Contacts of the helix formed by residues 1006 - 1013 (chain X) in PDB entry 2OO8
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 ALA1006 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1004X TRP 3.8 0.6 + - - -
1005X MET* 1.3 74.7 - - - +
1007X ILE* 1.3 67.5 + - - +
1008X GLU* 3.2 29.2 - - - +
1009X SER* 2.9 16.9 + - - +
1010X LEU* 3.0 11.1 + - - +
1019X SER* 3.8 15.3 + - - -
1022X TRP* 3.5 38.7 - - + +
1023X SER* 4.8 1.4 + - - -
1082X ARG* 3.9 0.2 - - - +
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Residues in contact with ILE1007 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1005X MET 3.8 1.0 + - - -
1006X ALA* 1.3 72.5 - - - +
1008X GLU* 1.3 60.6 + - - +
1010X LEU* 3.1 15.0 + - + +
1011X ASN* 2.9 48.5 + - - +
1022X TRP* 3.6 31.1 - - + -
1051X LEU* 4.3 15.9 - - + +
1052X PRO* 4.1 23.6 - - + -
1056X ARG* 3.9 14.8 - - - +
1077X GLU* 4.4 27.8 - - + +
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Residues in contact with GLU1008 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1006X ALA* 3.4 14.7 - - - +
1007X ILE* 1.3 79.6 + - - +
1009X SER* 1.3 59.9 + - - +
1011X ASN* 4.6 0.7 - - - +
1012X TYR* 2.9 35.7 + - + +
1014X VAL* 3.2 41.9 + - + +
1016X THR* 4.6 1.9 + - - -
1019X SER* 3.7 8.8 + - - -
1077X GLU 4.6 2.1 - - - +
1079X PRO* 3.7 21.1 - - + +
1082X ARG* 2.7 44.1 + - - -
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Residues in contact with SER1009 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1005X MET* 3.7 23.4 - - - +
1006X ALA 2.9 15.5 + - - -
1008X GLU* 1.3 78.3 - - - +
1010X LEU* 1.3 63.2 + - - +
1013X SER* 3.1 21.4 + - - +
1014X VAL 2.6 26.6 + - - +
1015X TYR* 3.9 17.6 + - - -
1019X SER* 3.6 19.9 + - - -
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Residues in contact with LEU1010 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1000X LEU* 6.1 1.4 - - - +
1002X VAL* 4.0 21.1 - - + +
1005X MET* 3.8 48.2 - - + +
1006X ALA 3.0 13.5 + - - +
1007X ILE* 3.5 13.9 - - + +
1009X SER* 1.3 77.1 - - - +
1011X ASN* 1.3 65.3 + - - +
1013X SER 5.1 0.2 + - - -
1048X TYR* 3.7 52.5 + - + +
1051X LEU* 4.0 23.3 - - + -
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Residues in contact with ASN1011 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1007X ILE* 2.9 35.2 + - - +
1008X GLU* 4.9 0.2 - - - -
1010X LEU* 1.3 87.5 - - - +
1012X TYR* 1.3 89.4 + - + +
1013X SER 3.8 0.4 - - - -
1048X TYR* 4.4 12.0 + - - +
1052X PRO* 4.7 9.3 - - - +
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Residues in contact with TYR1012 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1008X GLU* 2.9 23.1 + - + +
1011X ASN* 1.3 100.9 - - + +
1013X SER* 1.3 73.0 + - - +
1014X VAL* 3.1 16.8 + - + +
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Residues in contact with SER1013 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1009X SER 3.1 19.0 + - - -
1011X ASN 3.8 0.4 - - - -
1012X TYR* 1.3 80.1 - - - +
1014X VAL* 1.3 59.8 + - - +
1015X TYR* 3.4 29.5 + - - -
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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