Contacts of the helix formed by residues 763 - 769 (chain B) in PDB entry 4OL0
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 763 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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708B VAL* 5.9 0.2 - - - -
712B GLY* 3.8 10.1 - - - -
718B ARG* 3.0 25.8 + - - +
759B PHE* 2.7 34.0 + - - +
762B ARG* 1.3 74.6 - - - +
764B PRO* 1.3 69.1 - - - +
765B VAL 3.5 1.1 - - - -
766B THR* 2.6 34.0 + - - +
767B LEU* 3.7 11.6 + - - +
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Residues in contact with PRO 764 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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718B ARG* 5.1 1.3 - - - +
759B PHE 4.1 1.1 - - - +
760B ILE* 3.4 26.5 - - + +
761B GLN 4.5 3.4 - - - +
762B ARG 3.9 4.7 - - - +
763B SER* 1.3 89.7 - - - +
765B VAL* 1.3 60.4 + - + +
767B LEU* 3.3 3.5 + - - +
768B LEU* 2.8 36.8 + - + +
805B THR* 3.5 28.9 - - + +
812B GLU* 5.8 1.1 - - - +
814B ASP* 4.9 7.6 - - - +
818B ARG* 4.0 20.4 - - + +
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Residues in contact with VAL 765 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
763B SER 3.5 0.4 - - - -
764B PRO* 1.3 77.8 - - + +
766B THR* 1.3 65.2 + - - +
768B LEU* 3.7 6.0 - - - +
769B ARG* 2.9 41.8 + - + +
814B ASP* 3.9 19.7 - - + +
817B LEU* 3.3 37.2 - - + -
818B ARG* 3.8 23.1 - - + -
821B LEU* 4.3 3.1 - - + -
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Residues in contact with THR 766 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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718B ARG* 3.8 32.7 + - + +
719B GLN* 5.0 2.9 - - - +
722B LEU* 3.7 36.4 - - + +
759B PHE* 5.0 5.6 - - + -
763B SER* 2.6 28.2 + - - +
764B PRO 3.3 0.6 - - - -
765B VAL* 1.3 79.5 - - - +
767B LEU* 1.3 60.4 + - - +
769B ARG* 3.8 3.0 + - - +
770B SER* 3.5 19.1 + - - -
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Residues in contact with LEU 767 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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722B LEU* 4.8 0.9 - - - -
725B LEU* 3.9 23.8 - - + -
756B ALA* 4.1 11.2 - - + +
759B PHE* 3.8 31.0 - - + -
760B ILE* 3.7 28.9 - - + -
763B SER 3.7 5.9 + - - +
764B PRO 3.3 7.2 + - - +
766B THR* 1.3 76.9 - - - +
768B LEU* 1.3 65.6 + - + +
769B ARG 3.0 2.5 - - - -
770B SER* 2.7 32.3 + - - +
772B VAL* 3.9 7.9 - - + -
773B VAL* 3.4 27.5 - - + +
776B ILE* 4.4 5.2 - - + -
798B PHE* 4.8 6.7 - - + -
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Residues in contact with LEU 768 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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760B ILE* 3.6 26.7 - - + -
764B PRO 2.8 22.8 + - - +
765B VAL 3.2 3.6 + - - +
767B LEU* 1.3 76.9 - - - +
769B ARG* 1.3 58.0 + - - +
770B SER 4.3 0.7 - - - +
773B VAL* 4.0 22.3 - - + +
802B LEU* 3.9 15.0 - - + -
805B THR* 4.0 13.0 - - + -
818B ARG* 4.1 13.5 - - + +
821B LEU* 3.8 43.7 - - + +
822B ILE* 3.8 25.8 - - + +
825B VAL* 4.7 11.0 - - + +
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Residues in contact with ARG 769 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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765B VAL* 2.9 31.6 + - - +
766B THR* 4.1 3.6 - - - +
768B LEU* 1.3 75.6 - - - +
770B SER* 1.3 62.2 + - - +
817B LEU* 3.7 26.7 - - - +
821B LEU* 4.1 21.8 - - + -
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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