Contacts of the helix formed by residues 225 - 230 (chain F) in PDB entry 6CP3
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 225 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B LYS* 4.8 7.2 - - + -
302B TYR* 3.6 18.4 - - + +
19F ALA* 4.8 7.9 - - + -
63F ALA 4.7 1.1 - - - +
64F MET 5.3 0.2 - - - +
65F ASP* 3.5 12.3 - - - +
66F GLY* 3.4 34.3 - - - +
223F ASN 3.7 4.0 - - - +
224F GLU* 1.3 100.8 - - - +
226F PRO* 1.3 69.4 - - + +
227F GLY 2.8 11.6 + - - +
228F ALA* 3.0 14.6 + - - +
229F ARG 4.1 0.7 + - - -
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Residues in contact with PRO 226 (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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302B TYR* 4.9 7.9 - - + -
19F ALA* 3.8 21.1 - - + -
224F GLU 3.9 0.2 - - - -
225F PRO* 1.3 85.7 - - + +
227F GLY* 1.3 62.4 + - - +
228F ALA 3.2 0.7 - - - -
229F ARG* 3.6 16.5 - - - +
230F ALA* 3.4 7.1 + - - +
264F ALA* 3.3 27.5 - - + +
267F GLU* 3.2 40.4 - - + +
268F VAL* 4.0 16.5 - - + +
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Residues in contact with GLY 227 (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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19F ALA* 4.9 1.6 - - - +
62F ILE* 3.8 23.4 - - - +
63F ALA 3.3 20.9 + - - -
64F MET* 3.3 23.3 - - - +
225F PRO 2.8 2.2 + - - -
226F PRO* 1.3 81.3 - - - +
228F ALA* 1.3 61.7 + - - +
230F ALA* 3.6 5.5 + - - +
231F ARG* 3.6 9.0 - - - +
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Residues in contact with ALA 228 (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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64F MET* 3.6 23.4 + - - +
98F VAL* 3.8 27.2 - - + +
220F GLY* 6.1 1.1 - - - -
224F GLU* 3.8 23.1 - - + +
225F PRO 3.0 10.9 + - - +
227F GLY* 1.3 75.8 - - - +
229F ARG* 1.3 60.8 + - + +
231F ARG 3.1 2.9 + - - -
232F VAL* 2.9 32.2 + - - +
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Residues in contact with ARG 229 (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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301B PHE* 4.0 29.3 - - - -
302B TYR* 3.5 23.0 - - - +
187F VAL* 4.1 3.7 - - + +
188F GLY* 4.3 21.1 - - - +
220F GLY 4.8 3.1 - - - +
221F GLN 4.0 23.3 - - - +
222F MET* 4.5 5.9 + - - +
224F GLU* 3.6 17.1 + - + +
225F PRO 4.1 0.2 + - - -
226F PRO* 3.6 16.1 + - - +
227F GLY 3.4 0.4 - - - -
228F ALA* 1.3 76.9 - - + +
230F ALA* 1.3 59.0 + - - +
231F ARG 3.2 1.4 + - - -
232F VAL* 3.8 15.7 + - + +
233F ALA 5.0 0.3 + - - -
260F ARG* 4.2 17.6 + - - +
261F PHE* 3.6 19.9 - - - -
263F GLN* 5.7 2.6 - - - +
264F ALA* 3.7 16.8 - - + +
267F GLU* 2.6 34.5 + - - -
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Residues in contact with ALA 230 (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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62F ILE* 6.0 3.8 - - + -
226F PRO 3.4 15.5 + - - +
227F GLY* 4.1 4.9 - - - +
228F ALA 3.2 1.0 - - - -
229F ARG* 1.3 77.7 - - - +
231F ARG* 1.3 92.4 + - - +
234F LEU* 4.1 0.9 - - - +
261F PHE* 3.1 30.7 - - + +
264F ALA* 3.5 20.8 - - + +
265F GLY* 4.7 2.5 - - - +
268F VAL* 5.9 3.1 - - + -
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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