Contacts of the helix formed by residues 208 - 218 (chain J) in PDB entry 6O81
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 LYS 208 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209F ARG* 5.4 6.1 - - - +
100J ASP* 3.4 20.2 - - - +
101J VAL* 5.4 0.8 - - - +
121J PHE* 3.6 27.4 - - - -
125J ASP* 4.4 19.0 + - - -
126J ALA 3.6 15.9 + - - -
127J SER* 3.5 17.7 + - - +
207J LEU* 1.3 78.0 - - - +
209J LYS* 1.3 71.7 + - + +
210J TYR* 3.4 34.6 - - + +
211J ILE* 3.3 15.6 + - + +
212J VAL* 3.4 12.7 + - - +
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Residues in contact with LYS 209 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94J TYR* 3.6 13.6 + - - -
97J LEU* 3.8 41.3 - - + -
98J LYS* 4.7 11.9 - - - +
99J THR* 4.3 13.9 - - - +
100J ASP* 3.9 8.3 + - - +
208J LYS* 1.3 80.6 - - + +
210J TYR* 1.3 59.0 + - - +
212J VAL* 3.3 7.8 - - + +
213J ASP* 2.8 64.7 + - - +
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Residues in contact with TYR 210 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127J SER* 3.5 11.9 + - - -
208J LYS* 3.6 29.6 - - + +
209J LYS* 1.3 75.7 - - - +
211J ILE* 1.3 81.3 + - + +
213J ASP* 3.4 12.9 - - + +
214J PHE* 2.9 29.6 + - + +
261J LEU* 3.5 35.9 - - + +
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Residues in contact with ILE 211 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127J SER* 3.4 28.0 - - - +
128J LEU* 5.5 3.8 - - + -
207J LEU* 3.7 24.2 - - + -
208J LYS* 3.5 17.7 - - + +
209J LYS 3.2 0.6 - - - -
210J TYR* 1.3 106.6 - - + +
212J VAL* 1.3 58.2 + - + +
214J PHE* 3.2 10.3 + - + +
215J LEU* 2.9 29.2 + - + +
228J LEU* 5.2 11.0 - - + +
232J LEU* 5.7 6.3 - - + -
261J LEU* 5.1 6.5 - - + -
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Residues in contact with VAL 212 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90J LEU* 4.0 30.3 - - + +
94J TYR* 4.1 10.3 - - + -
97J LEU* 3.8 29.2 - - + -
101J VAL* 4.3 13.7 - - + -
207J LEU* 4.4 13.7 - - + -
208J LYS 3.4 10.5 + - - +
209J LYS* 3.3 20.2 - - + +
211J ILE* 1.3 75.0 - - + +
213J ASP* 1.3 59.6 + - - +
215J LEU* 3.6 14.9 - - + +
216J MET* 2.9 28.6 + - - +
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Residues in contact with ASP 213 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94J TYR* 2.4 35.9 + - - +
209J LYS* 2.8 50.3 + - - +
210J TYR* 3.4 12.8 - - + +
211J ILE 3.2 0.2 - - - -
212J VAL* 1.3 76.2 - - - +
214J PHE* 1.3 57.1 + - - +
216J MET* 3.3 3.3 + - - +
217J GLU* 2.9 27.8 + - - +
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Residues in contact with PHE 214 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210J TYR* 2.9 18.8 + - + +
211J ILE* 3.2 9.6 + - + +
213J ASP* 1.3 73.8 - - - +
215J LEU* 1.3 60.7 + - - +
217J GLU* 3.6 9.5 - - + -
218J ASN* 2.8 46.8 + - + +
231J TYR* 3.6 46.4 - + - -
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Residues in contact with LEU 215 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87J ALA* 3.5 40.4 - - + +
90J LEU* 3.8 26.9 - - + -
91J ARG* 3.9 14.7 - - + +
211J ILE* 2.9 19.5 + - + +
212J VAL* 3.6 14.6 - - + +
213J ASP 3.3 0.2 - - - -
214J PHE* 1.3 81.2 - - - +
216J MET* 1.3 59.9 + - - +
218J ASN* 2.9 24.2 - - - +
219J GLY* 4.1 2.9 + - - -
221J ILE* 5.1 9.0 - - + -
224J ILE* 5.0 8.5 - - + -
227J GLU* 6.4 0.9 - - + -
228J LEU* 5.3 9.9 - - + -
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Residues in contact with MET 216 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91J ARG* 5.1 9.0 - - + -
94J TYR* 4.1 35.7 - - + -
212J VAL 2.9 17.6 + - - +
213J ASP 3.7 4.5 - - - +
215J LEU* 1.3 79.4 - - - +
217J GLU* 1.3 61.2 + - - +
219J GLY* 4.7 3.6 + - - -
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Residues in contact with GLU 217 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213J ASP 2.9 16.8 + - - +
214J PHE* 3.3 13.4 + - + +
216J MET* 1.3 78.2 - - - +
218J ASN* 1.3 56.4 + - - +
219J GLY 3.9 1.8 + - - -
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Residues in contact with ASN 218 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214J PHE* 2.8 38.3 + - + +
215J LEU* 2.9 17.6 - - - +
217J GLU* 1.3 76.8 - - - +
219J GLY* 1.3 55.9 + - - +
220J SER* 3.2 12.4 + - - +
221J ILE* 4.0 12.0 + - + +
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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