - +
222H ARG* 3.1 11.6 + - - +
223H ASP 3.0 0.6 - - - -
224H ALA* 1.3 79.0 - - - +
226H ASP* 1.3 63.3 + - - +
227H PRO* 3.2 13.4 - - - +
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Residues in contact with ASP 226 (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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222H ARG 3.1 12.1 + - - +
223H ASP* 3.3 15.1 + - - +
224H ALA 5.0 0.5 - - - -
225H ALA* 1.3 71.7 - - - +
227H PRO* 1.3 71.5 - - - +
228H THR* 2.5 43.1 + - - +
229H SER* 3.3 27.0 + - - +
231H ARG* 4.9 2.3 - - - -
240H TYR* 5.8 4.7 - - - -
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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