Contacts of the helix formed by residues 211 - 217 (chain F) in PDB entry 6P59
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 211 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22F TRP* 3.8 10.5 - - - -
111F ASP* 3.0 20.9 + - - -
141F PHE* 4.5 4.3 - - - -
143F ARG* 3.2 29.0 - - - +
209F PHE 3.2 2.9 + - - -
210F PRO* 1.3 72.8 - - - +
212F LEU* 1.3 58.2 + - - +
214F TYR* 3.3 18.9 + - - +
215F LEU* 3.0 24.4 + - - +
302F GOL 3.2 20.7 + - - -
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Residues in contact with LEU 212 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22F TRP* 3.6 34.3 - - + +
68F ILE* 4.8 2.7 - - + -
70F VAL* 3.8 31.0 - - + -
90F LEU* 4.1 14.8 - - + -
107F PRO* 3.6 14.9 - - + +
110F ALA* 3.4 27.8 - - + -
111F ASP* 3.2 11.8 + - - +
114F ILE* 4.2 18.4 - - + -
210F PRO 4.2 1.1 - - - +
211F SER* 1.3 70.3 - - - +
213F ALA* 1.3 59.6 + - - +
215F LEU* 3.0 10.5 + - + -
216F CYS* 2.9 34.7 + - - -
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Residues in contact with ALA 213 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107F PRO* 3.5 13.9 - - + +
108F ILE* 4.3 26.9 - - + -
111F ASP* 3.1 19.3 + - - +
143F ARG* 3.8 20.0 - - - +
146F ARG* 5.8 1.8 - - - +
211F SER* 3.8 0.9 - - - +
212F LEU* 1.3 76.5 - - - +
214F TYR* 1.3 56.7 + - - +
216F CYS 4.0 0.2 - - - -
217F GLY* 3.1 26.3 + - - -
219F LEU* 4.3 7.0 - - + +
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Residues in contact with TYR 214 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F LYS* 3.4 46.5 + - + -
21F GLN* 2.4 46.5 + - + -
22F TRP* 5.9 4.9 - + + -
25F LEU* 6.0 2.7 - - + -
143F ARG* 3.7 25.0 - - - +
211F SER* 3.3 22.2 + - - +
212F LEU 3.2 0.6 - - - -
213F ALA* 1.3 78.6 - - - +
215F LEU* 1.3 65.9 + - + +
216F CYS 3.5 0.3 + - - -
217F GLY 3.6 6.4 + - - +
219F LEU* 3.8 16.8 - - + -
302F GOL 3.7 31.2 - - - -
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Residues in contact with LEU 215 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F VAL* 3.1 25.0 - - + +
18F LYS* 3.9 32.2 - - + +
19F ILE* 4.0 22.0 - - + -
22F TRP* 3.7 40.2 - - + -
70F VAL* 4.3 5.2 - - + -
72F THR* 5.2 3.4 - - + -
88F ALA* 4.2 18.8 - - + -
211F SER 3.0 14.3 + - - +
212F LEU* 3.0 23.5 + - + +
214F TYR* 1.3 80.2 - - - +
216F CYS* 1.3 63.8 + - - +
217F GLY 3.5 0.6 - - - +
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Residues in contact with CYS 216 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C ASN* 2.9 27.6 + - - +
12F TRP* 3.7 26.8 - - + -
14F VAL* 3.8 7.6 - - - -
88F ALA* 4.3 12.3 - - - -
90F LEU* 3.5 32.1 - - - -
107F PRO* 3.6 22.7 - - + -
212F LEU* 2.9 16.4 + - - +
213F ALA 4.0 0.4 - - - -
215F LEU* 1.3 82.7 - - - +
217F GLY* 1.3 57.4 + - - +
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Residues in contact with GLY 217 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C ASN* 4.9 0.9 - - - -
18F LYS* 3.8 12.1 - - - -
213F ALA 3.1 19.3 + - - -
214F TYR 3.6 10.4 + - - +
215F LEU 3.5 2.4 - - - +
216F CYS* 1.3 77.4 - - - +
218F THR* 1.3 58.5 + - - -
219F LEU* 2.8 24.6 + - - +
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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